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Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani NL, Dymek M, Desai H, Hausler R, Hicks B, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ. Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival. J Natl Cancer Inst 2024; 116:149-159. [PMID: 37688579 PMCID: PMC10777667 DOI: 10.1093/jnci/djad183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear. METHODS Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival. RESULTS We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3). CONCLUSIONS BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Kaufman
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L Conkrite
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
| | - Gonzalo Lopez
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Randall
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maiah H Dent
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance M Farra
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Neil L Menghani
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malwina Dymek
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Hausler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Belynda Hicks
- Cancer Genome Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A Cole
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kristopher R Bosse
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun S Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John M Maris
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon J Diskin
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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2
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Liu Z, Luo Y, Kirimunda S, Verboom M, Onabajo OO, Gouveia MH, Ogwang MD, Kerchan P, Reynolds SJ, Tenge CN, Were PA, Kuremu RT, Wekesa WN, Masalu N, Kawira E, Kinyera T, Otim I, Legason ID, Nabalende H, Dhudha H, Ayers LW, Bhatia K, Goedert JJ, Cole N, Luo W, Liu J, Manning M, Hicks B, Prokunina-Olsson L, Chagaluka G, Johnston WT, Mutalima N, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Molyneux EM, Newton R, Hsing AW, Mensah JE, Adjei AA, Hutchinson A, Carrington M, Yeager M, Blasczyk R, Chanock SJ, Raychaudhuri S, Mbulaiteye SM. Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma. Commun Biol 2024; 7:41. [PMID: 38182727 PMCID: PMC10770398 DOI: 10.1038/s42003-023-05701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Burkitt lymphoma (BL) is responsible for many childhood cancers in sub-Saharan Africa, where it is linked to recurrent or chronic infection by Epstein-Barr virus or Plasmodium falciparum. However, whether human leukocyte antigen (HLA) polymorphisms, which regulate immune response, are associated with BL has not been well investigated, which limits our understanding of BL etiology. Here we investigate this association among 4,645 children aged 0-15 years, 800 with BL, enrolled in Uganda, Tanzania, Kenya, and Malawi. HLA alleles are imputed with accuracy >90% for HLA class I and 85-89% for class II alleles. BL risk is elevated with HLA-DQA1*04:01 (adjusted odds ratio [OR] = 1.61, 95% confidence interval [CI] = 1.32-1.97, P = 3.71 × 10-6), with rs2040406(G) in HLA-DQA1 region (OR = 1.43, 95% CI = 1.26-1.63, P = 4.62 × 10-8), and with amino acid Gln at position 53 versus other variants in HLA-DQA1 (OR = 1.36, P = 2.06 × 10-6). The associations with HLA-DQA1*04:01 (OR = 1.29, P = 0.03) and rs2040406(G) (OR = 1.68, P = 0.019) persist in mutually adjusted models. The higher risk rs2040406(G) variant for BL is associated with decreased HLA-DQB1 expression in eQTLs in EBV transformed lymphocytes. Our results support the role of HLA variation in the etiology of BL and suggest that a promising area of research might be understanding the link between HLA variation and EBV control.
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Affiliation(s)
- Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Yang Luo
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel Kirimunda
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Murielle Verboom
- Institute of Transfusion Medicine and Transplant Engineering, Hanover, Germany
| | - Olusegun O Onabajo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mateus H Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Martin D Ogwang
- St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Kuluva Hospital, Arua, Uganda
| | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Constance N Tenge
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Moi University College of Health Sciences, Eldoret, Kenya
| | - Pamela A Were
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Robert T Kuremu
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Moi University College of Health Sciences, Eldoret, Kenya
| | - Walter N Wekesa
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Esther Kawira
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Tobias Kinyera
- St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Ismail D Legason
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Kuluva Hospital, Arua, Uganda
| | - Hadijah Nabalende
- St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Herry Dhudha
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathan Cole
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michelle Manning
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - George Chagaluka
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - W Thomas Johnston
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - George N Liomba
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - Collins Mitambo
- National Health Sciences Research Committee, Research Department, Ministry of Health, Lilongwe, Malawi
| | - Elizabeth M Molyneux
- Departments of Pediatrics and Surgery, Kamuzu University of Health Sciences (formerly College of Medicine), University of Malawi, Blantyre, Malawi
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hanover, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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3
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Hong HG, Gouveia MH, Ogwang MD, Kerchan P, Reynolds SJ, Tenge CN, Were PA, Kuremu RT, Wekesa WN, Masalu N, Kawira E, Kinyera T, Wang X, Zhou J, Leal TP, Otim I, Legason ID, Nabalende H, Dhudha H, Mumia M, Baker FS, Okusolubo T, Ayers LW, Bhatia K, Goedert JJ, Woo J, Manning M, Cole N, Luo W, Hicks B, Chagaluka G, Johnston WT, Mutalima N, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Molyneux EM, Newton R, Hutchinson A, Yeager M, Adeyemo AA, Thein SL, Rotimi CN, Chanock SJ, Prokunina-Olsson L, Mbulaiteye SM. Sickle cell allele HBB-rs334(T) is associated with decreased risk of childhood Burkitt lymphoma in East Africa. Am J Hematol 2024; 99:113-123. [PMID: 38009642 PMCID: PMC10872868 DOI: 10.1002/ajh.27149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/30/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023]
Abstract
Burkitt lymphoma (BL) is an aggressive B-cell lymphoma that significantly contributes to childhood cancer burden in sub-Saharan Africa. Plasmodium falciparum, which causes malaria, is geographically associated with BL, but the evidence remains insufficient for causal inference. Inference could be strengthened by demonstrating that mendelian genes known to protect against malaria-such as the sickle cell trait variant, HBB-rs334(T)-also protect against BL. We investigated this hypothesis among 800 BL cases and 3845 controls in four East African countries using genome-scan data to detect polymorphisms in 22 genes known to affect malaria risk. We fit generalized linear mixed models to estimate odds ratios (OR) and 95% confidence intervals (95% CI), controlling for age, sex, country, and ancestry. The ORs of the loci with BL and P. falciparum infection among controls were correlated (Spearman's ρ = 0.37, p = .039). HBB-rs334(T) was associated with lower P. falciparum infection risk among controls (OR = 0.752, 95% CI 0.628-0.9; p = .00189) and BL risk (OR = 0.687, 95% CI 0.533-0.885; p = .0037). ABO-rs8176703(T) was associated with decreased risk of BL (OR = 0.591, 95% CI 0.379-0.992; p = .00271), but not of P. falciparum infection. Our results increase support for the etiological correlation between P. falciparum and BL risk.
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Affiliation(s)
- Hyokyoung G. Hong
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mateus H. Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Martin D. Ogwang
- EMBLEM Study, St. Mary’s Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- EMBLEM Study, Kuluva Hospital, Arua, Uganda
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Pamela A. Were
- EMBLEM Study, Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Robert T. Kuremu
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Walter N. Wekesa
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Esther Kawira
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Tobias Kinyera
- EMBLEM Study, St. Mary’s Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Xunde Wang
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USAs
| | - Jiefu Zhou
- Department of Statistics and Probability, Michigan State University, MI, USA
| | - Thiago Peixoto Leal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Isaac Otim
- EMBLEM Study, St. Mary’s Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Ismail D. Legason
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
- EMBLEM Study, Kuluva Hospital, Arua, Uganda
| | - Hadijah Nabalende
- EMBLEM Study, St. Mary’s Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Herry Dhudha
- EMBLEM Study, Bugando Medical Center, Mwanza, Tanzania
| | - Mediatrix Mumia
- EMBLEM Study, Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Francine S. Baker
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Temiloluwa Okusolubo
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USAs
| | - Leona W. Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Joshua Woo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Michelle Manning
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - George Chagaluka
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - W Thomas Johnston
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - George N. Liomba
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Elizabeth M. Molyneux
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Adebowale A. Adeyemo
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USAs
| | - Charles N. Rotimi
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
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Hassan E, Hicks B, Tabet T, Farina N. Factors associated with dementia attitudes in an adolescent cohort: Structural Equation Modelling. Cogent Psychol 2023; 10:23311908.2023.2235125. [PMID: 38304300 PMCID: PMC7615582 DOI: 10.1080/23311908.2023.2235125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/06/2023] [Indexed: 02/03/2024] Open
Abstract
Objective Dementia-related stigma is a key barrier to people living well with dementia, leading to social isolation and poor well-being. Adolescents represent an under-researched group that will become future carers and healthcare workers for the estimated 83.2 million people who will be living with dementia by 2030. Understanding the factors involved in dementia attitude formation in adolescents is useful for the development of evidence-based anti-stigma initiatives. This study aims to identify predictors of dementia attitudes in adolescents. Methods This is a cross-sectional study using secondary data analysis. 470 participants aged 12-15 years old from secondary schools in the Southeast of England, United Kingdom completed validated questionnaires relating to dementia attitudes (KIDS and Brief A-ADS) as well as demographic information. Multiple regressions were employed as well as a path analysis via a structural equation model to test for direct and mediatory effects. Results Multiple regression models revealed that being female, having higher levels of contact with dementia, and higher levels of empathy are positively associated with dementia attitudes in adolescents (p<0.05). Within the accepted structural equation model, empathy was a key mediator between contact and dementia attitudes. Conclusion This study highlights the pivotal role that contact with dementia can have in influencing dementia attitudes in adolescents with empathy serving as a mediator between contact and dementia attitudes. Interventions that use contact should consider how to stimulate empathetic responses to ultimately shape dementia attitudes.
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Zhou W, Fischer A, Ogwang MD, Luo W, Kerchan P, Reynolds SJ, Tenge CN, Were PA, Kuremu RT, Wekesa WN, Masalu N, Kawira E, Kinyera T, Otim I, Legason ID, Nabalende H, Ayers LW, Bhatia K, Goedert JJ, Gouveia MH, Cole N, Hicks B, Jones K, Hummel M, Schlesner M, Chagaluka G, Mutalima N, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Molyneux EM, Newton R, Glaser S, Kretzmer H, Manning M, Hutchinson A, Hsing AW, Tettey Y, Adjei AA, Chanock SJ, Siebert R, Yeager M, Prokunina-Olsson L, Machiela MJ, Mbulaiteye SM. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa. Nat Commun 2023; 14:8081. [PMID: 38057307 PMCID: PMC10700489 DOI: 10.1038/s41467-023-43881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin-MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma (P-values = 5.7×10-11 and 3.74×10-2, respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC, while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.
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Affiliation(s)
- Weiyin Zhou
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | | | - Wen Luo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Constance N Tenge
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Pamela A Were
- EMBLEM Study, Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Robert T Kuremu
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Walter N Wekesa
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Esther Kawira
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Tobias Kinyera
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Ismail D Legason
- EMBLEM Study, Kuluva Hospital, Arua, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Hadijah Nabalende
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mateus H Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Berlin, Germany
- Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Mathias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, University of Augsburg, Augsburg, Germany
| | - George Chagaluka
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - George N Liomba
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Collins Mitambo
- Research Department, Ministry of Health, P.O. Box 30377, Lilongwe 3, Malawi
| | - Elizabeth M Molyneux
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michelle Manning
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, Palo Alto, CA, USA
| | - Yao Tettey
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Meredith Yeager
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.
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Felton H, Schiffmann O, Goudswaard M, Gopsill J, Snider C, Real R, McClenaghan A, Hicks B. Maker communities and the COVID-19 pandemic: a longitudinal analysis of Thingiverse's response to supply shortages. R Soc Open Sci 2023; 10:230790. [PMID: 37771964 PMCID: PMC10523067 DOI: 10.1098/rsos.230790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
The COVID-19 pandemic profoundly affected various aspects of daily life, particularly the supply and demand of essential goods, resulting in critical shortages. This included personal protective equipment for medical professionals and the general public. To address these shortages, online 'maker communities' emerged, aiming to develop and locally manufacture critical products. While some organized efforts existed, the majority of initiatives originated from individuals and groups on platforms like Thingiverse. This paper presents a longitudinal analysis of Thingiverse, one of the largest maker community websites, to examine the pandemic's effects. Our findings reveal a surge in community output during the initial lockdown periods in major contributing nations (primarily those in the Western Hemisphere), followed by a subsequent decline. Additionally, throughout 2020, pandemic-related products dominated uploads and interactions during this period. Based on these observations, we propose recommendations to expedite the community's ability to support local, national and international responses to future disasters.
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Affiliation(s)
- H. Felton
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - O. Schiffmann
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - M. Goudswaard
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - J. Gopsill
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - C. Snider
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - R. Real
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - A. McClenaghan
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
| | - B. Hicks
- Design Manufacturing Futures Laboratory, Department of Mechanical Engineering, University of Bristol, Bristol BS8 1TR, UK
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7
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Koutros S, Kiemeney LA, Pal Choudhury P, Milne RL, Lopez de Maturana E, Ye Y, Joseph V, Florez-Vargas O, Dyrskjøt L, Figueroa J, Dutta D, Giles GG, Hildebrandt MAT, Offit K, Kogevinas M, Weiderpass E, McCullough ML, Freedman ND, Albanes D, Kooperberg C, Cortessis VK, Karagas MR, Johnson A, Schwenn MR, Baris D, Furberg H, Bajorin DF, Cussenot O, Cancel-Tassin G, Benhamou S, Kraft P, Porru S, Carta A, Bishop T, Southey MC, Matullo G, Fletcher T, Kumar R, Taylor JA, Lamy P, Prip F, Kalisz M, Weinstein SJ, Hengstler JG, Selinski S, Harland M, Teo M, Kiltie AE, Tardón A, Serra C, Carrato A, García-Closas R, Lloreta J, Schned A, Lenz P, Riboli E, Brennan P, Tjønneland A, Otto T, Ovsiannikov D, Volkert F, Vermeulen SH, Aben KK, Galesloot TE, Turman C, De Vivo I, Giovannucci E, Hunter DJ, Hohensee C, Hunt R, Patel AV, Huang WY, Thorleifsson G, Gago-Dominguez M, Amiano P, Golka K, Stern MC, Yan W, Liu J, Li SA, Katta S, Hutchinson A, Hicks B, Wheeler WA, Purdue MP, McGlynn KA, Kitahara CM, Haiman CA, Greene MH, Rafnar T, Chatterjee N, Chanock SJ, Wu X, Real FX, Silverman DT, Garcia-Closas M, Stefansson K, Prokunina-Olsson L, Malats N, Rothman N. Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights. Eur Urol 2023; 84:127-137. [PMID: 37210288 PMCID: PMC10330197 DOI: 10.1016/j.eururo.2023.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Genomic regions identified by genome-wide association studies (GWAS) for bladder cancer risk provide new insights into etiology. OBJECTIVE To identify new susceptibility variants for bladder cancer in a meta-analysis of new and existing genome-wide genotype data. DESIGN, SETTING, AND PARTICIPANTS Data from 32 studies that includes 13,790 bladder cancer cases and 343,502 controls of European ancestry were used for meta-analysis. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSES Log-additive associations of genetic variants were assessed using logistic regression models. A fixed-effects model was used for meta-analysis of the results. Stratified analyses were conducted to evaluate effect modification by sex and smoking status. A polygenic risk score (PRS) was generated on the basis of known and novel susceptibility variants and tested for interaction with smoking. RESULTS AND LIMITATIONS Multiple novel bladder cancer susceptibility loci (6p.22.3, 7q36.3, 8q21.13, 9p21.3, 10q22.1, 19q13.33) as well as improved signals in three known regions (4p16.3, 5p15.33, 11p15.5) were identified, bringing the number of independent markers at genome-wide significance (p < 5 × 10-8) to 24. The 4p16.3 (FGFR3/TACC3) locus was associated with a stronger risk for women than for men (p-interaction = 0.002). Bladder cancer risk was increased by interactions between smoking status and genetic variants at 8p22 (NAT2; multiplicative p value for interaction [pM-I] = 0.004), 8q21.13 (PAG1; pM-I = 0.01), and 9p21.3 (LOC107987026/MTAP/CDKN2A; pM-I = 0.02). The PRS based on the 24 independent GWAS markers (odds ratio per standard deviation increase 1.49, 95% confidence interval 1.44-1.53), which also showed comparable results in two prospective cohorts (UK Biobank, PLCO trial), revealed an approximately fourfold difference in the lifetime risk of bladder cancer according to the PRS (e.g., 1st vs 10th decile) for both smokers and nonsmokers. CONCLUSIONS We report novel loci associated with risk of bladder cancer that provide clues to its biological underpinnings. Using 24 independent markers, we constructed a PRS to stratify lifetime risk. The PRS combined with smoking history, and other established risk factors, has the potential to inform future screening efforts for bladder cancer. PATIENT SUMMARY We identified new genetic markers that provide biological insights into the genetic causes of bladder cancer. These genetic risk factors combined with lifestyle risk factors, such as smoking, may inform future preventive and screening strategies for bladder cancer.
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Affiliation(s)
- Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Parichoy Pal Choudhury
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; American Cancer Society, Atlanta, GA, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Evangelina Lopez de Maturana
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | | | - Vijai Joseph
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jonine Figueroa
- Usher Institute, University of Edinburgh, Edinburgh, UK; Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Diptavo Dutta
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Demetrius Albanes
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Victoria K Cortessis
- Department of Population and Public Health Sciences, Epidemiology and Genetics, University of Southern California, Los Angeles, CA, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Helena Furberg
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Paris, France; GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Simone Benhamou
- INSERM U1018, Research Centre on Epidemiology and Population Health, Villejuif, France
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stefano Porru
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Angela Carta
- Department of Diagnostics and Public Health, Section of Occupational Medicine, University of Verona, Verona, Italy
| | - Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tony Fletcher
- London School of Hygiene and Tropical Medicine, London, UK
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jack A Taylor
- Epidemiology Branch and Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Stephanie J Weinstein
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Teo
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Anne E Kiltie
- Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Adonina Tardón
- Department of Preventive Medicine, Universidad de Oviedo, ISPA and CIBERESP, Spain
| | - Consol Serra
- Center for Research in Occupational Health, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institut, CIBERESP, Barcelona, Spain
| | - Alfredo Carrato
- Department of Medicine, Alcalá University, IRYCIS, CIBERONC, Madrid, Spain
| | | | - Josep Lloreta
- Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alan Schned
- Department of Pathology, Dartmouth Medical School, Hanover, NH, USA
| | - Petra Lenz
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | | | - Thomas Otto
- Department of Urology, Rheinland Klinikum, Lukaskrankenhaus, Neuss, Germany
| | | | - Frank Volkert
- Department of Urology, Evangelic Hospital, Paul Gerhardt Foundation, Lutherstadt Wittenberg, Germany
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katja K Aben
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands; Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Chancellor Hohensee
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rebecca Hunt
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alpa V Patel
- Population Science, American Cancer Society, Atlanta, GA, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saude, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Amiano
- Ministry of Health of the Basque Government, Sub Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain; Biodonostia Health Research Institute, Epidemiology of Chronic and Communicable Diseases Group, San Sebastian, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shengchao Alfred Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shilpa Katta
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Mark P Purdue
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Katherine A McGlynn
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xifeng Wu
- Zhejiang University, Hangzhou, China
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain; Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Montserrat Garcia-Closas
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Shi J, Shiraishi K, Choi J, Matsuo K, Chen TY, Dai J, Hung RJ, Chen K, Shu XO, Kim YT, Landi MT, Lin D, Zheng W, Yin Z, Zhou B, Song B, Wang J, Seow WJ, Song L, Chang IS, Hu W, Chien LH, Cai Q, Hong YC, Kim HN, Wu YL, Wong MP, Richardson BD, Funderburk KM, Li S, Zhang T, Breeze C, Wang Z, Blechter B, Bassig BA, Kim JH, Albanes D, Wong JYY, Shin MH, Chung LP, Yang Y, An SJ, Zheng H, Yatabe Y, Zhang XC, Kim YC, Caporaso NE, Chang J, Ho JCM, Kubo M, Daigo Y, Song M, Momozawa Y, Kamatani Y, Kobayashi M, Okubo K, Honda T, Hosgood DH, Kunitoh H, Patel H, Watanabe SI, Miyagi Y, Nakayama H, Matsumoto S, Horinouchi H, Tsuboi M, Hamamoto R, Goto K, Ohe Y, Takahashi A, Goto A, Minamiya Y, Hara M, Nishida Y, Takeuchi K, Wakai K, Matsuda K, Murakami Y, Shimizu K, Suzuki H, Saito M, Ohtaki Y, Tanaka K, Wu T, Wei F, Dai H, Machiela MJ, Su J, Kim YH, Oh IJ, Lee VHF, Chang GC, Tsai YH, Chen KY, Huang MS, Su WC, Chen YM, Seow A, Park JY, Kweon SS, Chen KC, Gao YT, Qian B, Wu C, Lu D, Liu J, Schwartz AG, Houlston R, Spitz MR, Gorlov IP, Wu X, Yang P, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Ji BT, Wichmann HE, Christiani DC, Rennert G, Arnold S, Brennan P, McKay J, Field JK, Shete SS, Le Marchand L, Liu G, Andrew A, Kiemeney LA, Zienolddiny-Narui S, Grankvist K, Johansson M, Cox A, Taylor F, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Jeon HS, Jiang SS, Sung JS, Chen CH, Hsiao CF, Jung YJ, Guo H, Hu Z, Burdett L, Yeager M, Hutchinson A, Hicks B, Liu J, Zhu B, Berndt SI, Wu W, Wang J, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Wang WC, Xu J, Guan P, Tan W, Yu CJ, Yang G, Sihoe ADL, Chen Y, Choi YY, Kim JS, Yoon HI, Park IK, Xu P, He Q, Wang CL, Hung HH, Vermeulen RCH, Cheng I, Wu J, Lim WY, Tsai FY, Chan JKC, Li J, Chen H, Lin HC, Jin L, Liu J, Sawada N, Yamaji T, Wyatt K, Li SA, Ma H, Zhu M, Wang Z, Cheng S, Li X, Ren Y, Chao A, Iwasaki M, Zhu J, Jiang G, Fei K, Wu G, Chen CY, Chen CJ, Yang PC, Yu J, Stevens VL, Fraumeni JF, Chatterjee N, Gorlova OY, Hsiung CA, Amos CI, Shen H, Chanock SJ, Rothman N, Kohno T, Lan Q. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population. Nat Commun 2023; 14:3043. [PMID: 37236969 PMCID: PMC10220065 DOI: 10.1038/s41467-023-38196-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Young Tae Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Clinical Epidemiology and Center of Evidence Based Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Li-Hsin Chien
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Maria Pik Wong
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Brian Douglas Richardson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shilan Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Biostatistics, Bioinformatics & Biomathematics, Georgetown University Medical Center, Washington, DC, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jin Hee Kim
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yasushi Yatabe
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Medical Oncology and Cancer Center, and Center for Advanced Medicine against Cancer, Shiga University of Medical Science, Shiga, Japan
| | - Minsun Song
- Department of Statistics & Research Institute of Natural Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Kobayashi
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Okubo
- Department of Thoracic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dean H Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yuichiro Ohe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kenji Takeuchi
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kimihiro Shimizu
- Department of Surgery, Division of General Thoracic Surgery, Shinshu University School of Medicine Asahi, Nagano, Japan
| | - Hiroyuki Suzuki
- Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoichi Ohtaki
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Tangchun Wu
- Institute of Occupational Medicine and Ministry of Education Key Lab for Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasuneup, Republic of Korea
- Department of Internal Medicine, Chonnam National Univerisity Medical School, Gwangju, Republic of Korea
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Gee-Chen Chang
- School of Medicine and Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ying-Huang Tsai
- Department of Respiratory Therapy, Chang Gung University, Taoyuan, Taiwan
- Department of Pulmonary and Critical Care, Xiamen Chang Gung Hospital, Xiamen, China
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, E-Da Cancer Hospital, I-Shou University and Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wu-Chou Su
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, and school of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
- Jeonnam Regional Cancer Center, Chonnam National University, Hwasun, Republic of Korea
| | - Kun-Chieh Chen
- Department of Internal Medicine, Division of Pulmonary Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency of Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Margaret R Spitz
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Ivan P Gorlov
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
| | - Xifeng Wu
- School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stig E Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Angela Risch
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
- Helmholtz Center Munich, Institute of Epidemiology, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | | | | | | | - Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Sanjay S Shete
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | | | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | | | | | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Washington State University College of Pharmacy, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Shih Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Junwen Wang
- Department of Biochemistry, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Genomic Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Li
- Department of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Chang Hyun Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Gong Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | | | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jun Suk Kim
- Department of Internal Medicine, Division of Medical Oncology, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho-Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel (Group) Corporation Staff-Worker Hospital, Wuhan, China
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsiao-Han Hung
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Roel C H Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, China
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Qujing, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hsien-Chih Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Rockville, MD, USA
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
- Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Ann Chao
- Center for Global Health, National Cancer Institute, Bethesda, MD, USA
| | - Motoki Iwasaki
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | | | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Olga Y Gorlova
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Christopher I Amos
- Department of Medicine, Section of Epidemiology and Population Science, Institute for Clinical and Translational Research, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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9
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Gomez MF, Byrd DA, Hogue SR, Burns JR, Smith N, Sampson J, Loftfield E, Warner A, Dagnall C, Jones K, Hicks B, Wan Y, Kim Y, Xu J, Sinha R, Vogtmann E. Abstract 3055: Associations of the mucosal microbiome and circulating bile acids with colorectal adenoma among average-risk women. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: The gut microbiome (GM) and the metabolites it produces and regulates, such as bile acids (BAs), may act individually or interact to influence colorectal cancer development. We used data from a multi-center screening study to investigate the associations of the normal colon tissue microbiome and circulating BAs with colorectal adenoma.
Methods: We used data from the multi-center Colorectal Neoplasia Screening with Colonoscopy in Average-Risk Women Regional Navy/Army Medical Centers study (CONCeRN), comprising women undergoing complete colonoscopies. We individually matched women with adenoma (n=165 cases) to those without adenoma (n=311 controls). We extracted DNA using the Animal Tissue DNA Extraction Kit (AutoGene) and sequenced the V4 region of the 16S rRNA gene to characterize normal colonic mucosal bacteria, including alpha and beta diversity, taxonomic abundance, and co-abundance groups (CAGs). Fasting serum collected before colonoscopy underwent targeted quantitative liquid chromatography-tandem mass spectrometry to measure 13 primary and secondary BAs. We used multivariable conditional logistic regression, partial Pearson’s correlations, and linear regression to estimate interrelationships among the GM, BAs, and adenoma.
Results: Multiple genera were statistically significantly associated with adenomas. For example, for the centered log-ratio transformed relative abundance of Phascolarctobacterium, Parvimonas, and Porphymonas, the ORs (95% CIs) were 0.75 (0.60-0.95, P=0.02), 0.71 (0.55-0.92; P=0.01), and 0.67 (0.49-0.93; P=0.02), respectively. A CAG comprising phylum Firmicutes, Actinobacteria, Proteobacteria, and Fusobacteria was less abundant among cases than controls (log2folddiff=-0.80, P=0.002). Alpha and beta diversity associations were close to null and not statistically significant. However, alpha diversity metrics were inversely associated with primary BAs [e.g., for Shannon (R2=-0.13, P=0.01)] and positively associated with secondary BAs [e.g., for Shannon (R2=0.16, P=0.001)]. Though no circulating BAs were statistically significantly associated with adenomas, those in the highest relative to lowest tertile of taurine-conjugated (TC) BAs, primary BAs, and secondary BAs had a 44% (95% CI: 0.85-2.46), 24% (95% CI: 0.73-2.12), and 11% (95% CI: 0.61-2.01) higher odds of adenoma, respectively. We found that TCBAs, primary BAs, and secondary BAs were inversely associated with the abundance of Parvimonas [e.g., for TCBAs (R2=-0.11, P=0.02)] and Porphyromonas [e.g., for TCBAs (R2=-0.11, P=0.02)].
Conclusions: We found short-chain fatty acid-producing and oral-originating bacteria were inversely associated with adenomas. Our oral bacteria findings are contrary to findings from prior studies. Our findings suggest potential interrelationships among the GM and BAs in adenoma development.
Citation Format: Maria F. Gomez, Doratha A. Byrd, Stephanie R. Hogue, Jessica R. Burns, Nathan Smith, Joshua Sampson, Erikka Loftfield, Andrew Warner, Casey Dagnall, Kristine Jones, Belynda Hicks, Yunhu Wan, Youngchul Kim, Jin Xu, Rashmi Sinha, Emily Vogtmann. Associations of the mucosal microbiome and circulating bile acids with colorectal adenoma among average-risk women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3055.
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Affiliation(s)
| | | | | | | | | | - Joshua Sampson
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Erikka Loftfield
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Andrew Warner
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Casey Dagnall
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Kristine Jones
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Belynda Hicks
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Yunhu Wan
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | | | - Jin Xu
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | - Rashmi Sinha
- 2National Cancer Institute, National Institute of Health, Rockville, MD
| | - Emily Vogtmann
- 2National Cancer Institute, National Institute of Health, Rockville, MD
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10
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Koka H, Bodelon C, Horvath S, Lee PMY, Wang D, Song L, Zhang T, Hurson AN, Guida JL, Zhu B, Bailey-Whyte M, Wang F, Wu C, Tsang KH, Tsoi YK, Chan WC, Law SH, Hung RKW, Tse GM, Yuen KKW, Karlins E, Jones K, Vogt A, Zhu B, Hutchinson A, Hicks B, Garcia-Closas M, Chanock S, Barnholtz-Sloan J, Tse LA, Yang XR. DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer. Clin Epigenetics 2023; 15:55. [PMID: 36991516 PMCID: PMC10062015 DOI: 10.1186/s13148-023-01465-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Few studies have examined epigenetic age acceleration (AA), the difference between DNA methylation (DNAm) predicted age and chronological age, in relation to somatic genomic features in paired cancer and normal tissue, with less work done in non-European populations. In this study, we aimed to examine DNAm age and its associations with breast cancer risk factors, subtypes, somatic genomic profiles including mutation and copy number alterations and other aging markers in breast tissue of Chinese breast cancer (BC) patients from Hong Kong. METHODS We performed genome-wide DNA methylation profiling of 196 tumor and 188 paired adjacent normal tissue collected from Chinese BC patients in Hong Kong (HKBC) using Illumina MethylationEPIC array. The DNAm age was calculated using Horvath's pan-tissue clock model. Somatic genomic features were based on data from RNA sequencing (RNASeq), whole-exome sequencing (WES), and whole-genome sequencing (WGS). Pearson's correlation (r), Kruskal-Wallis test, and regression models were used to estimate associations of DNAm AA with somatic features and breast cancer risk factors. RESULTS DNAm age showed a stronger correlation with chronological age in normal (Pearson r = 0.78, P < 2.2e-16) than in tumor tissue (Pearson r = 0.31, P = 7.8e-06). Although overall DNAm age or AA did not vary significantly by tissue within the same individual, luminal A tumors exhibited increased DNAm AA (P = 0.004) while HER2-enriched/basal-like tumors exhibited markedly lower DNAm AA (P = < .0001) compared with paired normal tissue. Consistent with the subtype association, tumor DNAm AA was positively correlated with ESR1 (Pearson r = 0.39, P = 6.3e-06) and PGR (Pearson r = 0.36, P = 2.4e-05) gene expression. In line with this, we found that increasing DNAm AA was associated with higher body mass index (P = 0.039) and earlier age at menarche (P = 0.035), factors that are related to cumulative exposure to estrogen. In contrast, variables indicating extensive genomic instability, such as TP53 somatic mutations, high tumor mutation/copy number alteration burden, and homologous repair deficiency were associated with lower DNAm AA. CONCLUSIONS Our findings provide additional insights into the complexity of breast tissue aging that is associated with the interaction of hormonal, genomic, and epigenetic mechanisms in an East Asian population.
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Affiliation(s)
- Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- San Diego Institute of Science, Alto Labs, San Diego, CA, USA
| | - Priscilla Ming Yi Lee
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong., Prince of Wales Hospital, Sha Tin, N.T., Hong Kong SAR, China
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Amber N Hurson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Jennifer Lyn Guida
- Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Maeve Bailey-Whyte
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- School of Medicine, University of Limerick, Limerick, Ireland
| | - Feng Wang
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong., Prince of Wales Hospital, Sha Tin, N.T., Hong Kong SAR, China
| | - Cherry Wu
- Department of Pathology, North District Hospital, Hong Kong, China
| | - Koon Ho Tsang
- Department of Pathology, Yan Chai Hospital, Hong Kong, China
| | - Yee-Kei Tsoi
- Department of Surgery, North District Hospital, Hong Kong, China
| | - W C Chan
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Sze Hong Law
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Ray Ka Wai Hung
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Jill Barnholtz-Sloan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lap Ah Tse
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong., Prince of Wales Hospital, Sha Tin, N.T., Hong Kong SAR, China.
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.
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11
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Wonnacott L, Banerjee S, Hicks B, Daley S. Understanding the experience of time for dementia education programme on undergraduate radiography students. Radiography (Lond) 2023; 29 Suppl 1:S46-S51. [PMID: 36922325 DOI: 10.1016/j.radi.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
INTRODUCTION Dementia is a global health priority, which requires the healthcare workforce to have the necessary attitudes and skills to deliver person-centred care to people with dementia. Radiographers have frequent contact with people with dementia, and undergraduate training is potentially an optimal time to deliver dementia education. Time for Dementia is an education programme in which undergraduate healthcare students visit a person with dementia and their carer over a two-year period to gain an in-depth understanding of the condition. The aim of this study was to understand undergraduate radiography students' experiences of undertaking the Time for Dementia (TFD) programme. METHODS Two focus groups were undertaken with 14 radiography students who were half-way through the TFD programme. Data was analysed using thematic analysis. RESULTS Three key themes were constructed from the analysis: A Holistic Learning Experience, Transferring Learning into Practice and Preparedness & Expectations. Participants discussed the value from learning directly from people with dementia and their carers, reporting an increase in their awareness and understanding of dementia as well as the impact of caring for somebody with the condition. Participants were able to identify learning to take into practice such as person-centred care, compassion, and patience. Challenges to learning were also identified. CONCLUSIONS This study suggests that a longitudinal, experiential education programme provides radiography students with the opportunity to develop a more holistic understanding of dementia and the impact it may have on the individual and their family members. IMPLICATIONS FOR PRACTICE Experiential dementia teaching is of value to radiography students, however preparation and learning support should fit with previous personal and teaching experience.
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Affiliation(s)
| | - S Banerjee
- Faculty of Health, University of Plymouth, UK
| | - B Hicks
- Centre of Dementia Studies, Brighton and Sussex Medical School, UK
| | - S Daley
- Centre of Dementia Studies, Brighton and Sussex Medical School, UK.
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12
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Byrd DA, Vogtmann E, Ortega-Villa AM, Wan Y, Gomez M, Hogue S, Warner A, Zhu B, Dagnall C, Jones K, Hicks B, Albert PS, Murphy G, Sinha R. Prospective and Cross-sectional Associations of the Rectal Tissue Microbiome with Colorectal Adenoma Recurrence. Cancer Epidemiol Biomarkers Prev 2023; 32:435-443. [PMID: 36525653 PMCID: PMC9992132 DOI: 10.1158/1055-9965.epi-22-0608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The gut microbiome is plausibly associated with colorectal cancer risk; however, previous studies mostly investigated this association cross-sectionally. We investigated cross-sectional and prospective associations of the rectal tissue microbiome with adenoma recurrence in the Polyp Prevention Trial (PPT). METHODS PPT is a 4-year randomized clinical trial of the effect of a dietary intervention on adenoma recurrence among community members. We extracted DNA from rectal biopsies at baseline, end of year 1, and end of year 4 among 455 individuals and sequenced the V4 region of the 16S rRNA gene. At each timepoint, we investigated associations of alpha diversity, beta diversity, and presence and relative abundance of select taxa with adenoma recurrence using multivariable logistic regression. RESULTS Variation in beta diversity was primarily explained by subject and minimally by year of collection or time between biopsy and colonoscopy. Cross-sectionally, year 4 alpha diversity was strongly, inversely associated with adenoma prevalence [ORQ3 vs. Q1 Shannon index = 0.40 (95% confidence interval, CI: 0.21-0.76)]. Prospective alpha diversity associations (i.e., baseline/year 1 alpha diversity with adenoma recurrence 3-4 years later) were weak or null, as were cross-sectional and prospective beta diversity-adenoma associations. Bacteroides abundance was more strongly, positively associated with adenoma prevalence cross-sectionally than prospectively. CONCLUSIONS Rectal tissue microbiome profiles may be associated with prevalent adenomas, with little evidence supporting prospective associations. IMPACT Additional prospective studies, with serial fecal and tissue samples, to explore microbiome-colorectal cancer associations are needed. Eventually, it may be possible to use microbiome characteristics as intervenable risk factors or screening tools.
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Affiliation(s)
- Doratha A. Byrd
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ana M. Ortega-Villa
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Maria Gomez
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Stephanie Hogue
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andrew Warner
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Casey Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Paul S. Albert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Gwen Murphy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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13
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Bai J, Shi J, Zhang Y, Li C, Xiong Y, Koka H, Wang D, Zhang T, Song L, Luo W, Zhu B, Hicks B, Hutchinson A, Kirk E, Troester MA, Li M, Shen Y, Ma T, Wang J, Liu X, Wang S, Gui S, McMaster ML, Chanock SJ, Parry DM, Goldstein AM, Yang XR. Gene Expression Profiling Identifies Two Chordoma Subtypes Associated with Distinct Molecular Mechanisms and Clinical Outcomes. Clin Cancer Res 2023; 29:261-270. [PMID: 36260525 DOI: 10.1158/1078-0432.ccr-22-1865] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/30/2022] [Accepted: 10/17/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE Chordoma is a rare bone tumor with a high recurrence rate and limited treatment options. The aim of this study was to identify molecular subtypes of chordoma that may improve clinical management. EXPERIMENTAL DESIGN We conducted RNA sequencing in 48 tumors from patients with Chinese skull-base chordoma and identified two major molecular subtypes. We then replicated the classification using a NanoString panel in 48 patients with chordoma from North America. RESULTS Tumors in one subtype were more likely to have somatic mutations and reduced expression in chromatin remodeling genes, such as PBRM1 and SETD2, whereas the other subtype was characterized by the upregulation of genes in epithelial-mesenchymal transition and Sonic Hedgehog pathways. IHC staining of top differentially expressed genes between the two subtypes in 312 patients with Chinese chordoma with long-term follow-up data showed that the expression of some markers such as PTCH1 was significantly associated with survival outcomes. CONCLUSIONS Our findings may improve the understanding of subtype-specific tumorigenesis of chordoma and inform clinical prognostication and targeted options.
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Affiliation(s)
- Jiwei Bai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Yujia Xiong
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Erin Kirk
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina
| | - Mingxuan Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yutao Shen
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tianshun Ma
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Junmei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Xing Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China
| | - Shuai Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Mary L McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Dilys M Parry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland
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14
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Astiazaran-Symonds E, Graham C, Kim J, Tucker MA, Ingvar C, Helgadottir H, Pastorino L, van Doorn R, Sampson JN, Zhu B, Bruno W, Queirolo P, Fornarini G, Sciallero S, Carter B, Hicks B, Hutchinson A, Jones K, Stewart DR, Chanock SJ, Freedman ND, Landi MT, Höiom V, Puig S, Gruis N, Yang XR, Ghiorzo P, Goldstein AM. Gene-Level Associations in Patients With and Without Pathogenic Germline Variants in CDKN2A and Pancreatic Cancer. JCO Precis Oncol 2022; 6:e2200145. [PMID: 36409970 PMCID: PMC10166474 DOI: 10.1200/po.22.00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/28/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is a component of familial melanoma due to germline pathogenic variants (GPVs) in CDKN2A. However, it is unclear what role this gene or other genes play in its etiology. MATERIALS AND METHODS We analyzed 189 cancer predisposition genes using parametric rare-variant association (RVA) tests and nonparametric permutation tests to identify gene-level associations in PDAC for patients with (CDKN2A+) and without (CDKN2A-) GPV. Exome sequencing was performed on 84 patients with PDAC, 47 CDKN2A+ and 37 CDKN2A-. After variant filtering, various RVA tests and permutation tests were run separately by CDKN2A status. Genes with the strongest nominal associations were evaluated in patients with PDAC from The Cancer Genome Atlas and the UK Biobank (UKB). A secondary analysis including only GPV from UKB was also performed. RESULTS In RVA tests, ERCC4 and RET showed the most compelling evidence as plausible PDAC candidate genes for CDKN2A+ patients. In contrast, the findings in CDKN2A- patients provided evidence for HMBS, EPCAM, and MRE11 as potential new candidate genes and confirmed ATM, BRCA2, and PALB2 as PDAC genes, consistent with findings in The Cancer Genome Atlas and the UKB. As expected, CDKN2A- patients were more likely to harbor GPVs from the 189 genes investigated. When including only GPVs from UKB, significant associations with PDAC were seen for ATM, BRCA2, and CDKN2A. CONCLUSION These results suggest that variants in other genes likely play a role in PDAC in all patients and that PDAC in CDKN2A+ patients has a distinct etiology from PDAC in CDKN2A- patients.
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Affiliation(s)
- Esteban Astiazaran-Symonds
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- National Human Genome Research Institute, NIH, Bethesda, MD
- Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | - Cole Graham
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | | | - Hildur Helgadottir
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Melanoma Sarcoma and Rare Tumors, IEO European Institute of Oncology, Milano, Italy
| | - Giuseppe Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | - Veronica Höiom
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Susana Puig
- Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona and CIBERER, Barcelona, Spain
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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15
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Xia B, Biswas K, Foo TK, Torres T, Riedel-Topper M, Southon E, Kang Z, Huo Y, Reid S, Stauffer S, Zhou W, Zhu B, Koka H, Yepes S, Brodie SA, Jones K, Vogt A, Zhu B, Cater B, Freedman ND, Hicks B, Yeager M, Chanock SJ, Couch F, Parry DM, Monteiro AN, Goldstein AM, Carvalho MA, Sharan SK, Yang XR. Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma. Hum Mutat 2022; 43:1396-1407. [PMID: 35762214 PMCID: PMC9444938 DOI: 10.1002/humu.24427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022]
Abstract
Chordoma is a rare bone tumor with genetic risk factors largely unknown. We conducted a whole-exome sequencing (WES) analysis of germline DNA from 19 familial chordoma cases in five pedigrees and 137 sporadic chordoma patients and identified 17 rare germline variants in PALB2 and BRCA2, whose products play essential roles in homologous recombination (HR) and tumor suppression. One PALB2 variant showed disease cosegregation in a family with four affected people or obligate gene carrier. Chordoma cases had a significantly increased burden of rare variants in both genes when compared to population-based controls. Four of the six PALB2 variants identified from chordoma patients modestly affected HR function and three of the 11 BRCA2 variants caused loss of function in experimental assays. These results, together with previous reports of abnormal morphology and Brachyury expression of the notochord in Palb2 knockout mouse embryos and genomic signatures associated with HR defect and HR gene mutations in advanced chordomas, suggest that germline mutations in PALB2 and BRCA2 may increase chordoma susceptibility. Our data shed light on the etiology of chordoma and support the previous finding that PARP-1 inhibitors may be a potential therapy for some chordoma patients.
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Affiliation(s)
- Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Thiago Torres
- Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro 20230-130, Brazil
| | - Maximilian Riedel-Topper
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Yanying Huo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Sally Yepes
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Seth A. Brodie
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Aurelie Vogt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Brian Cater
- American Cancer Society, Inc, Atlanta, GA 30303, USA
| | - Neal D. Freedman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Fergus Couch
- Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dilys M. Parry
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Marcelo A. Carvalho
- Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro 20230-130, Brazil
- Instituto Federal do Rio de Janeiro - IFRJ, Rio de Janeiro 20270-021, Brazil
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD, USA
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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16
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Yepes S, Tucker MA, Koka H, Xiao Y, Zhang T, Jones K, Vogt A, Burdette L, Luo W, Zhu B, Hutchinson A, Yeager M, Hicks B, Brown KM, Freedman ND, Chanock SJ, Goldstein AM, Yang XR. Integrated Analysis of Coexpression and Exome Sequencing to Prioritize Susceptibility Genes for Familial Cutaneous Melanoma. J Invest Dermatol 2022; 142:2464-2475.e5. [PMID: 35181301 PMCID: PMC9378750 DOI: 10.1016/j.jid.2022.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 11/17/2022]
Abstract
The application of whole-exome sequencing has led to the identification of high- and moderate-risk variants that contribute to cutaneous melanoma susceptibility. However, confirming disease-causing variants remains challenging. We applied a gene coexpression network analysis to prioritize the candidate genes identified from whole-exome sequencing of 34 melanoma-prone families, with at least three affected members sequenced per family (N = 119 cases). A coexpression network was constructed from genotype-tissue expression project, skin melanoma from the cancer genome atlas, and primary melanocyte cultures. We performed module-specific enrichment and focused on modules associated with pigmentation processes because they are the best-studied and most well-known risk factors for melanoma susceptibility. We found that pigmentation-associated modules across the four expression datasets examined were enriched for well-known melanoma susceptibility genes plus genes associated with pigmentation. We also used network properties to prioritize genes within pigmentation modules as candidate susceptibility genes. Integrating information from coexpression network analysis and variant prioritization, we identified 36 genes (such as DCT, TPCN2, TRPM1, ATP10A, and EPHA5) as potential melanoma risk genes in the families. Our approach also allowed us to link families with private gene mutations on the basis of gene coexpression patterns and thereby may provide an innovative perspective in gene identification in high-risk families.
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Affiliation(s)
- Sally Yepes
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | - Margaret A Tucker
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hela Koka
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Wen Luo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Bin Zhu
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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17
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McReynolds LJ, Rafati M, Wang Y, Ballew BJ, Kim J, Williams VV, Zhou W, Hendricks RM, Dagnall C, Freedman ND, Carter B, Strollo S, Hicks B, Zhu B, Jones K, Paczesny S, Marsh SGE, Spellman SR, He M, Wang T, Lee SJ, Savage SA, Gadalla SM. Genetic testing in severe aplastic anemia is required for optimal hematopoietic cell transplant outcomes. Blood 2022; 140:909-921. [PMID: 35776903 PMCID: PMC9412004 DOI: 10.1182/blood.2022016508] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with severe aplastic anemia (SAA) can have an unrecognized inherited bone marrow failure syndrome (IBMFS) because of phenotypic heterogeneity. We curated germline genetic variants in 104 IBMFS-associated genes from exome sequencing performed on 732 patients who underwent hematopoietic cell transplant (HCT) between 1989 and 2015 for acquired SAA. Patients with pathogenic or likely pathogenic (P/LP) variants fitting known disease zygosity patterns were deemed unrecognized IBMFS. Carriers were defined as patients with a single P/LP variant in an autosomal recessive gene or females with an X-linked recessive P/LP variant. Cox proportional hazard models were used for survival analysis with follow-up until 2017. We identified 113 P/LP single-nucleotide variants or small insertions/deletions and 10 copy number variants across 42 genes in 121 patients. Ninety-one patients had 105 in silico predicted deleterious variants of uncertain significance (dVUS). Forty-eight patients (6.6%) had an unrecognized IBMFS (33% adults), and 73 (10%) were carriers. No survival difference between dVUS and acquired SAA was noted. Compared with acquired SAA (no P/LP variants), patients with unrecognized IBMFS, but not carriers, had worse survival after HCT (IBMFS hazard ratio [HR], 2.13; 95% confidence interval[CI], 1.40-3.24; P = .0004; carriers HR, 0.96; 95% CI, 0.62-1.50; P = .86). Results were similar in analyses restricted to patients receiving reduced-intensity conditioning (n = 448; HR IBMFS = 2.39; P = .01). The excess mortality risk in unrecognized IBMFS attributed to death from organ failure (HR = 4.88; P < .0001). Genetic testing should be part of the diagnostic evaluation for all patients with SAA to tailor therapeutic regimens. Carriers of a pathogenic variant in an IBMFS gene can follow HCT regimens for acquired SAA.
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Affiliation(s)
| | | | | | - Bari J Ballew
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Casey Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Brian Carter
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Sara Strollo
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Steven G E Marsh
- Anthony Nolan Research Institute and University College London Cancer Institute, London, United Kingdom
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Meilun He
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research and
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI; and
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research and
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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18
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Ruan E, Nemeth E, Moffitt R, Sandoval L, Machiela MJ, Freedman ND, Huang WY, Wong W, Chen KL, Park B, Jiang K, Hicks B, Liu J, Russ D, Minasian L, Pinsky P, Chanock SJ, Garcia-Closas M, Almeida JS. PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. Bioinformatics 2022; 38:4434-4436. [PMID: 35900159 PMCID: PMC9890300 DOI: 10.1093/bioinformatics/btac531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION The Division of Cancer Epidemiology and Genetics (DCEG) and the Division of Cancer Prevention (DCP) at the National Cancer Institute (NCI) have recently generated genome-wide association study (GWAS) data for multiple traits in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Genomic Atlas project. The GWAS included 110 000 participants. The dissemination of the genetic association data through a data portal called GWAS Explorer, in a manner that addresses the modern expectations of FAIR reusability by data scientists and engineers, is the main motivation for the development of the open-source JavaScript software development kit (SDK) reported here. RESULTS The PLCO GWAS Explorer resource relies on a public stateless HTTP application programming interface (API) deployed as the sole backend service for both the landing page's web application and third-party analytical workflows. The core PLCOjs SDK is mapped to each of the API methods, and also to each of the reference graphic visualizations in the GWAS Explorer. A few additional visualization methods extend it. As is the norm with web SDKs, no download or installation is needed and modularization supports targeted code injection for web applications, reactive notebooks (Observable) and node-based web services. AVAILABILITY AND IMPLEMENTATION code at https://github.com/episphere/plco; project page at https://episphere.github.io/plco.
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Affiliation(s)
- Eric Ruan
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Erika Nemeth
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Lorena Sandoval
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Wendy Wong
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Kai-Ling Chen
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Brian Park
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Kevin Jiang
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel Russ
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Lori Minasian
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Paul Pinsky
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
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19
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Zhu B, Joo L, Zhang T, Koka H, Lee D, Shi J, Lee P, Wang D, Wang F, Chan WC, Law SH, Tsoi YK, Tse GM, Lai SW, Wu C, Yang S, Yang Chan EY, Shan Wong SY, Wang M, Song L, Jones K, Zhu B, Hutchinson A, Hicks B, Prokunina-Olsson L, Garcia-Closas M, Chanock S, Tse LA, Yang XR. Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients. HGG Adv 2022; 3:100076. [PMID: 35047861 PMCID: PMC8756551 DOI: 10.1016/j.xhgg.2021.100076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/30/2021] [Indexed: 12/24/2022] Open
Abstract
Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data to characterize somatic copy number alterations (SCNAs) and mutation profiles in 98 Hong Kong BC (HKBC) patients and compared with those from The Cancer Genome Atlas of European ancestry (TCGA-EA, N = 686), which had similar distributions of age at diagnosis and PAM50 subtypes as in HKBC. We developed a two-sample Poisson model to compare driver gene selection pressure, which reflects the effect sizes of cancer driver genes, while accounting for differences in sample size, sequencing platforms, depths, and mutation calling methods. We found that somatic mutation and SCNA profiles were overall very similar between HKBC and TCGA-EA. The selection pressure for small insertions and deletions (indels) in GATA3 (false discovery rate (FDR) corrected p < 0.01) and single-nucleotide variants (SNVs) in TP53 (nominal p = 0.02, FDR corrected p = 0.28) was lower in HKBC than in TCGA-EA. Among the 13 signatures of single-base substitutions (SBS) that are common in BC, we found a suggestively higher contribution of SBS18 and a lower contribution of SBS1 in HKBC than in TCGA-EA, while the two APOBEC-induced signatures showed similar prevalence. Our results suggest that the genomic landscape of BC was largely very similar between HKBC and TCGA-EA, despite suggestive differences in some driver genes and mutational signatures that warrant future investigations in large and diverse Asian populations.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lijin Joo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - DongHyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Priscilla Lee
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Feng Wang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing-cheong Chan
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Sze Hong Law
- Department of Surgery, North District Hospital, Hong Kong, China
- Department of Pathology, Yan Chai Hospital, Hong Kong, China
| | - Yee-kei Tsoi
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Gary M. Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Shui Wun Lai
- Department of Pathology, North District Hospital, Hong Kong, China
| | - Cherry Wu
- Department of Pathology, North District Hospital, Hong Kong, China
| | - Shuyuan Yang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Emily Ying Yang Chan
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Samuel Yeung Shan Wong
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lap Ah Tse
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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20
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Dalmasso B, Pastorino L, Nathan V, Shah NN, Palmer JM, Howlie M, Johansson PA, Freedman ND, Carter BD, Beane-Freeman L, Hicks B, Molven A, Helgadottir H, Sankar A, Tsao H, Stratigos AJ, Helsing P, Van Doorn R, Gruis NA, Visser M, Wadt KAW, Mann G, Holland EA, Nagore E, Potrony M, Puig S, Menin C, Peris K, Fargnoli MC, Calista D, Soufir N, Harland M, Bishop T, Kanetsky PA, Elder DE, Andreotti V, Vanni I, Bruno W, Höiom V, Tucker MA, Yang XR, Andresen PA, Adams DJ, Landi MT, Hayward NK, Goldstein AM, Ghiorzo P. Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia. Genet Med 2021; 23:2087-2095. [PMID: 34262154 PMCID: PMC8553617 DOI: 10.1038/s41436-021-01240-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Ataxia-Telangiectasia Mutated (ATM) has been implicated in the risk of several cancers, but establishing a causal relationship is often challenging. Although ATM single-nucleotide polymorphisms have been linked to melanoma, few functional alleles have been identified. Therefore, ATM impact on melanoma predisposition is unclear. METHODS From 22 American, Australian, and European sites, we collected 2,104 familial, multiple primary (MPM), and sporadic melanoma cases who underwent ATM genotyping via panel, exome, or genome sequencing, and compared the allele frequency (AF) of selected ATM variants classified as loss-of-function (LOF) and variants of uncertain significance (VUS) between this cohort and the gnomAD non-Finnish European (NFE) data set. RESULTS LOF variants were more represented in our study cohort than in gnomAD NFE, both in all (AF = 0.005 and 0.002, OR = 2.6, 95% CI = 1.56-4.11, p < 0.01), and familial + MPM cases (AF = 0.0054 and 0.002, OR = 2.97, p < 0.01). Similarly, VUS were enriched in all (AF = 0.046 and 0.033, OR = 1.41, 95% CI = 1.6-5.09, p < 0.01) and familial + MPM cases (AF = 0.053 and 0.033, OR = 1.63, p < 0.01). In a case-control comparison of two centers that provided 1,446 controls, LOF and VUS were enriched in familial + MPM cases (p = 0.027, p = 0.018). CONCLUSION This study, describing the largest multicenter melanoma cohort investigated for ATM germline variants, supports the role of ATM as a melanoma predisposition gene, with LOF variants suggesting a moderate-risk.
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Affiliation(s)
- B Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy.
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
| | - L Pastorino
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - V Nathan
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - N N Shah
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - J M Palmer
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - M Howlie
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - P A Johansson
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - N D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - B D Carter
- American Cancer Society, Atlanta, GA, USA
| | - L Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - B Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - A Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - H Helgadottir
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - A Sankar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - H Tsao
- Wellman Center for Photomedicine, Department of Dermatology, MGH Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - A J Stratigos
- First Department of Dermatology-Venereology, Andreas Sygros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - P Helsing
- Department of Dermatology, Oslo University Hospital, Oslo, Norway
| | - R Van Doorn
- Department Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - N A Gruis
- Department Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - M Visser
- Department Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - K A W Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - G Mann
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, Australia
| | - E A Holland
- Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, Australia
| | - E Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - M Potrony
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - S Puig
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Dermatology Department, Melanoma Unit, HospitalClínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - C Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - K Peris
- Institute of Dermatology, Catholic University of the Sacred Heart, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - M C Fargnoli
- Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - D Calista
- Dermatology Unit, Maurizio Bufalini Hospital, Cesena, Italy
| | - N Soufir
- Dépatement de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, Paris, France
| | - M Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - T Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - P A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - D E Elder
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - V Andreotti
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - I Vanni
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - W Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - V Höiom
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - M A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - X R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - P A Andresen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - D J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - M T Landi
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - N K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - A M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - P Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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21
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Wu Z, Han Y, Caporaso JG, Bokulich N, Mohamadkhani A, Moayyedkazemi A, Hua X, Kamangar F, Wan Y, Suman S, Zhu B, Hutchinson A, Dagnall C, Jones K, Hicks B, Shi J, Malekzadeh R, Abnet CC, Pourshams A, Vogtmann E. Cigarette Smoking and Opium Use in Relation to the Oral Microbiota in Iran. Microbiol Spectr 2021; 9:e0013821. [PMID: 34523990 PMCID: PMC8557864 DOI: 10.1128/spectrum.00138-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022] Open
Abstract
Cigarettes and opium contain chemicals and particulate matter that may modify the oral microbiota. This study aimed to investigate the association between cigarette and opium use with the oral microbiota. A total of 558 participants were recruited from Iran between 2011 and 2015. Individuals were categorized as never cigarette nor opium users, ever cigarette-only smokers, ever opium-only users, and ever both cigarette and opium users. Participants provided saliva samples for 16S rRNA gene sequencing. Logistic regression, microbiome regression-based kernel association test (MiRKAT), and zero-inflated beta regression models were calculated. For every increase in 10 observed amplicon sequence variants (ASVs), the odds for being a cigarette-only smoker, opium-only user, and both user compared to never users decreased by 9% (odds ratio [OR] = 0.91; 95% confidence interval [95% CI] = 0.86 to 0.97), 13% (OR = 0.87; 95% CI = 0.75 to 1.01), and 12% (OR = 0.88; 95% CI = 0.80 to 0.96), respectively. The microbial communities differed by cigarette and opium use as indicated by MiRKAT models testing the three beta-diversity matrices (P < 0.05 for all). Three genera were less likely and one genus was more likely to be detected in cigarette-only smokers or opium-only users than in never users. The relative abundance of the phylum Actinobacteria (never, 14.78%; both, 21.20%) was higher and the phyla Bacteroidetes (never, 17.63%; both, 11.62%) and Proteobacteria (never, 9.06%; both, 3.70%) were lower in users of both cigarettes and opium, while the phylum Firmicutes (never, 54.29%; opium, 65.49%) was higher in opium-only users. Cigarette and opium use was associated with lower alpha-diversity, overall oral microbiota community composition, and both the presence and relative abundance of multiple taxa. IMPORTANCE Cigarette smoking and opium use are associated with periodontal disease caused by specific bacteria such as Porphyromonas gingivalis, which suggests a link between cigarette smoking and opium use and the oral microbiota. Alterations of the oral microbiota in cigarette smokers compared to nonsmokers have been reported, but this has not been studied across diverse populations. Additionally, the association of opium use with the oral microbiota has not been investigated to date. We conducted this study to investigate differences in the oral microbiota between ever users of cigarettes only, opium only, and both cigarettes and opium and never users of cigarettes and opium in Iran. Lower alpha-diversity, distinct overall oral microbial communities, and the presence and relative abundance of multiple taxa have been found for users of cigarettes and/or opium.
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Affiliation(s)
- Zeni Wu
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Yongli Han
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Nicholas Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ashraf Mohamadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Moayyedkazemi
- Department of Internal Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
- Liver and Pancreatobiliary Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Xing Hua
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Farin Kamangar
- Department of Biology, School of Computer, Mathematical, and Natural Sciences, Morgan State University, Baltimore, Maryland, USA
| | - Yunhu Wan
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Shalabh Suman
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Digestive Disease Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Christian C. Abnet
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Akram Pourshams
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Liver and Pancreatobiliary Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
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22
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Shern JF, Selfe J, Izquierdo E, Patidar R, Chou HC, Song YK, Yohe ME, Sindiri S, Wei J, Wen X, Rudzinski ER, Barkauskas DA, Lo T, Hall D, Linardic CM, Hughes D, Jamal S, Jenney M, Chisholm J, Brown R, Jones K, Hicks B, Angelini P, George S, Chesler L, Hubank M, Kelsey A, Gatz SA, Skapek SX, Hawkins DS, Shipley JM, Khan J. Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium. J Clin Oncol 2021; 39:2859-2871. [PMID: 34166060 PMCID: PMC8425837 DOI: 10.1200/jco.20.03060] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood. Despite aggressive therapy, the 5-year survival rate for patients with metastatic or recurrent disease remains poor, and beyond PAX-FOXO1 fusion status, no genomic markers are available for risk stratification. We present an international consortium study designed to determine the incidence of driver mutations and their association with clinical outcome. PATIENTS AND METHODS Tumor samples collected from patients enrolled on Children's Oncology Group trials (1998-2017) and UK patients enrolled on malignant mesenchymal tumor and RMS2005 (1995-2016) trials were subjected to custom-capture sequencing. Mutations, indels, gene deletions, and amplifications were identified, and survival analysis was performed. RESULTS DNA from 641 patients was suitable for analyses. A median of one mutation was found per tumor. In FOXO1 fusion-negative cases, mutation of any RAS pathway member was found in > 50% of cases, and 21% had no putative driver mutation identified. BCOR (15%), NF1 (15%), and TP53 (13%) mutations were found at a higher incidence than previously reported and TP53 mutations were associated with worse outcomes in both fusion-negative and FOXO1 fusion-positive cases. Interestingly, mutations in RAS isoforms predominated in infants < 1 year (64% of cases). Mutation of MYOD1 was associated with histologic patterns beyond those previously described, older age, head and neck primary site, and a dismal survival. Finally, we provide a searchable companion database (ClinOmics), containing all genomic variants, and clinical annotation including survival data. CONCLUSION This is the largest genomic characterization of clinically annotated rhabdomyosarcoma tumors to date and provides prognostic genetic features that refine risk stratification and will be incorporated into prospective trials.
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MESH Headings
- Adolescent
- Adult
- Biomarkers, Tumor/genetics
- Child
- Child, Preschool
- DNA Mutational Analysis
- Databases, Genetic
- Disease Progression
- Female
- Gene Amplification
- Gene Deletion
- Gene Expression Profiling
- Genetic Predisposition to Disease
- Genomics
- Humans
- INDEL Mutation
- Infant
- Infant, Newborn
- Male
- Phenotype
- Predictive Value of Tests
- Progression-Free Survival
- Rhabdomyosarcoma, Alveolar/genetics
- Rhabdomyosarcoma, Alveolar/mortality
- Rhabdomyosarcoma, Alveolar/pathology
- Rhabdomyosarcoma, Alveolar/therapy
- Rhabdomyosarcoma, Embryonal/genetics
- Rhabdomyosarcoma, Embryonal/mortality
- Rhabdomyosarcoma, Embryonal/pathology
- Rhabdomyosarcoma, Embryonal/therapy
- Risk Assessment
- Risk Factors
- Time Factors
- Transcriptome
- United Kingdom
- United States
- Young Adult
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Affiliation(s)
- Jack F. Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Elisa Izquierdo
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Rajesh Patidar
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Hsien-Chao Chou
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Young K. Song
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Sivasish Sindiri
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Jun Wei
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Erin R. Rudzinski
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Donald A. Barkauskas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA
- Children's Oncology Group, Monrovia, CA
| | - Tammy Lo
- Children's Oncology Group, Monrovia, CA
| | | | | | - Debbie Hughes
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Sabri Jamal
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Meriel Jenney
- Cardiff and Vale UHB, Paeds Oncology, Cardiff, United Kingdom
| | - Julia Chisholm
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Rebecca Brown
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sally George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Michael Hubank
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Anna Kelsey
- Department of Paediatric Histopathology, Manchester University NHS Foundation Trust Royal Manchester Childrens Hospital, Manchester, United Kingdom
| | - Susanne A. Gatz
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Stephen X. Skapek
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Douglas S. Hawkins
- Department of Pediatrics, Seattle Children's Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA
| | - Janet M. Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
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Landi MT, Synnott NC, Rosenbaum J, Zhang T, Zhu B, Shi J, Zhao W, Kebede M, Sang J, Choi J, Mendoza L, Pacheco M, Hicks B, Caporaso NE, Abubakar M, Gordenin DA, Wedge DC, Alexandrov LB, Rothman N, Lan Q, Garcia-Closas M, Chanock SJ. Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers. Am J Epidemiol 2021; 190:962-976. [PMID: 33712835 DOI: 10.1093/aje/kwaa234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Epidemiologic studies often rely on questionnaire data, exposure measurement tools, and/or biomarkers to identify risk factors and the underlying carcinogenic processes. An emerging and promising complementary approach to investigate cancer etiology is the study of somatic "mutational signatures" that endogenous and exogenous processes imprint on the cellular genome. These signatures can be identified from a complex web of somatic mutations thanks to advances in DNA sequencing technology and analytical algorithms. This approach is at the core of the Sherlock-Lung study (2018-ongoing), a retrospective case-only study of over 2,000 lung cancers in never-smokers (LCINS), using different patterns of mutations observed within LCINS tumors to trace back possible exposures or endogenous processes. Whole genome and transcriptome sequencing, genome-wide methylation, microbiome, and other analyses are integrated with data from histological and radiological imaging, lifestyle, demographic characteristics, environmental and occupational exposures, and medical records to classify LCINS into subtypes that could reveal distinct risk factors. To date, we have received samples and data from 1,370 LCINS cases from 17 study sites worldwide and whole-genome sequencing has been completed on 1,257 samples. Here, we present the Sherlock-Lung study design and analytical strategy, also illustrating some empirical challenges and the potential for this approach in future epidemiologic studies.
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Yepes S, Shah NN, Bai J, Koka H, Li C, Gui S, McMaster ML, Xiao Y, Jones K, Wang M, Vogt A, Zhu B, Zhu B, Hutchinson A, Yeager M, Hicks B, Carter B, Freedman ND, Beane-Freeman L, Chanock SJ, Zhang Y, Parry DM, Yang XR, Goldstein AM. Rare Germline Variants in Chordoma-Related Genes and Chordoma Susceptibility. Cancers (Basel) 2021; 13:cancers13112704. [PMID: 34070849 PMCID: PMC8197919 DOI: 10.3390/cancers13112704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Chordoma is an extremely rare bone cancer that has not been fully characterized and few risk factors have been identified, highlighting the need for improving our understanding of the disease biology. Our study aims to identify chordoma susceptibility genes by investigating 265 genes involved in chordoma-related signaling pathways and other biological processes on germline DNA of 138 chordoma patients of European ancestry compared to internal control datasets and general population databases. Results were intersected with whole genome sequencing data from 80 skull-base chordoma patients of Chinese ancestry. Several rare loss-of-function and predicted deleterious missense variants were enriched in chordoma cases in both datasets, suggesting a complex model of pathways potentially involved in chordoma development and susceptibility, warranting further investigation in larger studies. Abstract Background: Chordoma is a rare bone cancer with an unknown etiology. TBXT is the only chordoma susceptibility gene identified to date; germline single nucleotide variants and copy number variants in TBXT have been associated with chordoma susceptibility in familial and sporadic chordoma. However, the genetic susceptibility of chordoma remains largely unknown. In this study, we investigated rare germline genetic variants in genes involved in TBXT/chordoma-related signaling pathways and other biological processes in chordoma patients from North America and China. Methods: We identified variants that were very rare in general population and internal control datasets and showed evidence for pathogenicity in 265 genes in a whole exome sequencing (WES) dataset of 138 chordoma patients of European ancestry and in a whole genome sequencing (WGS) dataset of 80 Chinese patients with skull base chordoma. Results: Rare and likely pathogenic variants were identified in 32 of 138 European ancestry patients (23%), including genes that are part of notochord development, PI3K/AKT/mTOR, Sonic Hedgehog, SWI/SNF complex and mesoderm development pathways. Rare pathogenic variants in COL2A1, EXT1, PDK1, LRP2, TBXT and TSC2, among others, were also observed in Chinese patients. Conclusion: We identified several rare loss-of-function and predicted deleterious missense variants in germline DNA from patients with chordoma, which may influence chordoma predisposition and reflect a complex susceptibility, warranting further investigation in large studies.
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Affiliation(s)
- Sally Yepes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Correspondence: (S.Y.); (A.M.G.)
| | - Nirav N. Shah
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Jiwei Bai
- Beijing Tiantan Hospital, Beijing 100070, China; (J.B.); (C.L.); (S.G.); (Y.Z.)
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Chuzhong Li
- Beijing Tiantan Hospital, Beijing 100070, China; (J.B.); (C.L.); (S.G.); (Y.Z.)
| | - Songbai Gui
- Beijing Tiantan Hospital, Beijing 100070, China; (J.B.); (C.L.); (S.G.); (Y.Z.)
| | - Mary Lou McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Brian Carter
- American Cancer Society, Inc, Atlanta, GA 30303, USA;
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Yazhuo Zhang
- Beijing Tiantan Hospital, Beijing 100070, China; (J.B.); (C.L.); (S.G.); (Y.Z.)
| | - Dilys M. Parry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (N.N.S.); (H.K.); (M.L.M.); (Y.X.); (K.J.); (M.W.); (A.V.); (B.Z.); (B.Z.); (A.H.); (M.Y.); (B.H.); (N.D.F.); (L.B.-F.); (S.J.C.); (D.M.P.); (X.R.Y.)
- Correspondence: (S.Y.); (A.M.G.)
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Morton LM, Karyadi D, Stewart C, Bogdanova T, Dawson E, Steinberg M, Dai J, Hartley S, Schonfeld S, Sampson J, Maruvka Y, Kapoor V, Ramsden D, Carvajal-Garcia J, Perou C, Parker J, Krznaric M, Yeager M, Boland J, Hutchinson A, Hicks B, Dagnall C, Gastier-Foster J, Bowen J, Lee O, Machiela M, Cahoon E, Brenner A, Mabuchi K, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Hatch M, de Gonzalez AB, Thomas G, Tronko M, Getz G, Chanock S. Abstract PO-055: Molecular characterization of papillary thyroid cancer in relation to ionizing radiation dose following the Chernobyl accident. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.radsci21-po-055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The 1986 Chernobyl nuclear power plant accident increased papillary thyroid cancer (PTC) incidence in surrounding regions, particularly for 131I-exposed children. To investigate the contribution of environmental radiation to PTC characteristics and improve understanding of radiation-induced carcinogenesis, we analyzed genomic, transcriptomic, and epigenomic characteristics of 440 pathologically-confirmed fresh-frozen PTCs from Ukraine (359 with estimated childhood or in utero 131I exposure and 81 from unexposed children born after March 1987) and matched normal tissue (non-tumor thyroid tissue and/or blood). Mean age at PTC was 28.0 years (range: 10.0-45.6). Among 131I-exposed individuals, mean radiation dose was 250 mGy (range: 11.0-8,800). In multivariable models adjusted for age at PTC and sex, we observed radiation dose-dependent enrichment of fusion drivers (P=6.6 × 10−8), nearly all occurring in the MAPK pathway, as well as increases in small deletions (P=8.0 × 10−9) and simple/balanced structural variants (P=1.2 × 10−14). Further analyses demonstrated even stronger associations for those small deletions and simple/balanced structural variants that were clonal and bore hallmarks of non-homologous end-joining repair (deletions: P=4.9 × 10−31; simple/balanced structural variants: P=5.5 × 10−19). In contrast, radiation dose was not associated with subclonal small deletions (P=0.82) or subclonal simple/balanced structural variants (P=0.91). Additionally, radiation dose was not associated with TINS (locally templated insertions), which are characteristic of alt-end-joining repair (P=0.69). The effects of radiation on genomic alterations with more pronounced for those younger at exposure. Analyses generally were consistent with a linear radiation dose-response for all molecular characteristics except clonal small deletions. Analyses of transcriptomic and epigenomic features demonstrated strong associations with the PTC driver gene but not radiation dose. Our results point to DNA double-strand breaks as early carcinogenic events that subsequently enable PTC growth following environmental radiation exposure.
Citation Format: Lindsay M. Morton, Danielle Karyadi, Chip Stewart, Tetiana Bogdanova, Eric Dawson, Mia Steinberg, Jieqiong Dai, Stephen Hartley, Sara Schonfeld, Joshua Sampson, Yosi Maruvka, Vidushi Kapoor, Dale Ramsden, Juan Carvajal-Garcia, Chuck Perou, Joel Parker, Marko Krznaric, Meredith Yeager, Joseph Boland, Amy Hutchinson, Belynda Hicks, Casey Dagnall, Julie Gastier-Foster, Jay Bowen, Olivia Lee, Mitchell Machiela, Elizabeth Cahoon, Alina Brenner, Kiyohiko Mabuchi, Vladimir Drozdovitch, Sergii Masiuk, Mykola Chepurny, Liudmyla Yu Zurnadzhy, Maureen Hatch, Amy Berrington de Gonzalez, Gerry Thomas, Mykola Tronko, Gad Getz, Stephen Chanock. Molecular characterization of papillary thyroid cancer in relation to ionizing radiation dose following the Chernobyl accident [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-055.
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Affiliation(s)
- Lindsay M. Morton
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Danielle Karyadi
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Tetiana Bogdanova
- 3V.P.Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine,
| | - Eric Dawson
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mia Steinberg
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Jieqiong Dai
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Stephen Hartley
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sara Schonfeld
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joshua Sampson
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Vidushi Kapoor
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Dale Ramsden
- 5University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Chuck Perou
- 5University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joel Parker
- 5University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Meredith Yeager
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Joseph Boland
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Amy Hutchinson
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Belynda Hicks
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Casey Dagnall
- 4Frederick National Laboratory for Cancer Research, Bethesda, MD
| | | | - Jay Bowen
- 8Nationwide Children's Hospital, Columbus, OH
| | - Olivia Lee
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mitchell Machiela
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Elizabeth Cahoon
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Alina Brenner
- 9Radiation Effects Research Foundation, Hiroshima, Japan,
| | - Kiyohiko Mabuchi
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Sergii Masiuk
- 10National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine,
| | - Mykola Chepurny
- 10National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine,
| | - Liudmyla Yu Zurnadzhy
- 3V.P.Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine,
| | - Maureen Hatch
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Gerry Thomas
- 11Imperial College London, Charing Cross Hospital, London, United Kingdom
| | - Mykola Tronko
- 3V.P.Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine,
| | - Gad Getz
- 2Broad Institute of MIT and Harvard, Boston, MA
| | - Stephen Chanock
- 1National Cancer Institute, National Institutes of Health, Bethesda, MD
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Bai J, Shi J, Li C, Wang S, Zhang T, Hua X, Zhu B, Koka H, Wu HH, Song L, Wang D, Wang M, Zhou W, Ballew BJ, Zhu B, Hicks B, Mirabello L, Parry DM, Zhai Y, Li M, Du J, Wang J, Zhang S, Liu Q, Zhao P, Gui S, Goldstein AM, Zhang Y, Yang XR. Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival. Nat Commun 2021; 12:757. [PMID: 33536423 PMCID: PMC7859411 DOI: 10.1038/s41467-021-21026-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Chordoma is a rare bone tumor with an unknown etiology and high recurrence rate. Here we conduct whole genome sequencing of 80 skull-base chordomas and identify PBRM1, a SWI/SNF (SWItch/Sucrose Non-Fermentable) complex subunit gene, as a significantly mutated driver gene. Genomic alterations in PBRM1 (12.5%) and homozygous deletions of the CDKN2A/2B locus are the most prevalent events. The combination of PBRM1 alterations and the chromosome 22q deletion, which involves another SWI/SNF gene (SMARCB1), shows strong associations with poor chordoma-specific survival (Hazard ratio [HR] = 10.55, 95% confidence interval [CI] = 2.81-39.64, p = 0.001) and recurrence-free survival (HR = 4.30, 95% CI = 2.34-7.91, p = 2.77 × 10-6). Despite the low mutation rate, extensive somatic copy number alterations frequently occur, most of which are clonal and showed highly concordant profiles between paired primary and recurrence/metastasis samples, indicating their importance in chordoma initiation. In this work, our findings provide important biological and clinical insights into skull-base chordoma.
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Affiliation(s)
- Jiwei Bai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Shuai Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Ho-Hsiang Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bari J Ballew
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Dilys M Parry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Yixuan Zhai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mingxuan Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jiang Du
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Junmei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Shuheng Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Anshan Central Hospital, Anshan, China
| | - Qian Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Peng Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China.
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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27
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Yepes S, Tucker MA, Koka H, Xiao Y, Jones K, Vogt A, Burdette L, Luo W, Zhu B, Hutchinson A, Yeager M, Hicks B, Freedman ND, Chanock SJ, Goldstein AM, Yang XR. Using whole-exome sequencing and protein interaction networks to prioritize candidate genes for germline cutaneous melanoma susceptibility. Sci Rep 2020; 10:17198. [PMID: 33057211 PMCID: PMC7560829 DOI: 10.1038/s41598-020-74293-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Although next-generation sequencing has demonstrated great potential for novel gene discovery, confirming disease-causing genes after initial discovery remains challenging. Here, we applied a network analysis approach to prioritize candidate genes identified from whole-exome sequencing analysis of 98 cutaneous melanoma patients from 27 families. Using a network propagation method, we ranked candidate genes by their similarity to known disease genes in protein-protein interaction networks and identified gene clusters with functional connectivity. Using this approach, we identified several new candidate susceptibility genes that warrant future investigations such as NGLY1, IL1RN, FABP2, PRKDC, and PROSER2. The propagated network analysis also allowed us to link families that did not have common underlying genes but that carried variants in genes that interact on protein-protein interaction networks. In conclusion, our study provided an analysis perspective for gene prioritization in the context of genetic heterogeneity across families and prioritized top potential candidate susceptibility genes in our dataset.
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Affiliation(s)
- Sally Yepes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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28
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Gouveia MH, Otim I, Ogwang MD, Wang M, Zhu B, Cole N, Luo W, Hicks B, Jones K, Oehl-Huber K, Ayers LW, Pittaluga S, Legason ID, Nabalende H, Kerchan P, Kinyera T, Kawira E, Brubaker G, Levin AG, Guertler L, Kim J, Stewart DR, Adde M, Magrath I, Bergen AW, Reynolds SJ, Yeager M, Bhatia K, Adeyemo AA, Prokunina-Olsson L, Dean M, Shriner D, Rotimi CN, Chanock S, Siebert R, Mbulaiteye SM. Endemic Burkitt Lymphoma in second-degree relatives in Northern Uganda: in-depth genome-wide analysis suggests clues about genetic susceptibility. Leukemia 2020; 35:1209-1213. [PMID: 33051549 PMCID: PMC8024190 DOI: 10.1038/s41375-020-01052-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/11/2020] [Accepted: 09/29/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Mateus H Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Isaac Otim
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | - Mingyi Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kathrin Oehl-Huber
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Tobias Kinyera
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Esther Kawira
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Glen Brubaker
- Inter-Church Medical Assistance Mission, Baltimore, MD, USA
| | - Arthur G Levin
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Lutz Guertler
- Max von Pettenkofer Institute, LMU University of München, München, Germany
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Melissa Adde
- International Network for Cancer Treatment, Brussels, Belgium
| | - Ian Magrath
- International Network for Cancer Treatment, Brussels, Belgium
| | - Andrew W Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.
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29
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Kiely M, Tse LA, Koka H, Wang D, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Zhang H, Karlins E, Zhu B, Hutchinson A, Hicks B, Zhu B, Yang XR. Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients. Epigenetics 2020; 16:677-691. [PMID: 32970968 PMCID: PMC8143246 DOI: 10.1080/15592294.2020.1819661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Age-related DNA methylation is a potential mechanism contributing to breast cancer development. Studies of primarily Caucasian women have identified many CpG sites of age-related methylation in non-diseased breast tissue possibly driving cancer development over time. There is a paucity of studies involving Asian women whose ages at breast cancer onset are usually younger than Caucasians. We identified the 181 most consistent age-related methylation events in non-diseased breast tissue across published studies. Age-related methylation events were measured in adjacent normal and breast tumour tissue in an exclusively Asian population at the previously identified age-related methylation sites. Age-related methylation was found in 118 probes in adjacent normal breast tissue. Methylation of 99% of these sites was increased with age and predominantly located on CpG islands in promoter regions. To ascertain biological relevance to breast cancer, we focused on the 37 sites with overall higher methylation in tumour compared to adjacent normal samples. Some sites positively related to age, including AQP5 and CORO6, inversely correlated with gene expression. Several others have known involvement in suppression of carcinogenesis including GPC5 and SST, suggesting that perturbation of epigenetic regulation at these sites due to ageing may contribute to the progression of carcinogenesis. This study highlights an age-related methylation landscape in non-tumour tissue, consistent not just across studies, but also across different populations. We present candidate age-related methylation sites warranting further investigation as potential epigenetic drivers of breast cancer. They may serve as potential targets of site-specific demethylation intervention strategies for the prevention of age-related breast cancer.
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Affiliation(s)
- Maeve Kiely
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lap Ah Tse
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Priscilla Lee
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- North District Hospital, Hong Kong, China
| | | | | | | | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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30
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Hicks B, Veronesi G, Ferrario M, Cesana G, Iacoviello L, Palmieri L, Kuulasmaa K, Soderberg S, Sans S, Kee F. Differential susceptibility to allostatic load and educational inequalities in coronary heart disease. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Differential exposure to lifestyle factors may mediate the association between education and cardiovascular disease (CVD). However, differential susceptibility (the effect of exposure to the same “dose” of risk factors differs across groups) may also elevate CVD risk but the causal pathways remain unclear. Allostatic Load (AL) is a marker of cumulative biological burden resulting from mal-adaptation to chronic stressors. We aimed to examine the role of differential exposure and susceptibility to AL and other factors in coronary heart disease (CHD) educational gradients in Europe.
Methods
51,328 35-74-year-old participants originally free of CVD from 21 European cohorts in the BiomarCaRE consortium were identified and followed for a median of 10 years to their first CHD event. We defined an AL score as the sum of z-scores of 8 markers from the cardiovascular, metabolic, and inflammatory systems. To investigate the mediating role of AL (and smoking, alcohol and BMI) on educational differences in CHD incidence we applied marginal structural models and three-way decomposition on gender-specific additive hazards models.
Results
AL was a significant mediator of the association between educational status and CHD. The highest proportion mediated was observed in women, with 28% (95%CI 20% to 44%) attributable to differential exposure and 8% (95%CI 0% to 16%) to differential susceptibility. In men, AL mediated 16% of the increased CHD risk in the less educated, with 2% (95%CI 0%-6%) attributable to differential susceptibility. The effects of smoking, alcohol and BMI were relatively small for men and women, with a limited role of differential susceptibility.
Conclusions
While we found evidence of differential susceptibility to AL on CHD, effects were modest and the mediating effect of AL (and other lifestyle factors) was predominately via differential exposure. Controlling disproportionate exposure to AL may help reduce CHD morbidity among those with lower education.
Key messages
Educational inequalities in coronary heart disease in Europe were predominantly driven by differential exposure rather than susceptibility to allostatic load and other lifestyle factors. Controlling disproportionate exposure to AL may help reduce coronary heart disease morbidity among those with lower education.
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Affiliation(s)
- B Hicks
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G Veronesi
- Research Center in Epidemiology and Preventive Medicine, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - M Ferrario
- Research Center in Epidemiology and Preventive Medicine, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - G Cesana
- Research Centre on Public Health, Department of Medicine, University of Milano Bicocca, Monza, Italy
| | - L Iacoviello
- Research Center in Epidemiology and Preventive Medicine, Department of Medicine and Surgery, University of Insubria, Varese, Italy
- Department of Epidemiology and Prevention, IRCCS Neuromed, Pozzilli, Italy
| | - L Palmieri
- Department of Cardiovascular, Endocrine-metabolic Disease, National Institutes of Health-ISS, Rome, Italy
| | - K Kuulasmaa
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - S Soderberg
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - S Sans
- Catalan Department of Health, Catalan Department of Health, Barcelona, Spain
| | - F Kee
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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31
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Koka H, Zhu B, Tse SLA, Wang D, Kiely M, Guida JL, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Karlins E, Zhu B, Hutchinson A, Hicks B, Yang XR. Abstract 146: DNA methylation age of paired tumor-normal breast tissue in Chinese women with breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Epigenetic age, captured by DNA methylation changes, is thought to be more informative with respect to disease risk and progression, than chronological age. A few studies have associated epigenetic age acceleration (EAA), the difference between DNA methylation age (DNAm age) and chronological age, with BC risk and subtypes. However, most of these studies were conducted in Western populations. In this study, we examined EAA in an Asian population, in which BC incidence rate is lower and age at BC onset is younger compared to most Western populations.
Methods: We performed genome-wide DNA methylation profiling of 97 tumor and 89 paired distant normal tissue samples collected from BC patients in Hong Kong (HK) using an Illumina MethylationEPIC array. Two independent datasets were used to compare results: The Cancer Genome Atlas (TCGA, n=525 tumor and n=88 adjacent normal) and healthy women from the Komen tissue bank (n=59). DNAm age was calculated using Horvath's model based on 353 CpGs. The significance of EAA was tested using a simple linear regression model. We also used a multivariate regression model to test for equality of slopes (EAA rates) among different BC subtypes or datasets, considering interaction terms between age and subtype/dataset.
Results: The average age at BC diagnosis was 58 years old (range: 33-81) and the distribution of the molecular subtype based on PAM50 was 43.0%, 29.1%, and 27.9% for luminal A, luminal B, and HER2-enriched/basal tumors, respectively. As expected, DNAm age showed a stronger correlation with chronological age in normal tissue (r=0.78, p<.0001) than in tumor tissue (r=0.27, p=0.0075). The average EAAs in normal and tumor samples were 9.43 and 6.02 years, respectively. Among different BC subtypes, EAA in normal tissue did not vary by subtypes. However, in tumor samples, luminal patients showed positive EAA (average 10/13 years in luminal A/B, respectively), while HER2-enriched/basal patients showed a negative EAA (average -8 years), although the rate of EAA did not vary significantly by subtype. Analyses on TCGA data produced consistent results. When comparing the rate of DNAm acceleration in normal tissue of HK, TCGA, and Komen, HK patients had a significantly different rate (βHK=0.46) compared to TCGA (βTCGA=0.65, p=0.001) and Komen (βKomen=0.80, p<.0001).
Conclusion: Consistent with previous studies, we found that EAA in tumor samples varied across tumor subtypes. We also found that HK BC patients' epigenetic age accelerated at a different rate compared to predominantly white TCGA and Komen women, suggesting a potential racial biological difference. Large studies in other Asian populations are warranted to confirm our findings, which may provide biological insight into racial heterogeneity of BC, especially with regard to age at onset.
Citation Format: Hela Koka, Bin Zhu, Shelly Lap Ah Tse, Difei Wang, Maeve Kiely, Jennifer Lyn Guida, Priscilla Lee, Feng Wang, Cherry Wu, Koon Ho Tsang, Wing-cheong Chan, Sze Hong Law, Eric Karlins, Bin Zhu, Amy Hutchinson, Belynda Hicks, Xiaohong R. Yang. DNA methylation age of paired tumor-normal breast tissue in Chinese women with breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 146.
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Affiliation(s)
- Hela Koka
- 1National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Bin Zhu
- 1National Cancer Institute, NIH, DHHS, Bethesda, MD
| | | | - Difei Wang
- 1National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Maeve Kiely
- 1National Cancer Institute, NIH, DHHS, Bethesda, MD
| | | | - Priscilla Lee
- 2The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- 2The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- 2The Chinese University of Hong Kong, Hong Kong, China
| | - Koon Ho Tsang
- 2The Chinese University of Hong Kong, Hong Kong, China
| | | | - Sze Hong Law
- 2The Chinese University of Hong Kong, Hong Kong, China
| | - Eric Karlins
- 3Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bin Zhu
- 1National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Amy Hutchinson
- 3Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Belynda Hicks
- 3Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
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32
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Micheletti SJ, Bryc K, Ancona Esselmann SG, Freyman WA, Moreno ME, Poznik GD, Shastri AJ, Beleza S, Mountain JL, Agee M, Aslibekyan S, Auton A, Bell R, Clark S, Das S, Elson S, Fletez-Brant K, Fontanillas P, Gandhi P, Heilbron K, Hicks B, Hinds D, Huber K, Jewett E, Jiang Y, Kleinman A, Lin K, Litterman N, McCreight J, McIntyre M, McManus K, Mozaffari S, Nandakumar P, Noblin L, Northover C, O’Connell J, Petrakovitz A, Pitts S, Shelton J, Shringarpure S, Tian C, Tung J, Tunney R, Vacic V, Wang X, Zare A. Genetic Consequences of the Transatlantic Slave Trade in the Americas. Am J Hum Genet 2020; 107:265-277. [PMID: 32707084 PMCID: PMC7413858 DOI: 10.1016/j.ajhg.2020.06.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/15/2020] [Indexed: 01/07/2023] Open
Abstract
According to historical records of transatlantic slavery, traders forcibly deported an estimated 12.5 million people from ports along the Atlantic coastline of Africa between the 16th and 19th centuries, with global impacts reaching to the present day, more than a century and a half after slavery's abolition. Such records have fueled a broad understanding of the forced migration from Africa to the Americas yet remain underexplored in concert with genetic data. Here, we analyzed genotype array data from 50,281 research participants, which-combined with historical shipping documents-illustrate that the current genetic landscape of the Americas is largely concordant with expectations derived from documentation of slave voyages. For instance, genetic connections between people in slave trading regions of Africa and disembarkation regions of the Americas generally mirror the proportion of individuals forcibly moved between those regions. While some discordances can be explained by additional records of deportations within the Americas, other discordances yield insights into variable survival rates and timing of arrival of enslaved people from specific regions of Africa. Furthermore, the greater contribution of African women to the gene pool compared to African men varies across the Americas, consistent with literature documenting regional differences in slavery practices. This investigation of the transatlantic slave trade, which is broad in scope in terms of both datasets and analyses, establishes genetic links between individuals in the Americas and populations across Atlantic Africa, yielding a more comprehensive understanding of the African roots of peoples of the Americas.
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33
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Wang M, Luo W, Jones K, Bian X, Williams R, Higson H, Wu D, Hicks B, Yeager M, Zhu B. SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach. Sci Rep 2020; 10:12898. [PMID: 32732891 PMCID: PMC7393490 DOI: 10.1038/s41598-020-69772-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.
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Affiliation(s)
- Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA.
| | - Wen Luo
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Xiaopeng Bian
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
| | - Russell Williams
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Herbert Higson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Dongjing Wu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, Frederick National Laboratory for Cancer Research, Frederick, MD, 20877, USA.
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34
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Hua X, Zhao W, Pesatori AC, Consonni D, Caporaso NE, Zhang T, Zhu B, Wang M, Jones K, Hicks B, Song L, Sampson J, Wedge DC, Shi J, Landi MT. Genetic and epigenetic intratumor heterogeneity impacts prognosis of lung adenocarcinoma. Nat Commun 2020; 11:2459. [PMID: 32424208 PMCID: PMC7235245 DOI: 10.1038/s41467-020-16295-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Intratumor heterogeneity (ITH) of genomic alterations may impact prognosis of lung adenocarcinoma (LUAD). Here, we investigate ITH of somatic copy number alterations (SCNAs), DNA methylation, and point mutations in lung cancer driver genes in 292 tumor samples from 84 patients with LUAD. LUAD samples show substantial SCNA and methylation ITH, and clonal architecture analyses present congruent evolutionary trajectories for SCNAs and DNA methylation aberrations. Methylation ITH mapping to gene promoter areas or tumor suppressor genes is low. Moreover, ITH composed of genetic and epigenetic mechanisms altering the same cancer driver genes is shown in several tumors. To quantify ITH for valid statistical association analyses, we develope an average pairwise ITH index (APITH), which does not depend on the number of samples per tumor. Both APITH indexes for SCNAs and methylation aberrations show significant associations with poor prognosis. This study further establishes the important clinical implications of genetic and epigenetic ITH in LUAD. Many tumors are known to be heterogeneous. Here, the authors examined multiple samples from 84 patients with lung adenocarcinoma and demonstrate that the intratumor heterogeneity of methylation and copy number associates with poor prognosis.
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Affiliation(s)
- Xing Hua
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Wei Zhao
- Integrative Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Angela C Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Occupational Health Unit, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Occupational Health Unit, Milan, Italy
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Tongwu Zhang
- Integrative Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Mingyi Wang
- Cancer Genome Research Laboratory, Leidos Biomedical Research Inc., Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genome Research Laboratory, Leidos Biomedical Research Inc., Bethesda, MD, USA
| | - Belynda Hicks
- Cancer Genome Research Laboratory, Leidos Biomedical Research Inc., Bethesda, MD, USA
| | - Lei Song
- Cancer Genome Research Laboratory, Leidos Biomedical Research Inc., Bethesda, MD, USA
| | - Joshua Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - David C Wedge
- Big Data Institute, Old Road Campus, Oxford, UK.,Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Maria Teresa Landi
- Integrative Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.
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35
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McReynolds LJ, Wang Y, Thompson AS, Ballew BJ, Kim J, Alter BP, Hicks B, Zhu B, Jones K, Spellman SR, Wang T, Lee SJ, Savage SA, Gadalla SM. Population Frequency of Fanconi Pathway Gene Variants and Their Association with Survival After Hematopoietic Cell Transplantation for Severe Aplastic Anemia. Biol Blood Marrow Transplant 2020; 26:817-822. [PMID: 31982544 PMCID: PMC7243455 DOI: 10.1016/j.bbmt.2020.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 01/15/2020] [Indexed: 11/17/2022]
Abstract
Severe aplastic anemia (SAA) is most frequently immune-mediated; however, rare inherited bone marrow failure syndromes, such as Fanconi anemia (FA), may be causal and can present as aplastic anemia (AA). FA is primarily an autosomal recessive disorder caused by the presence of 2 pathogenic variants in a single FA/BRCA DNA repair pathway gene. Patients with SAA often undergo genetic testing during clinical evaluation that may identify single deleterious alleles in FA pathway genes. We quantified the rate of germline single deleterious alleles in 22 FA genes using both a general population database (3234 variants, 125,748 exomes) and in a cohort of patients with SAA undergoing hematopoietic cell transplantation (HCT) (21 variants in 730 patients). The variants were classified as deleterious using in silico tools (REVEL, MetaSVM, VEP) and database resources (ClinVar, LOVD-FA). We found similar rates of single deleterious alleles in FA genes in both groups (2.6% and 2.9%). The presence of a single deleterious variant in a gene for FA in SAA HCT recipients did not affect the overall survival after HCT (hazard ratio, 0.85; 95% CI, 0.37 to 1.95; P = 0.71), or post-HCT cancer risk (P = 0.52). Our results demonstrate that the identification of a germline monoallelic deleterious variant in an FA gene in patients with idiopathic SAA does not influence the outcome of HCT. Our findings suggest that there is no need for special treatment considerations for patients with SAA and a single deleterious FA allele identified on genetic testing.
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Affiliation(s)
- Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Youjin Wang
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Ashley S Thompson
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Bari J Ballew
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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36
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Landi MT, Bishop DT, MacGregor S, Machiela MJ, Stratigos AJ, Ghiorzo P, Brossard M, Calista D, Choi J, Fargnoli MC, Zhang T, Rodolfo M, Trower AJ, Menin C, Martinez J, Hadjisavvas A, Song L, Stefanaki I, Scolyer R, Yang R, Goldstein AM, Potrony M, Kypreou KP, Pastorino L, Queirolo P, Pellegrini C, Cattaneo L, Zawistowski M, Gimenez-Xavier P, Rodriguez A, Elefanti L, Manoukian S, Rivoltini L, Smith BH, Loizidou MA, Del Regno L, Massi D, Mandala M, Khosrotehrani K, Akslen LA, Amos CI, Andresen PA, Avril MF, Azizi E, Soyer HP, Bataille V, Dalmasso B, Bowdler LM, Burdon KP, Chen WV, Codd V, Craig JE, Dębniak T, Falchi M, Fang S, Friedman E, Simi S, Galan P, Garcia-Casado Z, Gillanders EM, Gordon S, Green A, Gruis NA, Hansson J, Harland M, Harris J, Helsing P, Henders A, Hočevar M, Höiom V, Hunter D, Ingvar C, Kumar R, Lang J, Lathrop GM, Lee JE, Li X, Lubiński J, Mackie RM, Malt M, Malvehy J, McAloney K, Mohamdi H, Molven A, Moses EK, Neale RE, Novaković S, Nyholt DR, Olsson H, Orr N, Fritsche LG, Puig-Butille JA, Qureshi AA, Radford-Smith GL, Randerson-Moor J, Requena C, Rowe C, Samani NJ, Sanna M, Schadendorf D, Schulze HJ, Simms LA, Smithers M, Song F, Swerdlow AJ, van der Stoep N, Kukutsch NA, Visconti A, Wallace L, Ward SV, Wheeler L, Sturm RA, Hutchinson A, Jones K, Malasky M, Vogt A, Zhou W, Pooley KA, Elder DE, Han J, Hicks B, Hayward NK, Kanetsky PA, Brummett C, Montgomery GW, Olsen CM, Hayward C, Dunning AM, Martin NG, Evangelou E, Mann GJ, Long G, Pharoah PDP, Easton DF, Barrett JH, Cust AE, Abecasis G, Duffy DL, Whiteman DC, Gogas H, De Nicolo A, Tucker MA, Newton-Bishop JA, Peris K, Chanock SJ, Demenais F, Brown KM, Puig S, Nagore E, Shi J, Iles MM, Law MH. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility. Nat Genet 2020; 52:494-504. [PMID: 32341527 PMCID: PMC7255059 DOI: 10.1038/s41588-020-0611-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 cases of melanoma (67% newly genotyped) and 375,188 controls identified 54 significant (P < 5 × 10-8) loci with 68 independent single nucleotide polymorphisms. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with GWAS of nevus count and hair color, and transcriptome association approaches, uncovered 31 potential secondary loci for a total of 85 cutaneous melanoma susceptibility loci. These findings provide insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation and telomere maintenance, together with identifying potential new pathways for cutaneous melanoma pathogenesis.
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Affiliation(s)
- Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander J Stratigos
- Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Paola Ghiorzo
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Myriam Brossard
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Concetta Fargnoli
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Adam J Trower
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Andreas Hadjisavvas
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Stefanaki
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Richard Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rose Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miriam Potrony
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Katerina P Kypreou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Lorenza Pastorino
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Medical Oncology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Cristina Pellegrini
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Cattaneo
- Pathology Unit, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pol Gimenez-Xavier
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Arantxa Rodriguez
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Maria A Loizidou
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Laura Del Regno
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Mario Mandala
- Department of Oncology, Giovanni XXIII Hospital, Bergamo, Italy
| | - Kiarash Khosrotehrani
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Per A Andresen
- Department of Pathology, Molecular Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marie-Françoise Avril
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service de Dermatologie, Université Paris Descartes, Paris, France
| | - Esther Azizi
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv, Israel
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H Peter Soyer
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Bruna Dalmasso
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Lisa M Bowdler
- Sample Processing, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Wei V Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eitan Friedman
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarah Simi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Pilar Galan
- Université Paris 13, Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Institut National de la Santé et de la Recherche Médicale (INSERM U1153), Institut National de la Recherche Agronomique (INRA U1125), Conservatoire National des Arts et Métiers, Communauté d'Université Sorbonne Paris Cité, Bobigny, France
| | - Zaida Garcia-Casado
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Elizabeth M Gillanders
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Scott Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Adele Green
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- CRUK Manchester Institute, Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mark Harland
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jessica Harris
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Per Helsing
- Department of Dermatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anjali Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marko Hočevar
- Department of Surgical Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Lund, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Julie Lang
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - G Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Jan Lubiński
- International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Rona M Mackie
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
- Department of Public Health, University of Glasgow, Glasgow, UK
| | - Maryrose Malt
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Kerrie McAloney
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hamida Mohamdi
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Anders Molven
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Rachel E Neale
- Cancer Aetiology & Prevention, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Dale R Nyholt
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Håkan Olsson
- Department of Oncology/Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nicholas Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Lars G Fritsche
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona,CIBERER, Barcelona, Spain
| | - Abrar A Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Graham L Radford-Smith
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- University of Queensland School of Medicine, Herston Campus, Brisbane, Queensland, Australia
| | | | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Casey Rowe
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Marianna Sanna
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
- German Consortium Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Hans-Joachim Schulze
- Department of Dermatology, Fachklinik Hornheide, Institute for Tumors of the Skin, University of Münster, Münster, Germany
| | - Lisa A Simms
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, The University of Queensland, St Lucia, Queensland, Australia
- Mater Research Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Fengju Song
- Departments of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, P. R. China
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nicole A Kukutsch
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sarah V Ward
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lawrie Wheeler
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Michael Malasky
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - David E Elder
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chad Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, Sydney, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgina Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore Hospital, Sydney, Australia
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | | | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Cancer Epidemiology and Prevention Research, Sydney School of Public Health, Sydney, Australia
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - David L Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Helen Gogas
- First Department of Internal Medicine, Laikon General Hospital Greece, National and Kapodistrian University of Athens, Athens, Greece
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Ketty Peris
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florence Demenais
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK.
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM. Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia. Am J Hum Genet 2020; 106:264-271. [PMID: 32004448 PMCID: PMC7010969 DOI: 10.1016/j.ajhg.2020.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
Severe aplastic anemia (SAA) is a rare disorder characterized by hypoplastic bone marrow and progressive pancytopenia. The etiology of acquired SAA is not understood but is likely related to abnormal immune responses and environmental exposures. We conducted a genome-wide association study of individuals with SAA genetically matched to healthy controls in discovery (359 cases, 1,396 controls) and validation sets (175 cases, 1,059 controls). Combined analyses identified linked SNPs in distinct blocks within the major histocompatibility complex on 6p21. The top SNP encodes p.Met76Val in the P4 binding pocket of the HLA class II gene HLA-DPB1 (rs1042151A>G, odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50-2.03, p = 1.94 × 10-13) and was associated with HLA-DP cell surface expression in healthy individuals (p = 2.04 × 10-6). Phylogenetic analyses indicate that Val76 is not monophyletic and likely occurs in conjunction with different HLA-DP binding groove conformations. Imputation of HLA-DPB1 alleles revealed increased risk of SAA associated with Val76-encoding alleles DPB1∗03:01, (OR 1.66, p = 1.52 × 10-7), DPB1∗10:01 (OR 2.12, p = 0.0003), and DPB1∗01:01 (OR 1.60, p = 0.0008). A second SNP near HLA-B, rs28367832G>A, reached genome-wide significance (OR 1.49, 95% CI 1.22-1.78, p = 7.27 × 10-9) in combined analyses; the association remained significant after excluding cases with clonal copy-neutral loss-of-heterozygosity affecting class I HLA genes (8.6% of cases and 0% of controls). SNPs in the HLA class II gene HLA-DPB1 and possibly class I (HLA-B) are associated with SAA. The replacement of Met76 to Val76 in certain HLA-DPB1 alleles might influence risk of SAA through mechanisms involving DP peptide binding specificity, expression, and/or other factors affecting DP function.
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Affiliation(s)
- Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weiyin Zhou
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shengchao Alfred Li
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Veron Ramsuran
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Aurelie Vogt
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Belynda Hicks
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Charles Chung
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Yawei Zhang
- Section of Surgical Outcomes and Epidemiology, Department of Surgery, Yale Medical School, New Haven, CT 06520, USA
| | - Lauren R Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, 30303, USA
| | - Michael Haagenson
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Youjin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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Vogtmann E, Han Y, Caporaso JG, Bokulich N, Mohamadkhani A, Moayyedkazemi A, Hua X, Kamangar F, Wan Y, Suman S, Zhu B, Hutchinson A, Dagnall C, Jones K, Hicks B, Shi J, Malekzadeh R, Abnet CC, Pourshams A. Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran. Cancer Med 2020; 9:797-806. [PMID: 31750624 PMCID: PMC6970053 DOI: 10.1002/cam4.2660] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/15/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Oral microbiota may be related to pancreatic cancer risk because periodontal disease, a condition linked to multiple specific microbes, has been associated with increased risk of pancreatic cancer. We evaluated the association between oral microbiota and pancreatic cancer in Iran. METHODS A total of 273 pancreatic adenocarcinoma cases and 285 controls recruited from tertiary hospitals and a specialty clinic in Tehran, Iran provided saliva samples and filled out a questionnaire regarding demographics and lifestyle characteristics. DNA was extracted from saliva and the V4 region of the 16S rRNA gene was PCR amplified and sequenced on the MiSeq. The sequencing data were processed using the DADA2 plugin in QIIME 2 and taxonomy was assigned against the Human Oral Microbiome Database. Logistic regression and MiRKAT models were calculated with adjustment for potential confounders. RESULTS No association was observed for alpha diversity with an average of 91.11 (standard deviation [SD] 2.59) sequence variants for cases and 89.42 (SD 2.58) for controls. However, there was evidence for an association between beta diversity and case status. The association between the Bray-Curtis dissimilarity and pancreatic cancer was particularly strong with a MiRKAT P-value of .000142 and specific principal coordinate vectors had strong associations with cancer risk. Several specific taxa were also associated with case status after adjustment for multiple comparisons. CONCLUSION The overall microbial community appeared to differ between pancreatic cancer cases and controls. Whether these reflect differences evident before development of pancreatic cancer will need to be evaluated in prospective studies.
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Affiliation(s)
- Emily Vogtmann
- Metabolic Epidemiology BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - Yongli Han
- Biostatistics BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - J. Gregory Caporaso
- Center for Applied Microbiome SciencePathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
| | - Nicholas Bokulich
- Center for Applied Microbiome SciencePathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
| | - Ashraf Mohamadkhani
- Digestive Oncology Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
| | - Alireza Moayyedkazemi
- Department of Internal MedicineLorestan University of Medical SciencesKhorramabadIran
- Liver and Pancreatobiliary Diseases Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
| | - Xing Hua
- Biostatistics BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - Farin Kamangar
- Department of BiologySchool of Computer, Mathematical, and Natural SciencesMorgan State UniversityBaltimoreMDUSA
| | - Yunhu Wan
- Biostatistics BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - Shalabh Suman
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Bin Zhu
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Amy Hutchinson
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Casey Dagnall
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Kristine Jones
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Belynda Hicks
- Cancer Genomics Research LaboratoryDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
- Leidos Biomedical Research Laboratory, Inc.Frederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Jianxin Shi
- Biostatistics BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - Reza Malekzadeh
- Digestive Oncology Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
- Digestive Disease Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
| | - Christian C. Abnet
- Metabolic Epidemiology BranchDivision of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMDUSA
| | - Akram Pourshams
- Digestive Oncology Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
- Liver and Pancreatobiliary Diseases Research CenterDigestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
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Zhu B, Tse LA, Wang D, Koka H, Zhang T, Abubakar M, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Li M, Li W, Wu S, Liu Z, Huang B, Zhang H, Tang E, Kan Z, Lee S, Park YH, Nam SJ, Wang M, Sun X, Jones K, Zhu B, Hutchinson A, Hicks B, Prokunina-Olsson L, Shi J, Garcia-Closas M, Chanock S, Yang XR. Immune gene expression profiling reveals heterogeneity in luminal breast tumors. Breast Cancer Res 2019; 21:147. [PMID: 31856876 PMCID: PMC6924001 DOI: 10.1186/s13058-019-1218-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/18/2019] [Indexed: 12/24/2022] Open
Abstract
Background Heterogeneity of immune gene expression patterns of luminal breast cancer (BC), which is clinically heterogeneous and overall considered as low immunogenic, has not been well studied especially in non-European populations. Here, we aimed at characterizing the immune gene expression profile of luminal BC in an Asian population and associating it with patient characteristics and tumor genomic features. Methods We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 luminal BC patients from Hong Kong using RNA-sequencing data and used unsupervised consensus clustering to stratify tumors. We then used luminal patients from The Cancer Genome Atlas (TCGA, N = 564) and a Korean breast cancer study (KBC, N = 112) as replication datasets. Results Based on the expression of 130 immune-related genes, luminal tumors were stratified into three distinct immune subtypes. Tumors in one subtype showed higher level of tumor-infiltrating lymphocytes (TILs), characterized by T cell gene activation, higher expression of immune checkpoint genes, higher nonsynonymous mutation burden, and higher APOBEC-signature mutations, compared with other luminal tumors. The high-TIL subtype was also associated with lower ESR1/ESR2 expression ratio and increasing body mass index. The comparison of the immune profile in tumor and matched normal tissue suggested a tumor-derived activation of specific immune responses, which was only seen in high-TIL patients. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in TCGA and KBC, although the pattern was more similar in Asian populations. The germline APOBEC3B deletion polymorphism, which is prevalent in East Asian populations and was previously linked to immune activation, was not associated with immune subtypes in our study. This result does not support the hypothesis that the germline APOBEC3B deletion polymorphism is the driving force for immune activation in breast tumors in Asian populations. Conclusion Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification and a subset of luminal BC patients may benefit from checkpoint immunotherapy, at least in Asian populations.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lap Ah Tse
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China.
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Priscilla Lee
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- North District Hospital, Hong Kong, China
| | | | | | | | - Mengjie Li
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China.,Vanderbilt University, Nashville, TN, USA
| | - Wentao Li
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Suyang Wu
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiguang Liu
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Bixia Huang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Eric Tang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Zhengyan Kan
- Pfizer Oncology Research, San Diego, CA, 92121, USA
| | | | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Seok Jin Nam
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xuezheng Sun
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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40
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Wang Y, Best A, Fernández-Torrón R, Alsaggaf R, Garcia-Puga M, Dagnall CL, Hicks B, Thompson M, Matheu Fernandez A, Zulaica Ijurco M, Greene MH, Lopez de Munain A, Gadalla SM. Leukocyte telomere length in patients with myotonic dystrophy type I: a pilot study. Ann Clin Transl Neurol 2019; 7:126-131. [PMID: 31808320 PMCID: PMC6952307 DOI: 10.1002/acn3.50954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 01/30/2023] Open
Abstract
Myotonic dystrophy type I (DM1) is an autosomal dominant disease of which clinical manifestations resemble premature aging. We evaluated the contribution of telomere length in pathogenesis in 361 DM1 patients (12 with serial measurements) and 223 unaffected relative controls using qPCR assay. While no differences in baseline leukocyte relative telomere length (RTL) was noted, the data suggested an accelerated RTL attrition in DM1 (discovery cohort: T/S change/year = −0.013 in DM1 vs. −0.005 in controls, P = 0.04); similar trend was noted in validation cohort. Further investigations are needed to examine the role of TL in the pathophysiology of DM1.
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Affiliation(s)
- Youjin Wang
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ana Best
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Roberto Fernández-Torrón
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Institute Carlos III, Madrid, Spain.,Neuroscience Area, Institute Biodonostia, San Sebastian, Spain
| | - Rotana Alsaggaf
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mone't Thompson
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Miren Zulaica Ijurco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Institute Carlos III, Madrid, Spain.,Neuroscience Area, Institute Biodonostia, San Sebastian, Spain
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Adolfo Lopez de Munain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Institute Carlos III, Madrid, Spain.,Neuroscience Area, Institute Biodonostia, San Sebastian, Spain.,Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain.,Department of Neurosciences, Universidad del País Vasco UPV-EHU, San Sebastian, Spain
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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41
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Knudtson KL, Carnahan RH, Hegstad-Davies RL, Fisher NC, Hicks B, Lopez PA, Meyn SM, Mische SM, Weis-Garcia F, White LD, Sol-Church K. Survey on Scientific Shared Resource Rigor and Reproducibility. J Biomol Tech 2019; 30:36-44. [PMID: 31452645 PMCID: PMC6657953 DOI: 10.7171/jbt.19-3003-001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions. The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research. In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development. In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research. The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility. These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines. These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.
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Affiliation(s)
| | | | | | - Nancy C. Fisher
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 20877
| | - Peter A. Lopez
- New York University, Langone Medical Center, New York, New York 10016, USA
| | - Susan M. Meyn
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Sheenah M. Mische
- New York University, Langone Medical Center, New York, New York 10016, USA
| | | | - Lisa D. White
- Baylor College Medicine, Houston, Texas 77030, USA; and
| | - Katia Sol-Church
- University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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42
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Wang Y, McReynolds LJ, Dagnall C, Katki HA, Spellman SR, Wang T, Hicks B, Freedman ND, Jones K, Lee SJ, Savage SA, Gadalla SM. Pre-transplant short telomeres are associated with high mortality risk after unrelated donor haematopoietic cell transplant for severe aplastic anaemia. Br J Haematol 2019; 188:309-316. [PMID: 31426123 DOI: 10.1111/bjh.16153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/20/2019] [Indexed: 11/28/2022]
Abstract
Telomeres are essential for chromosomal stability and markers of biological age. We evaluated the effect of pre-transplant short (<10th percentile-for-age) or very short (<5th or <1st percentile-for-age) leucocyte telomere length on survival after unrelated donor haematopoietic cell transplantation (HCT) for acquired severe aplastic anaemia (SAA). Patient pre-transplant blood samples and clinical data were available at the Center for International Blood and Marrow Transplant Research. We used quantitative real time polymerase chain reaction to measure relative telomere length (RTL) in 490 SAA patients who received HCT between 1990 and 2013 (median age = 20 years). One hundred and twelve patients (22·86%) had pre-HCT RTL <10th percentile-for-age, with the majority below the 5th percentile (N = 80, 71·43%). RTL <10th percentile-for-age was associated with a higher risk of post-HCT mortality (hazard ratio [HR] = 1·78, 95% confidence interval [CI]=1·18-2·69, P = 0·006) compared with RTL ≥50th percentile; no survival differences were noted in longer RTL categories (P > 0·10). Time-dependent effects for post-HCT mortality were only observed in relation to very short RTL; HR comparing RTL <5th versus ≥5th percentile = 1·38, P = 0·15 for the first 12 months after HCT, and HR = 3·91, P < 0·0001, thereafter, P-heterogeneity = 0·008; the corresponding HRs for RTL <1st versus ≥1st percentile = 1·29, P = 0·41, and HR = 5·18, P < 0·0001, P-heterogeneity = 0·005. The study suggests a potential role for telomere length in risk stratification of SAA patients in regard to their HCT survival.
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Affiliation(s)
- Youjin Wang
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.,Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hormuzd A Katki
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.,Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.,Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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43
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Wong JYY, Zhang H, Hsiung CA, Shiraishi K, Yu K, Matsuo K, Wong MP, Hong YC, Wang J, Seow WJ, Wang Z, Song M, Kim HN, Chang IS, Chatterjee N, Hu W, Wu C, Mitsudomi T, Zheng W, Kim JH, Seow A, Caporaso NE, Shin MH, Chung LP, An SJ, Wang P, Yang Y, Zheng H, Yatabe Y, Zhang XC, Kim YT, Cai Q, Yin Z, Kim YC, Bassig BA, Chang J, Ho JCM, Ji BT, Daigo Y, Ito H, Momozawa Y, Ashikawa K, Kamatani Y, Honda T, Hosgood HD, Sakamoto H, Kunitoh H, Tsuta K, Watanabe SI, Kubo M, Miyagi Y, Nakayama H, Matsumoto S, Tsuboi M, Goto K, Shi J, Song L, Hua X, Takahashi A, Goto A, Minamiya Y, Shimizu K, Tanaka K, Wei F, Matsuda F, Su J, Kim YH, Oh IJ, Song F, Su WC, Chen YM, Chang GC, Chen KY, Huang MS, Chien LH, Xiang YB, Park JY, Kweon SS, Chen CJ, Lee KM, Blechter B, Li H, Gao YT, Qian B, Lu D, Liu J, Jeon HS, Hsiao CF, Sung JS, Tsai YH, Jung YJ, Guo H, Hu Z, Wang WC, Chung CC, Burdett L, Yeager M, Hutchinson A, Berndt SI, Wu W, Pang H, Li Y, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Zhu M, Chen CH, Yang TY, Xu J, Guan P, Tan W, Wang CL, Hsin M, Sit KY, Ho J, Chen Y, Choi YY, Hung JY, Kim JS, Yoon HI, Lin CC, Park IK, Xu P, Wang Y, He Q, Perng RP, Chen CY, Vermeulen R, Wu J, Lim WY, Chen KC, Li YJ, Li J, Chen H, Yu CJ, Jin L, Chen TY, Jiang SS, Liu J, Yamaji T, Hicks B, Wyatt K, Li SA, Dai J, Ma H, Jin G, Song B, Wang Z, Cheng S, Li X, Ren Y, Cui P, Iwasaki M, Shimazu T, Tsugane S, Zhu J, Chen Y, Yang K, Jiang G, Fei K, Wu G, Lin HC, Chen HL, Fang YH, Tsai FY, Hsieh WS, Yu J, Stevens VL, Laird-Offringa IA, Marconett CN, Rieswijk L, Chao A, Yang PC, Shu XO, Wu T, Wu YL, Lin D, Chen K, Zhou B, Huang YC, Kohno T, Shen H, Chanock SJ, Rothman N, Lan Q. Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women. Genomics 2019; 112:1223-1232. [PMID: 31306748 DOI: 10.1016/j.ygeno.2019.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
Abstract
We investigated whether genetic susceptibility to tuberculosis (TB) influences lung adenocarcinoma development among never-smokers using TB genome-wide association study (GWAS) results within the Female Lung Cancer Consortium in Asia. Pathway analysis with the adaptive rank truncated product method was used to assess the association between a TB-related gene-set and lung adenocarcinoma using GWAS data from 5512 lung adenocarcinoma cases and 6277 controls. The gene-set consisted of 31 genes containing known/suggestive associations with genetic variants from previous TB-GWAS. Subsequently, we followed-up with Mendelian Randomization to evaluate the association between TB and lung adenocarcinoma using three genome-wide significant variants from previous TB-GWAS in East Asians. The TB-related gene-set was associated with lung adenocarcinoma (p = 0.016). Additionally, the Mendelian Randomization showed an association between TB and lung adenocarcinoma (OR = 1.31, 95% CI: 1.03, 1.66, p = 0.027). Our findings support TB as a causal risk factor for lung cancer development among never-smoking Asian women.
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Affiliation(s)
- Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Maria Pik Wong
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Jie Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Minsun Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Department of Statistics, Sookmyung Women's University, Seoul, Republic of Korea
| | - Hee Nam Kim
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Chen Wu
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Kinki University School of Medicine, Sayama, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Jin Hee Kim
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul, Republic of Korea
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Lap Ping Chung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
| | - She-Juan An
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ping Wang
- Department of Radiotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Central Hospital, Nagoya, Japan
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Young Tae Kim
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea; Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiang Chang
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - James Chung Man Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Japan; Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kyota Ashikawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takayuki Honda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideo Kunitoh
- Department of Medical Oncology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology and Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Shun-Ichi Watanabe
- Division of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, Kanagawa, Japan
| | - Shingo Matsumoto
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Japan
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita City, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita City, Japan
| | - Kimihiro Shimizu
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Kazumi Tanaka
- Department of Integrative Center of General Surgery, Gunma University Hospital, Gunma, Japan
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jian Su
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yeul Hong Kim
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - In-Jae Oh
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea; Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Gee-Chen Chang
- School of Medicine, Faculty of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Shyan Huang
- Department of Internal Medicine, E-Da Cancer Hospital, School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Li-Hsin Chien
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jae Yong Park
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea; Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea
| | - Chien-Jen Chen
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Kyoung-Mu Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Department of Environmental Health, Korea National Open University, Seoul, Republic of Korea
| | - Batel Blechter
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Haixin Li
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Biyun Qian
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Human Genetics, Genome Institute of Singapore, Singapore; School of Life Sciences, Anhui Medical University, Hefei, China
| | - Hyo-Sung Jeon
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jae Sook Sung
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yoo Jin Jung
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Huan Guo
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen-Chang Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Herbert Pang
- School of BioMedical Sciences, The University of Hong Kong, Hong Kong
| | - Yuqing Li
- Cancer Prevention Institute of California, Fremont, CA, USA
| | - Jin Eun Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Kyong Hwa Park
- Department of Internal Medicine, Division of Oncology/Hematology, College of Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul St Mary's Hospital, The Catholic University of Korea, Republic of Korea
| | - Li Liu
- Department of Oncology, Cancer Center, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - C H Kang
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chung-Hsing Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Wen Tan
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chih-Liang Wang
- Department of Pulmonary and Critical Care, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Michael Hsin
- Department of Cardiothoracic Surgery, Queen Mary Hospital, The University of Hong Kong, China
| | - Ko-Yung Sit
- Department of Cardiothoracic Surgery, Queen Mary Hospital, The University of Hong Kong, China
| | - James Ho
- Department of Medicine, The University of Hong Kong, China
| | - Ying Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yi Young Choi
- Cancer Research Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jen-Yu Hung
- Department of Internal Medicine, E-Da Cancer Hospital, School of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Jun Suk Kim
- Division of Medical Oncology, Department of Internal Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ho Il Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Chien-Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - In Kyu Park
- Department of Thoracic and Cardiovascular Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ping Xu
- Department of Oncology, Wuhan Iron and Steel Corporation Staff Worker Hospital, Wuhan, China
| | - Yuzhuo Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | | | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Junjie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Kun-Chieh Chen
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Jen Li
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Sanjiangdadao, Qujing, China
| | - Hongyan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tzu-Yu Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Gaithersburg, MD, USA
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bao Song
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Zhehai Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Sensen Cheng
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, Shenyang, China
| | - Ping Cui
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Junjie Zhu
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Ying Chen
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Kaiyun Yang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | | | - Ke Fei
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Hsien-Chin Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Hui-Ling Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yao-Huei Fang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Fang-Yu Tsai
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Wan-Shan Hsieh
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jinming Yu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Jinan, China
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Crystal N Marconett
- Department of Surgery, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda Rieswijk
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Ann Chao
- Center for Global Health, National Cancer Institute, Bethesda, MD, USA
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Tangchun Wu
- Department of Occupational and Environmental Health and Ministry of Education Key Lab for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Y L Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dongxin Lin
- Department of Etiology & Carcinogenesis and State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Yun-Chao Huang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Yunnan Cancer Center, Kunming, China
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Yepes S, Tucker M, Koka H, Jones K, Vogt A, Burdette L, Luo W, Zhu B, Yeager M, Hicks B, Freedman ND, Chanock SJ, Goldstein AM, Yang XR. Abstract 1638: Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Known cutaneous malignant melanoma (CMM) genes account for melanoma risk in less than 40% of melanoma-prone families, suggesting the existence of additional risk genes or other modifiers. Whole exome sequencing (WES) of high-risk families usually results in the identification of a large number of potential disease-causing genes. However, prioritizing these genes and finding the true disease-causing ones have been challenging. We hypothesize that physically interacting proteins might have a similar effect on cell function and therefore, might produce a shared phenotype or increase the risk when mutated. To test this hypothesis, we applied a network approach integrating WES and protein-protein interaction (PPI) data to detect and prioritize rare variants in melanoma-prone families.
Methods: We conducted WES analysis on germline DNA of 212 patients from 45 CMM families (2-5 affected people in a family) without known mutations. Variants that were rare (<1% in public and our in-house control datasets), loss-of-function or missense predicted to be deleterious, and showed complete disease co-segregation (present in all affected members within a family) were included in the network analysis. For this analysis, we only focused on genes that interact with known CMM genes (gene list in Goldstein AM, et al. Hum Mol Genet, 2017) which we used as seed proteins. We then applied a degree-aware algorithm (DADA) to rank the set of candidate genes from WES with respect to the set of known CMM genes using human PPI networks. The goal of DADA is to prioritize a candidate set of genes based on their association level with genes known to be related to the disease. Network proximity calculations of the candidates with respect to the seed set were based on Random Walk with Restarts method. We used high quality and scored human proteins interactions collected from InWeb_IM. In the primary analysis, the network contains 625,641 interactions, aggregated from 8 source databases and spanning 87% of reviewed human proteins. We also conducted additional analyses with CMM PPI subnetworks generated using high confidence interaction data from different sources to compare results.
Results: The WES analysis described above identified 546 genes that harbored rare variants, likely affect protein function and co-segregated in affected members in CMM families. After applying DADA across all networks, the rankings of these genes were fairly consistent. Top genes included both known CMM genes (such as MC1R, CDKN2B, KITLG, and TINF2) and genes that have not yet been associated with CMM susceptibility (such as FOXK1, AR, LEF1, RGL4, PABPC1, CHEK2, CTBP2, and BLM). These results highlight the importance of known CMM genes and their networks in CMM susceptibility, and demonstrate the potential value of network approaches in gene prioritization. Further evaluation of novel genes is in progress.
Citation Format: Sally Yepes, Margaret Tucker, Hela Koka, Kristine Jones, Aurelie Vogt, Laurie Burdette, Wen Luo, Bin Zhu, Meredith Yeager, Belynda Hicks, Neal D. Freedman, Stephen J. Chanock, Alisa M. Goldstein, Xiaohong R. Yang. Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1638.
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Khincha PP, Jones K, Teshome K, Hicks B, Mai PL, Savage SA. Abstract 4159: Gonadal mosaicism in a family with TP53-associated Li-Fraumeni syndrome. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer predisposition syndrome with exceptionally high lifetime cancer risks, caused primarily by germline pathogenic variants in TP53. Sarcomas, pre-menopausal breast cancer, brain tumors and adrenocortical carcinomas are the ‘core’ LFS cancers among a multitude of other cancers that can occur. Individuals with LFS are also at risk of developing multiple primary cancers over their lifetime. Clinical criteria have been established to denote LFS and ‘Li-Fraumeni like’ (LFL) families to facilitate genetic testing for TP53. De novo pathogenic germline variants in TP53 are estimated to cause between 7-25% of LFS. Gonadal mosaicism is an alternate explanation for presumed de novo variants and is yet to be described in LFS.
We present a proband who developed WHO grade II astrocytoma at age 18 years, who had a deceased brother with osteosarcoma diagnosed at age 13 years, and a healthy older sibling. The only other cancer history was leukemia at age 62 years in the paternal grandmother, who also had polycythemia vera. The family meets Eele’s criteria for LFL. The proband’s germline genetic testing revealed a heterozygous TP53 c.743G>A p.R248Q pathogenic variant. Subsequent clinical genetic testing of the parents failed to reveal the variant, and the proband was presumed to have a de novo variant. Given the characteristic LFS-associated cancers in the brothers, we investigated further and identified the same TP53 pathogenic variant in the brother’s osteosarcoma tissue and pathology-confirmed benign liver tissue. TP53 sequencing of the brother’s tumor did not show loss of heterozygosity. Parental relationships to the proband and brother were confirmed through STR-based identifiler profiling. Ultra-deep sequencing (>50,000x) of DNA derived from the parents’ blood, saliva and father’s benign colon polyp did not identify the variant, thus ruling out somatic mosaicism in the parents. We were unable to test gonadal tissues from the parents. In the setting of two siblings with the same pathogenic variant in TP53 which is absent in both parents, this family presents a case of assumed gonadal mosaicism resulting from a post-zygotic event.
The possibility of gonadal mosaicism presents complexity in genetic counselling of families with inherited disorders, and a conundrum in syndromes such as TP53-associated LFS where the presumed de novo rate is high and cancer risks are significantly elevated. The presented family suggests that further investigation of individuals with presumed de novo variation, especially in the setting of suspicious family cancer history, is required to accurately identify family members at-risk.
Citation Format: Payal P. Khincha, Kristine Jones, Kedest Teshome, Belynda Hicks, Phuong L. Mai, Sharon A. Savage. Gonadal mosaicism in a family with TP53-associated Li-Fraumeni syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4159.
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Affiliation(s)
| | | | | | | | - Phuong L. Mai
- 3University of Pittsburgh School of Medicine, Pittsburgh, PA
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Morton LM, Karyadi DM, Hartley S, Frone M, Sampson JN, Howell RM, Neglia JP, Arnold MA, Dagnall CL, Hicks B, Kristine J, Zhu B, Leisenring WM, Yasui Y, Bhatia S, Robison LL, Tucker MA, Armstrong GT, Chanock SJ. Subsequent neoplasm risk associated with rare variants in DNA repair and clinical radiation sensitivity syndrome genes: A report from the Childhood Cancer Survivor Study. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.10028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
10028 Background: Radiotherapy for childhood cancer is associated with strikingly elevated risk for developing subsequent neoplasms (SNs). Whether mutations in DNA repair and radiation sensitivity genes modulate SN risks is largely unknown. Methods: We conducted whole-exome sequencing in 5105 long-term childhood cancer survivors of European descent (mean follow-up = 32.7 years). SnpEff and ClinVar identified potentially damaging rare variants in 476 DNA repair or radiation sensitivity genes. Conditional logistic regression assessed SN risk associated with these variants aggregated by gene or pathway (N = 155 with ≥5 carriers). Controls were matched on sex, childhood cancer type and diagnosis age, radiation dose to the SN site, and survival. Exact p-values were calculated by permutation. Analyses used all survivors or subsets stratified on radiation dose. Results: A total of 1108 (21.7%) survivors developed at least one SN type known to be related to ionizing radiation exposure (e.g., breast cancer, basal cell carcinoma, meningioma, thyroid cancer, sarcoma). Radiation-related SN risk was associated with homologous recombination (HR) gene variants for SN sites that received > 0- < 10 Gy (20.9% cases, 11.0% controls; odds ratio [OR] = 2.20, 95% confidence interval [CI] 1.52-3.18; P = 1.41x10-4), most notably for FANCM (3.1% cases, 0.5% controls; OR = 9.91, 95%CI 3.73-26.4; P = 2.85x10-4). For radiation-related SNs at sites with higher doses (≥10 Gy), associations were not observed for the HR pathway (14.4% cases, 12.4% controls, P = 0.17) but were observed for two individual genes implicated in double-strand DNA break repair, EXO1 (1.8% cases, 0.4% controls; OR = 6.50, 95%CI 3.49-12.1; P = 7.43x10-4) and NEIL3 (0% cases, 1.0% controls; P = 3.23x10-4). Conclusions: In this discovery study, we identified dose-specific novel associations between SN risk after radiotherapy for childhood cancer and potentially damaging rare variants in genes involved in double-strand DNA break repair, particularly HR. If replicated, these results could impact long-term screening of childhood cancer survivors and risk-benefit assessments of treatment approaches.
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Affiliation(s)
- Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Megan Frone
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Rebecca M. Howell
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jones Kristine
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Yutaka Yasui
- St. Jude Children's Research Hospital, Memphis, TN
| | - Smita Bhatia
- University of Alabama at Birmingham, Birmingham, AL
| | | | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
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Bailey ST, Hicks B, Zhu B, Hu N, Taylor PR, Gulcher JR, Sun H, Lund J, Oliner K, Williams RT, Chanock SJ, Goldstein AM. SeqPlus sequencing methodology enables robust whole-genome sequencing, true variant detection, and novel genomic insights from archival esophageal carcinoma FFPE samples. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13016 Background: Whole-genome sequencing (WGS) of formalin-fixed, paraffin-embedded (FFPE) samples could enable novel insights from archival sample collections, yet robust FFPE WGS is challenged by fragmented DNA, uneven genomic coverage & sequencing artifacts attributed to FFPE fixation. We report our proprietary extraction & library preparation methodology (SeqPlus) with high quality, uniform WGS sequencing performance comparable to that from fresh-frozen samples. Methods: We analyzed 20 paired esophageal carcinoma (EC) samples i.e., primary tumors & matched germline samples to assess SeqPlus performance on 10-15-year-old FFPE tissues, measure variant concordance between WGS and a high-depth sequencing panel (269 genes, 400x coverage) & identify novel genomic features. Results: At a targeted 70x WGS tumor sequencing depth, 93% of the genome was covered by ³ 20 reads, 99% of bases had 10x coverage & average duplicate reads were 31%. We noted similar transition/transversion ratios & mutational spectra as from fresh-frozen EC specimens, suggesting that extraction & library preparation contributes to prior FFPE artifacts. Concordance of tumor-specific SNVs & indels derived from WGS & targeted panel was high at 86%. All 76 targeted panel-detected variants above the WGS limit of detection (mutant allele frequency [MAF] > 10%) were detected by WGS, 2 variants (2 tumors) were detected only by WGS, and 12 variants at MAF ≤ 6% (9 tumors) were only detected by the targeted panel. Tumor WGS yielded SNV, indels & CNV findings beyond variants detected by targeted sequencing. WGS enabled detection of 10.4 putative cancer variants per tumor compared to 12 variants per patient from frozen specimens and a median of 7 (up to 16) cancer-associated variants in genes outside the targeted panel. WGS copy number analysis revealed CCND1, EGFR, TP63, and SOX2amplification, CDKN2A/B deletion and additional unrecognized genomic aberrations. Conclusions: Our study reinforces the utility of high-quality, uniform WGS sequencing of archival FFPE cancer samples with SeqPlus and unlocks the potential for massive-scale retrospective genomic analysis of archived pathology samples with associated clinical & outcomes data.
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Affiliation(s)
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Bin Zhu
- National Cancer Institute DCEG, Biostatistics Branch, Bethesda, MD
| | - Nan Hu
- National Cancer Institute, Bethesda, MD
| | | | | | | | - Jim Lund
- WuXi NextCODE Genomics, Cambridge, MA
| | | | | | | | - Alisa M. Goldstein
- National Cancer Institute Division of Cancer Epidemiology & Genetics, Clinical Genetics Branch, Bethesda, MD
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Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies. Breast Cancer Res 2019; 21:62. [PMID: 31101124 PMCID: PMC6525390 DOI: 10.1186/s13058-019-1145-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date. METHODS We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing. RESULTS The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98). CONCLUSIONS Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.
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Affiliation(s)
- Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | | | - Joshua N. Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Belynda Hicks
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Eric Karlins
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Amy Hutchinson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Dallas English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Silvia Polidoro
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manuela Assumma
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Gianluca Severi
- CESP (U1018 INSERM, Équipe Générations et Santé), Facultés de médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Roger L. Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
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49
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McMaster ML, Sun C, Landi MT, Savage SA, Rotunno M, Yang XR, Jones K, Vogt A, Hutchinson A, Zhu B, Wang M, Hicks B, Thirunavukarason A, Stewart DR, Koutros S, Goldstein AM, Chanock SJ, Caporaso NE, Tucker MA, Goldin LR, Liu Y. Germline mutations in Protection of Telomeres 1 in two families with Hodgkin lymphoma. Br J Haematol 2019; 181:372-377. [PMID: 29693246 DOI: 10.1111/bjh.15203] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/29/2023]
Abstract
In a previous whole exome sequencing of patients from 41 families with Hodgkin lymphoma, we identified two families with distinct heterozygous rare coding variants in POT1 (D224N and Y36H), both in a highly conserved region of the gene. POT1 D224N mutant did not bind to a single-stranded telomere oligonucleotide in vitro suggesting the mutation perturbs POT1's ability to bind to the telomeric G-rich overhang. Human HT1080 cells expressing POT1 D224N and lymphoblastoid cells carrying Y36H both showed increased telomere length and fragility in comparison to wild type cells. This strongly suggests that mutant POT1 causes chromosome instability and may play a role in lymphomagenesis in these families.
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Affiliation(s)
- Mary L McMaster
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Chongkui Sun
- Laboratory of Molecular Gerontology, National Institute on Aging/National Institute of Health, Baltimore, MD, USA
| | - Maria T Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Melissa Rotunno
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Xiaohong R Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Aurélie Vogt
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Anand Thirunavukarason
- Laboratory of Molecular Gerontology, National Institute on Aging/National Institute of Health, Baltimore, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Alisa M Goldstein
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Margaret A Tucker
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Lynn R Goldin
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute; NIH, Bethesda, MD, USA
| | - Yie Liu
- Laboratory of Molecular Gerontology, National Institute on Aging/National Institute of Health, Baltimore, MD, USA
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50
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Kim J, Luo W, Wang M, Wegman-Ostrosky T, Frone MN, Johnston JJ, Nickerson ML, Rotunno M, Li SA, Achatz MI, Brodie SA, Dean M, de Andrade KC, Fortes FP, Gianferante M, Khincha P, McMaster ML, McReynolds LJ, Pemov A, Pinheiro M, Santiago KM, Alter BP, Caporaso NE, Gadalla SM, Goldin LR, Greene MH, Loud J, Yang XR, Freedman ND, Gapstur SM, Gaudet MM, Calista D, Ghiorzo P, Fargnoli MC, Nagore E, Peris K, Puig S, Landi MT, Hicks B, Zhu B, Liu J, Sampson JN, Chanock SJ, Mirabello LJ, Morton LM, Biesecker LG, Tucker MA, Savage SA, Goldstein AM, Stewart DR. Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls. Genome Med 2018; 10:99. [PMID: 30583724 PMCID: PMC6305568 DOI: 10.1186/s13073-018-0607-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Prior research has established that the prevalence of pathogenic/likely pathogenic (P/LP) variants across all of the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes is approximately 0.8–5%. We investigated the prevalence of P/LP variants in the 24 ACMG SF v2.0 cancer genes in a family-based cancer research cohort (n = 1173) and in cancer-free ethnicity-matched controls (n = 982). Methods We used InterVar to classify variants and subsequently conducted a manual review to further examine variants of unknown significance (VUS). Results In the 24 genes on the ACMG SF v2.0 list associated with a cancer phenotype, we observed 8 P/LP unique variants (8 individuals; 0.8%) in controls and 11 P/LP unique variants (14 individuals; 1.2%) in cases, a non-significant difference. We reviewed 115 VUS. The median estimated per-variant review time required was 30 min; the first variant within a gene took significantly (p = 0.0009) longer to review (median = 60 min) compared with subsequent variants (median = 30 min). The concordance rate was 83.3% for the variants examined by two reviewers. Conclusion The 115 VUS required database and literature review, a time- and labor-intensive process hampered by the difficulty in interpreting conflicting P/LP determinations. By rigorously investigating the 24 ACMG SF v2.0 cancer genes, our work establishes a benchmark P/LP variant prevalence rate in a familial cancer cohort and controls. Electronic supplementary material The online version of this article (10.1186/s13073-018-0607-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,División de Investigación, Instituto Nacional de Cancerología, 14080, Mexico City, Mexico
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Melissa Rotunno
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shengchao A Li
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Maria I Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,Centro de Oncologia, Hospital Sirio-Libanes, Sao Paulo, SP, 013050-050, Brazil
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Fernanda P Fortes
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Payal Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mary L McMaster
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Maisa Pinheiro
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Karina M Santiago
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lynn R Goldin
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Xiaohong R Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, IRCCS Ospedale Policinico San Martino, Genoa, Italy
| | | | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Ketty Peris
- Institute of Dermatology, Catholic University - Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clinic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain & Centro de Investigacion Biomedica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Maria Teresa Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, Human Genetics Program National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alisa M Goldstein
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
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