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Purdue MP, Dutta D, Machiela MJ, Gorman BR, Winter T, Okuhara D, Cleland S, Ferreiro-Iglesias A, Scheet P, Liu A, Wu C, Antwi SO, Larkin J, Zequi SC, Sun M, Hikino K, Hajiran A, Lawson KA, Cárcano F, Blanchet O, Shuch B, Nepple KG, Margue G, Sundi D, Diver WR, Folgueira MAAK, van Bokhoven A, Neffa F, Brown KM, Hofmann JN, Rhee J, Yeager M, Cole NR, Hicks BD, Manning MR, Hutchinson AA, Rothman N, Huang WY, Linehan WM, Lori A, Ferragu M, Zidane-Marinnes M, Serrano SV, Magnabosco WJ, Vilas A, Decia R, Carusso F, Graham LS, Anderson K, Bilen MA, Arciero C, Pellegrin I, Ricard S, Scelo G, Banks RE, Vasudev NS, Soomro N, Stewart GD, Adeyoju A, Bromage S, Hrouda D, Gibbons N, Patel P, Sullivan M, Protheroe A, Nugent FI, Fournier MJ, Zhang X, Martin LJ, Komisarenko M, Eisen T, Cunningham SA, Connolly DC, Uzzo RG, Zaridze D, Mukeria A, Holcatova I, Hornakova A, Foretova L, Janout V, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Gaborieau V, Abedi-Ardekani B, McKay J, Johansson M, Phouthavongsy L, Hayman L, Li J, Lungu I, Bezerra SM, Souza AG, Sares CTG, Reis RB, Gallucci FP, Cordeiro MD, Pomerantz M, Lee GSM, Freedman ML, Jeong A, Greenberg SE, Sanchez A, Thompson RH, Sharma V, Thiel DD, Ball CT, Abreu D, Lam ET, Nahas WC, Master VA, Patel AV, Bernhard JC, Freedman ND, Bigot P, Reis RM, Colli LM, Finelli A, Manley BJ, Terao C, Choueiri TK, Carraro DM, Houlston R, Eckel-Passow JE, Abbosh PH, Ganna A, Brennan P, Gu J, Chanock SJ. Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions. Nat Genet 2024:10.1038/s41588-024-01725-7. [PMID: 38671320 DOI: 10.1038/s41588-024-01725-7] [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] [Received: 08/08/2023] [Accepted: 03/13/2024] [Indexed: 04/28/2024]
Abstract
Here, in a multi-ancestry genome-wide association study meta-analysis of kidney cancer (29,020 cases and 835,670 controls), we identified 63 susceptibility regions (50 novel) containing 108 independent risk loci. In analyses stratified by subtype, 52 regions (78 loci) were associated with clear cell renal cell carcinoma (RCC) and 6 regions (7 loci) with papillary RCC. Notably, we report a variant common in African ancestry individuals ( rs7629500 ) in the 3' untranslated region of VHL, nearly tripling clear cell RCC risk (odds ratio 2.72, 95% confidence interval 2.23-3.30). In cis-expression quantitative trait locus analyses, 48 variants from 34 regions point toward 83 candidate genes. Enrichment of hypoxia-inducible factor-binding sites underscores the importance of hypoxia-related mechanisms in kidney cancer. Our results advance understanding of the genetic architecture of kidney cancer, provide clues for functional investigation and enable generation of a validated polygenic risk score with an estimated area under the curve of 0.65 (0.74 including risk factors) among European ancestry individuals.
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Affiliation(s)
- Mark P Purdue
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Diptavo Dutta
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Timothy Winter
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | | | | | - Paul Scheet
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aoxing Liu
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chao Wu
- Biosample Repository, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Samuel O Antwi
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - James Larkin
- Department of Medical Oncology, Royal Marsden NHS Foundation Trust, London, UK
| | - Stênio C Zequi
- Department of Urology, A.C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation INCIT-INOTE, São Paulo, Brazil
- Latin American Renal Cancer Group, São Paulo, Brazil
- Department of Surgery, Division of Urology, São Paulo Federal University, São Paulo, Brazil
| | - Maxine Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ali Hajiran
- Department of Urology, Division of Urologic Oncology, West Virginia University Cancer Institute, Morgantown, WV, USA
| | - Keith A Lawson
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Flavio Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Brian Shuch
- Department of Urology, UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Kenneth G Nepple
- Department of Urology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Gaëlle Margue
- Department of Urology, CHU Bordeaux, Bordeaux, France
| | - Debasish Sundi
- Department of Urology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Maria A A K Folgueira
- Departments of Radiology and Oncology, Comprehensive Center for Precision Oncology-C2PO, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas, Faculdade de Medicina Universidade de São Paulo, São Paulo, Brazil
| | - Adrie van Bokhoven
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jongeun Rhee
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Nathan R Cole
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Michelle R Manning
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | | | | | - Sérgio V Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Ana Vilas
- Department of Pathology, Hospital Pasteur, Montevideo, Uruguay
| | - Ricardo Decia
- Department of Urology, Hospital Pasteur, Montevideo, Uruguay
| | | | - Laura S Graham
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kyra Anderson
- Oncology Clinical Research Support Team, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mehmet A Bilen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Cletus Arciero
- Department of Surgery, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Solène Ricard
- Department of Urology, CHU Bordeaux, Bordeaux, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Department of Oncology, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naeem Soomro
- Department of Urology, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK
| | - Grant D Stewart
- Department of Urology, Western General Hospital, NHS Lothian, Edinburgh, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Adebanji Adeyoju
- Department of Urology, Stockport NHS Foundation Trust, Stockport, UK
| | - Stephen Bromage
- Department of Urology, Stockport NHS Foundation Trust, Stockport, UK
| | - David Hrouda
- Department of Urology, Imperial College Healthcare NHS Trust, London, UK
| | - Norma Gibbons
- Department of Urology, Imperial College Healthcare NHS Trust, London, UK
| | - Poulam Patel
- Division of Oncology, University of Nottingham, Nottingham, UK
| | - Mark Sullivan
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Andrew Protheroe
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Francesca I Nugent
- Department of Urology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | | | - Xiaoyu Zhang
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisa J Martin
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Maria Komisarenko
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sonia A Cunningham
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denise C Connolly
- Cancer Signaling and Microenvironment, Biosample Repository Facility, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Robert G Uzzo
- Department of Urology, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - David Zaridze
- Department of Clinical Epidemiology, N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeria
- Department of Clinical Epidemiology, N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- Department of Occupational Health and Toxicology, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Academy of Romanian Scientists, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, Clinical Hospital Center Dr Dragisa Misovic Dedinje, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organisation for Cancer Prevention and Research, Belgrade, Serbia
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | | | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lindsay Hayman
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jason Li
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Aline G Souza
- Departments of Medical Imaging, Hematology and Oncology, Division of Medical Oncology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Claudia T G Sares
- Departments of Surgery and Anatomy, Division of Urology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Rodolfo B Reis
- Departments of Surgery and Anatomy, Division of Urology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Fabio P Gallucci
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mauricio D Cordeiro
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gwo-Shu M Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Anhyo Jeong
- Department of Urology, UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Samantha E Greenberg
- Department of Population Sciences, Genetic Counseling Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Alejandro Sanchez
- Department of Surgery, Division of Urology, Huntsman Cancer Institute and University of Utah, Salt Lake City, UT, USA
| | | | - Vidit Sharma
- Department of Urology, Mayo Clinic, Rochester, MN, USA
| | - David D Thiel
- Department of Urology, Mayo Clinic, Jacksonville, FL, USA
| | - Colleen T Ball
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Diego Abreu
- Department of Urology, Hospital Pasteur, Montevideo, Uruguay
| | - Elaine T Lam
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - William C Nahas
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Viraj A Master
- Department of Urology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | | | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Pierre Bigot
- Department of Urology, CHU Angers, Angers, France
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Leandro M Colli
- Departament of Medical Image, Hematology and Oncology, Division of Medical Oncology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Antonio Finelli
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brandon J Manley
- Genitourinary Oncology Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dirce M Carraro
- Clinical and Functional Genomics Group, CIPE (International Research Center), A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Philip H Abbosh
- Department of Nuclear Dynamics and Cancer, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Jian Gu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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Wu Z, Pfeiffer RM, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Knight R, Biritwum R, Yarney J, Wiafe S, Awuah B, Nyarko K, Garcia-Closas M, Sinha R, Figueroa JD, Brinton LA, Trabert B, Vogtmann E. Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study. Microbiol Spectr 2023; 11:e0157223. [PMID: 37341612 PMCID: PMC10433996 DOI: 10.1128/spectrum.01572-23] [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: 04/24/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
The human fecal and oral microbiome may play a role in the etiology of breast cancer through modulation of endogenous estrogen metabolism. This study aimed to investigate associations of circulating estrogens and estrogen metabolites with the fecal and oral microbiome in postmenopausal African women. A total of 117 women with fecal (N = 110) and oral (N = 114) microbiome data measured by 16S rRNA gene sequencing, and estrogens and estrogen metabolites data measured by liquid chromatography tandem mass spectrometry were included. The outcomes were measures of the microbiome and the independent variables were the estrogens and estrogen metabolites. Estrogens and estrogen metabolites were associated with the fecal microbial Shannon index (global P < 0.01). In particular, higher levels of estrone (β = 0.36, P = 0.03), 2-hydroxyestradiol (β = 0.30, P = 0.02), 4-methoxyestrone (β = 0.51, P = 0.01), and estriol (β = 0.36, P = 0.04) were associated with higher levels of the Shannon index, while 16alpha-hydroxyestrone (β = -0.57, P < 0.01) was inversely associated with the Shannon index as indicated by linear regression. Conjugated 2-methoxyestrone was associated with oral microbial unweighted UniFrac as indicated by MiRKAT (P < 0.01) and PERMANOVA, where conjugated 2-methoxyestrone explained 2.67% of the oral microbial variability, but no other estrogens or estrogen metabolites were associated with any other beta diversity measures. The presence and abundance of multiple fecal and oral genera, such as fecal genera from families Lachnospiraceae and Ruminococcaceae, were associated with several estrogens and estrogen metabolites as indicated by zero-inflated negative binomial regression. Overall, we found several associations of specific estrogens and estrogen metabolites and the fecal and oral microbiome. IMPORTANCE Several epidemiologic studies have found associations of urinary estrogens and estrogen metabolites with the fecal microbiome. However, urinary estrogen concentrations are not strongly correlated with serum estrogens, a known risk factor for breast cancer. To better understand whether the human fecal and oral microbiome were associated with breast cancer risk via the regulation of estrogen metabolism, we conducted this study to investigate the associations of circulating estrogens and estrogen metabolites with the fecal and oral microbiome in postmenopausal African women. We found several associations of parent estrogens and several estrogen metabolites with the microbial communities, and multiple individual associations of estrogens and estrogen metabolites with the presence and abundance of multiple fecal and oral genera, such as fecal genera from families Lachnospiraceae and Ruminococcaceae, which have estrogen metabolizing properties. Future large, longitudinal studies to investigate the dynamic changes of the fecal and oral microbiome and estrogen relationship are needed.
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Affiliation(s)
- Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Doratha A. Byrd
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Casey L. Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Thomas U. Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | | | | | - Seth Wiafe
- School of Public Health, Loma Linda University, Loma Linda, California, USA
| | | | | | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jonine D. Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Britton Trabert
- Department of Obstetrics and Gynecology, University of Utah, and Huntsman Cancer Institute at the University of Utah, Salt Lake City, Utah, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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3
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Wu Z, Han Y, Wan Y, Hua X, Chill SS, Teshome K, Zhou W, Liu J, Wu D, Hutchinson A, Jones K, Dagnall CL, Hicks BD, Liao L, Hallen-Adams H, Shi J, Abnet CC, Sinha R, Chaturvedi A, Vogtmann E. Oral microbiome and risk of incident head and neck cancer: A nested case-control study. Oral Oncol 2023; 137:106305. [PMID: 36610232 PMCID: PMC9877180 DOI: 10.1016/j.oraloncology.2022.106305] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/26/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
OBJECTIVES This nested case-control study in the NIH-AARP Diet and Health Study was carried out to prospectively investigate the relationship of oral microbiome with head and neck cancer (HNC). MATERIALS AND METHODS 56 incident HNC cases were identified, and 112 controls were incidence-density matched to cases. DNA extracted from pre-diagnostic oral wash samples was whole-genome shotgun metagenomic sequenced to measure the overall oral microbiome. ITS2 gene qPCR was used to measure the presence of fungi. ITS2 gene sequencing was performed on ITS2 gene qPCR positive samples. We computed taxonomic and functional alpha-diversity and beta-diversity metrics. The presence and relative abundance of groups of red-complex (e.g., Porphyromonas gingivalis) and/or orange-complex (e.g., Fusobacterium nucleatum) periodontal pathogens were compared between cases and controls using conditional logistic regression models and MiRKAT. RESULTS Participants with higher taxonomic microbial alpha-diversity had a non-statistically significant decreased risk of HNC. No case-control differences were found for beta diversity by MiRKAT model (all p > 0.05). A greater relative abundance of red-complex periodontal pathogens (OR = 0.51, 95 % CI = 0.26-1.00), orange-complex (OR = 0.38, 95 % CI = 0.18-0.83), and both complexes' pathogens (OR = 0.32, 95 % CI = 0.14-0.75), were associated with reduced risk of HNC. The presence of oral fungi was also strongly associated with reduced risk of HNC compared with controls (OR = 0.39, 95 % CI = 0.17-0.92). CONCLUSION Greater taxonomic alpha-diversity, the presence of oral fungi, and the presence or relative abundance of multiple microbial species, including the red- and orange-complex periodontal pathogens, were associated with reduced risk of HNC. Future studies with larger sample sizes are needed to evaluate these associations.
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Affiliation(s)
- Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Yongli Han
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xing Hua
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Samantha S Chill
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Kedest Teshome
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dongjing Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Linda Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Heather Hallen-Adams
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Anil Chaturvedi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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4
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Yano Y, Vogtmann E, Shreves AH, Weinstein SJ, Black A, Diaz-Mayoral N, Wan Y, Zhou W, Hua X, Dagnall CL, Hutchinson A, Jones K, Hicks BD, Wyatt K, Brotzman M, Gerlanc N, Huang WY, Albert PS, Wentzensen N, Abnet CC. Evaluation of alcohol-free mouthwash for studies of the oral microbiome. PLoS One 2023; 18:e0284956. [PMID: 37104300 PMCID: PMC10138257 DOI: 10.1371/journal.pone.0284956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Oral bacteria play important roles in human health and disease. Oral samples collected using ethanol-containing mouthwash are widely used for oral microbiome studies. However, ethanol is flammable and not ideal for transportation/storage in large quantities, and some individuals may avoid ethanol due to the burning sensation or due to various personal, medical, religious, and/or cultural factors. Here, we compared ethanol-free and ethanol-containing mouthwashes using multiple microbiome metrics and assessed the stability of the mouthwash samples stored up to 10 days before processing. Forty volunteers provided oral wash samples collected using ethanol-free and ethanol-containing mouthwashes. From each sample, one aliquot was immediately frozen, one was stored at 4°C for 5 days and frozen, while the third aliquot was stored for 5 days at 4°C and 5 days at ambient temperature to mimic shipping delays and then frozen. DNA was extracted, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatic processing was performed using QIIME 2. Microbiome metrics measured in the two mouthwash types were very similar, with intraclass correlation coefficients (ICCs) for alpha and beta diversity metrics greater than 0.85. Relative abundances of some taxa were significantly different, but ICCs of the top four most abundant phyla and genera were high (> 0.75) for the comparability of the mouthwashes. Stability during delayed processing was also high for both mouthwashes based on alpha and beta diversity measures and relative abundances of the top four phyla and genera (ICCs ≥ 0.90). These results demonstrate ethanol-free mouthwash performs similarly to ethanol-containing mouthwash for microbial analyses, and both mouthwashes are stable for at least 10 days without freezing prior to laboratory processing. Ethanol-free mouthwash is suitable for collecting and shipping oral wash samples, and these results have important implications for planning future epidemiologic studies of the oral microbiome.
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Affiliation(s)
- Yukiko Yano
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emily Vogtmann
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alaina H Shreves
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Black
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Norma Diaz-Mayoral
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Yunhu Wan
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Weiyin Zhou
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Xing Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle Washington, United States of America
| | - Casey L Dagnall
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Belynda D Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kathleen Wyatt
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Michelle Brotzman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicole Gerlanc
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Wen-Yi Huang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Paul S Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Christian C Abnet
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
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5
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Sargen MR, Helgadottir H, Yang XR, Harland M, Hatton JN, Jones K, Hicks BD, Hutchinson A, Curry M, Tucker MA, Goldstein AM, Pfeiffer RM. Impact of Transcript (p16/p14ARF) Alteration on Cancer Risk in CDKN2A Germline Pathogenic Variant Carriers. JNCI Cancer Spectr 2022; 6:6767842. [PMID: 36269225 DOI: 10.1093/jncics/pkac074] [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] [Received: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Few studies have evaluated the relationship between CDKN2A germline pathogenic variants (GPV), transcript (p16, p14ARF) alteration, and cancer risk. METHODS Standardized incidence ratios (SIRs) comparing cancer risk to the general population were calculated for 385 CDKN2A GPV carriers from two large cohorts (259 United States and 126 Swedish individuals) using Poisson regression; statistical significance was defined as P<.002 (Bonferroni correction). Cumulative incidence is reported for melanoma and non-melanoma cancer. RESULTS Incidence was significantly increased for melanoma (SIR = 159.8, 95% confidence interval [CI] = 132.1 to 193.2), pancreatic cancer (SIR = 24.1, 95% CI = 14.7 to 39.4), head and neck squamous cell carcinoma (HNSCC; SIR = 16.2, 95% CI = 9.5 to 27.6), and lung cancer (SIR = 5.6, 95% CI = 3.4 to 9.1) in GPV carriers. Similar associations were observed with p16 alteration. Combined p16 and p14ARF alteration was associated with increased incidence of esophageal cancer (SIR = 16.7, 95% CI = 5.7 to 48.9) and malignant peripheral nerve sheath tumor (SIR = 113.0, 95% CI = 16.4 to 780.9), although cancer events were limited (n < 5 for each malignancy). Cumulative incidence at age 70 for melanoma and non-melanoma cancer was 68.3% (95% CI = 68.0 to 68.6) and 35.2% (95% CI = 34.9 to 35.6), respectively. 89% of smoking-related cancers (lung, HNSCC, pancreatic, esophageal) occurred in ever smokers. CONCLUSION These findings highlight the impact of p16 and p14ARF alteration on cancer risk. Smoking was an important risk factor for smoking-related cancers in our study.
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Affiliation(s)
- Michael R Sargen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Jessica N Hatton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Bethesda, Maryland, United States
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Bethesda, Maryland, United States
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Bethesda, Maryland, United States
| | - Michael Curry
- Information Management Services, Inc., Calverton, Maryland, United States
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
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6
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Wu Z, Byrd DA, Wan Y, Ansong D, Clegg-Lamptey JN, Wiafe-Addai B, Edusei L, Adjei E, Titiloye N, Dedey F, Aitpillah F, Oppong J, Vanderpuye V, Osei-Bonsu E, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Ahearn TU, Shi J, Knight R, Biritwum R, Yarney J, Seth Wiafe, Awuah B, Nyarko K, Figueroa JD, Sinha R, Garcia-Closas M, Brinton LA, Vogtmann E. The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study. Int J Cancer 2022; 151:1248-1260. [PMID: 35657343 PMCID: PMC9420782 DOI: 10.1002/ijc.34145] [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: 12/07/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/24/2022]
Abstract
The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faith's Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r = -.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls.
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Affiliation(s)
- Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Doratha A Byrd
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Casey L. Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Lab for Cancer Research, Frederick, MD USA
| | - Thomas U. Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | | | - Seth Wiafe
- School of Public Health, Loma Linda University, Loma Linda, CA, USA
| | | | | | - Jonine D. Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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7
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Vogtmann E, Hua X, Yu G, Purandare V, Hullings AG, Shao D, Wan Y, Li S, Dagnall CL, Jones K, Hicks BD, Hutchinson A, Caporaso JG, Wheeler W, Sandler DP, Beane Freeman LE, Liao LM, Huang WY, Freedman ND, Caporaso NE, Sinha R, Gail MH, Shi J, Abnet CC. The Oral Microbiome and Lung Cancer Risk: An Analysis of 3 Prospective Cohort Studies. J Natl Cancer Inst 2022; 114:1501-1510. [PMID: 35929779 PMCID: PMC9664178 DOI: 10.1093/jnci/djac149] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/08/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Previous studies suggested associations between the oral microbiome and lung cancer, but studies were predominantly cross-sectional and underpowered. METHODS Using a case-cohort design, 1306 incident lung cancer cases were identified in the Agricultural Health Study; National Institutes of Health-AARP Diet and Health Study; and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Referent subcohorts were randomly selected by strata of age, sex, and smoking history. DNA was extracted from oral wash specimens using the DSP DNA Virus Pathogen kit, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatics were conducted using QIIME 2. Hazard ratios and 95% confidence intervals were calculated using weighted Cox proportional hazards models. RESULTS Higher alpha diversity was associated with lower lung cancer risk (Shannon index hazard ratio = 0.90, 95% confidence interval = 0.84 to 0.96). Specific principal component vectors of the microbial communities were also statistically significantly associated with lung cancer risk. After multiple testing adjustment, greater relative abundance of 3 genera and presence of 1 genus were associated with greater lung cancer risk, whereas presence of 3 genera were associated with lower risk. For example, every SD increase in Streptococcus abundance was associated with 1.14 times the risk of lung cancer (95% confidence interval = 1.06 to 1.22). Associations were strongest among squamous cell carcinoma cases and former smokers. CONCLUSIONS Multiple oral microbial measures were prospectively associated with lung cancer risk in 3 US cohort studies, with associations varying by smoking history and histologic subtype. The oral microbiome may offer new opportunities for lung cancer prevention.
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Affiliation(s)
- Emily Vogtmann
- Correspondence to: Emily Vogtmann, PhD, MPH, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr, MSC 9768, Bethesda, MD 20892, USA (e-mail: )
| | | | - Guoqin Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Vaishnavi Purandare
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Autumn G Hullings
- Nutrition Department, University of North Carolina, Chapel Hill, NC, USA
| | - Dantong Shao
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc, Frederick, MD, USA
| | - Shilan Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, Washington, DC, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc, Frederick, MD, USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA,Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc, Frederick, MD, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Dale P Sandler
- Epidemiology Branch, Chronic Disease Epidemiology Group, National Institute for Environmental Health Science, Research Triangle Park, NC, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Linda M Liao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mitchell H Gail
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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8
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Ahearn TU, Choudhury PP, Derkach A, Wiafe-Addai B, Awuah B, Yarney J, Edusei L, Titiloye N, Adjei E, Vanderpuye V, Aitpillah F, Dedey F, Oppong J, Osei-Bonsu EB, Duggan MA, Brinton LA, Allen J, Luccarini C, Baynes C, Carvalho S, Dunning AM, Davis Lynn BC, Chanock SJ, Hicks BD, Yeager M, Chatterjee N, Biritwum R, Clegg-Lamptey JN, Nyarko K, Wiafe S, Ansong D, Easton DF, Figueroa JD, Garcia-Closas M. Breast Cancer Risk in Women from Ghana Carrying Rare Germline Pathogenic Mutations. Cancer Epidemiol Biomarkers Prev 2022; 31:1593-1601. [PMID: 35654374 DOI: 10.1158/1055-9965.epi-21-1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/09/2021] [Revised: 03/16/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Risk estimates for women carrying germline mutations in breast cancer susceptibility genes are mainly based on studies of European ancestry women. METHODS We investigated associations between pathogenic variants (PV) in 34 genes with breast cancer risk in 871 cases [307 estrogen receptor (ER)-positive, 321 ER-negative, and 243 ER-unknown] and 1,563 controls in the Ghana Breast Health Study (GBHS), and estimated lifetime risk for carriers. We compared results with those for European, Asian, and African American ancestry women. RESULTS The frequency of PV in GBHS for nine breast cancer genes was 8.38% in cases and 1.22% in controls. Relative risk estimates for overall breast cancer were: (OR, 13.70; 95% confidence interval (CI), 4.03-46.51) for BRCA1, (OR, 7.02; 95% CI, 3.17-15.54) for BRCA2, (OR, 17.25; 95% CI, 2.15-138.13) for PALB2, 5 cases and no controls carried TP53 PVs, and 2.10, (0.72-6.14) for moderate-risk genes combined (ATM, BARD1, CHEK2, RAD51C, RAD52D). These estimates were similar to those previously reported in other populations and were modified by ER status. No other genes evaluated had mutations associated at P < 0.05 with overall risk. The estimated lifetime risks for mutation carriers in BRCA1, BRCA2, and PALB2 and moderate-risk genes were 18.4%, 9.8%, 22.4%, and 3.1%, respectively, markedly lower than in Western populations with higher baseline risks. CONCLUSIONS We confirmed associations between PV and breast cancer risk in Ghanaian women and provide absolute risk estimates that could inform counseling in Ghana and other West African countries. IMPACT These findings have direct relevance for breast cancer genetic counseling for women in West Africa.
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Affiliation(s)
- Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Parichoy Pal Choudhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | | | | | | | | | | | | | | | - Máire A Duggan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Louise A Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Brittny C Davis Lynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | - Seth Wiafe
- Loma Linda University, School of Public Health, Loma Linda, California
| | | | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jonine D Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, United Kingdom
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9
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Wu Z, Han Y, Wan Y, Hua X, Dagnall CL, Jones K, Hutchinson A, Hicks BD, Zhou W, Liao L, Hallen-Adams H, Shi J, Abnet CC, Sinha R, Chaturvedi A, Vogtmann E. Abstract 687: The oral microbiome and the risk of head and neck cancer: A nested case-control study in the NIH-AARP. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-687] [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
Objective: This nested case-control study in the NIH-AARP Diet and Health Study was carried out to prospectively investigate the relationship of oral microbiome with head and neck cancer.
Methods: Among 34,262 participants with oral wash samples, 60 incident head and neck cancer cases were identified during a mean of 6.25±1.28 years of follow-up. Two controls were matched to each case by age at sample collection, sex, and baseline smoking history, and available controls were not diagnosed with head and neck cancer over follow-up. Whole genome shotgun metagenomic sequencing was used to measure the overall oral microbiome, and ITS2 gene qPCR was used to measure the presence of fungi in pre-diagnostic oral wash samples. ITS2 gene sequencing was performed on ITS2 qPCR positive samples. Taxonomic and functional alpha-diversity and beta-diversity metrics were computed. Presence/absence and relative abundance of groups of red- and/or orange-complex periodontal pathogens were also calculated. Conditional logistic regression models and MiRKAT were used to investigate the case-control associations.
Results: Participants with higher taxonomic microbial alpha-diversity had a decreased risk of head and neck cancer with odds ratios per every 10 observed species of 0.87 (95% CI=0.75-1.004, P=0.057), and per one unit of Faith’s PD and the Shannon index of 0.84 (95% CI=0.72-0.99, P=0.032) and 0.52 (95% CI=0.29-0.94, P=0.032), respectively. No case-control differences were found for beta diversity (all p>0.05). The presence of red-complex periodontal pathogens was non-significantly associated with reduced risk of head and neck cancer (OR=0.41, 95% CI=0.17-1.01, P=0.052). Greater relative abundance of red-complex (OR=0.29, 95% CI=0.09-0.94, P=0.040), orange-complex (OR=0.45, 95% CI=0.22-0.89, P=0.022), and both complexes combined (OR=0.46, 95% CI=0.25-0.82, P=0.009), were associated with reduced risk of head and neck cancer. The presence of oral fungi was also strongly associated with reduced risk of head and neck cancer compared with controls (OR=0.39, 95% CI=0.17-0.87, P=0.022).
Conclusions: Greater taxonomic alpha-diversity and the presence or relative abundance of multiple bacterial or fungal species, including the red- and orange-complex periodontal pathogens, were associated with reduced risk of head and neck cancer.
Citation Format: Zeni Wu, Yongli Han, Yunhu Wan, Xing Hua, Casey L. Dagnall, Kristine Jones, Amy Hutchinson, Belynda D. Hicks, Weiyin Zhou, Linda Liao, Heather Hallen-Adams, Jianxin Shi, Christian C. Abnet, Rashmi Sinha, Anil Chaturvedi, Emily Vogtmann. The oral microbiome and the risk of head and neck cancer: A nested case-control study in the NIH-AARP [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 687.
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Affiliation(s)
- Zeni Wu
- 1National Cancer Institute, Rockville, MD
| | - Yongli Han
- 1National Cancer Institute, Rockville, MD
| | - Yunhu Wan
- 1National Cancer Institute, Rockville, MD
| | - Xing Hua
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | - Linda Liao
- 1National Cancer Institute, Rockville, MD
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10
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Pearce EE, Alsaggaf R, Katta S, Dagnall C, Aubert G, Hicks BD, Spellman SR, Savage SA, Horvath S, Gadalla SM. Telomere length and epigenetic clocks as markers of cellular aging: a comparative study. GeroScience 2022; 44:1861-1869. [PMID: 35585300 DOI: 10.1007/s11357-022-00586-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 01/01/2022] [Accepted: 05/06/2022] [Indexed: 12/11/2022] Open
Abstract
Telomere length (TL) and DNA methylation-based epigenetic clocks are markers of biological age, but the relationship between the two is not fully understood. Here, we used multivariable regression models to evaluate the relationships between leukocyte TL (LTL; measured by qPCR [n = 635] or flow FISH [n = 144]) and five epigenetic clocks (Hannum, DNAmAge pan-tissue, PhenoAge, SkinBlood, or GrimAge clocks), or their epigenetic age acceleration measures in healthy adults (age 19-61 years). LTL showed statistically significant negative correlations with all clocks (qPCR: r = - 0.26 to - 0.32; flow FISH: r = - 0.34 to - 0.49; p < 0.001 for all). Yet, models adjusted for age, sex, and race revealed significant associations between three of five clocks (PhenoAge, GrimAge, and Hannum clocks) and LTL by flow FISH (p < 0.01 for all) or qPCR (p < 0.001 for all). Significant associations between age acceleration measures for the same three clocks and qPCR or flow FISH TL were also found (p < 0.01 for all). Additionally, LTL (by qPCR or flow FISH) showed significant associations with extrinsic epigenetic age acceleration (EEAA: p < 0.0001 for both), but not intrinsic epigenetic age acceleration (IEAA; p > 0.05 for both). In conclusion, the relationships between LTL and epigenetic clocks were limited to clocks reflecting phenotypic age. The observed association between LTL and EEAA reflects the ability of both measures to detect immunosenescence. The observed modest correlations between LTL and epigenetic clocks highlight a possible benefit from incorporating both measures in understanding disease etiology and prognosis.
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Affiliation(s)
- Emily E Pearce
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Rotana Alsaggaf
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shilpa Katta
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Geraldine Aubert
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, 55401, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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11
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Morton LM, Karyadi DM, Stewart C, Bogdanova TI, Dawson ET, Steinberg MK, Dai J, Hartley SW, Schonfeld SJ, Sampson JN, Maruvka YE, Kapoor V, Ramsden DA, Carvajal-Garcia J, Perou CM, Parker JS, Krznaric M, Yeager M, Boland JF, Hutchinson A, Hicks BD, Dagnall CL, Gastier-Foster JM, Bowen J, Lee O, Machiela MJ, Cahoon EK, Brenner AV, Mabuchi K, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Hatch M, Berrington de Gonzalez A, Thomas GA, Tronko MD, Getz G, Chanock SJ. Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident. Science 2021; 372:science.abg2538. [PMID: 33888599 DOI: 10.1126/science.abg2538] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
The 1986 Chernobyl nuclear power plant accident increased papillary thyroid carcinoma (PTC) incidence in surrounding regions, particularly for radioactive iodine (131I)-exposed children. We analyzed genomic, transcriptomic, and epigenomic characteristics of 440 PTCs from Ukraine (from 359 individuals with estimated childhood 131I exposure and 81 unexposed children born after 1986). PTCs displayed radiation dose-dependent enrichment of fusion drivers, nearly all in the mitogen-activated protein kinase pathway, and increases in small deletions and simple/balanced structural variants that were clonal and bore hallmarks of nonhomologous end-joining repair. Radiation-related genomic alterations were more pronounced for individuals who were younger at exposure. Transcriptomic and epigenomic features were strongly associated with driver events but not radiation dose. Our results point to DNA double-strand breaks as early carcinogenic events that subsequently enable PTC growth after environmental radiation exposure.
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Affiliation(s)
- Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Danielle M Karyadi
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tetiana I Bogdanova
- Laboratory of Morphology of the Endocrine System, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Eric T Dawson
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.,Nvidia Corporation, Santa Clara, CA 95051, USA
| | - Mia K Steinberg
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Jieqiong Dai
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Stephen W Hartley
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sara J Schonfeld
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Yosef E Maruvka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vidushi Kapoor
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joel S Parker
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Marko Krznaric
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London W6 8RF, UK
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Joseph F Boland
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH 43205, USA.,Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jay Bowen
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH 43205, USA
| | - Olivia Lee
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Elizabeth K Cahoon
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alina V Brenner
- Radiation Effects Research Foundation, Hiroshima 732-0815, Japan
| | - Kiyohiko Mabuchi
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Drozdovitch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sergii Masiuk
- Radiological Protection Laboratory, Institute of Radiation Hygiene and Epidemiology, National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv 04050, Ukraine
| | - Mykola Chepurny
- Radiological Protection Laboratory, Institute of Radiation Hygiene and Epidemiology, National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv 04050, Ukraine
| | - Liudmyla Yu Zurnadzhy
- Laboratory of Morphology of the Endocrine System, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Maureen Hatch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amy Berrington de Gonzalez
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gerry A Thomas
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London W6 8RF, UK
| | - Mykola D Tronko
- Department of Fundamental and Applied Problems of Endocrinology, V. P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv 04114, Ukraine
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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12
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Kim J, Gianferante M, Karyadi DM, Hartley SW, Frone MN, Luo W, Robison LL, Armstrong GT, Bhatia S, Dean M, Yeager M, Zhu B, Song L, Sampson JN, Yasui Y, Leisenring WM, Brodie SA, de Andrade KC, Fortes FP, Goldstein AM, Khincha PP, Machiela MJ, McMaster ML, Nickerson ML, Oba L, Pemov A, Pinheiro M, Rotunno M, Santiago K, Wegman-Ostrosky T, Diver WR, Teras L, Freedman ND, Hicks BD, Zhu B, Wang M, Jones K, Hutchinson AA, Dagnall C, Savage SA, Tucker MA, Chanock SJ, Morton LM, Stewart DR, Mirabello L. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in the Childhood Cancer Survivor Study. JNCI Cancer Spectr 2021; 5:pkab007. [PMID: 34308104 PMCID: PMC8023430 DOI: 10.1093/jncics/pkab007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/24/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Background Pediatric cancers are the leading cause of death by disease in children despite improved survival rates overall. The contribution of germline genetic susceptibility to pediatric cancer survivors has not been extensively characterized. We assessed the frequency of pathogenic or likely pathogenic (P/LP) variants in 5451 long-term pediatric cancer survivors from the Childhood Cancer Survivor Study. Methods Exome sequencing was conducted on germline DNA from 5451 pediatric cancer survivors (cases who survived ≥5 years from diagnosis; n = 5105 European) and 597 European cancer-free adults (controls). Analyses focused on comparing the frequency of rare P/LP variants in 237 cancer-susceptibility genes and a subset of 60 autosomal dominant high-to-moderate penetrance genes, for both case-case and case-control comparisons. Results Of European cases, 4.1% harbored a P/LP variant in high-to-moderate penetrance autosomal dominant genes compared with 1.3% in controls (2-sided P = 3 × 10-4). The highest frequency of P/LP variants was in genes typically associated with adult onset rather than pediatric cancers, including BRCA1/2, FH, PALB2, PMS2, and CDKN2A. A statistically significant excess of P/LP variants, after correction for multiple tests, was detected in patients with central nervous system cancers (NF1, SUFU, TSC1, PTCH2), Wilms tumor (WT1, REST), non-Hodgkin lymphoma (PMS2), and soft tissue sarcomas (SDHB, DICER1, TP53, ERCC4, FGFR3) compared with other pediatric cancers. Conclusion In long-term pediatric cancer survivors, we identified P/LP variants in cancer-susceptibility genes not previously associated with pediatric cancer as well as confirmed known associations. Further characterization of variants in these genes in pediatric cancer will be important to provide optimal genetic counseling for patients and their families.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Matthew Gianferante
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Megan N Frone
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship,
University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
- 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
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs,
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Fernanda P Fortes
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mary L McMaster
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Michael L Nickerson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Leatrisse Oba
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Alexander Pemov
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Karina Santiago
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Talia Wegman-Ostrosky
- Basic Research Subdirection, Instituto Nacional de
Cancerología (INCan), Mexico City, Mexico
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Lauren Teras
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
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13
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Alsaggaf R, Katta S, Wang T, Hicks BD, Zhu B, Spellman SR, Lee SJ, Horvath S, Gadalla SM. Epigenetic Aging and Hematopoietic Cell Transplantation in Patients With Severe Aplastic Anemia. Transplant Cell Ther 2021; 27:313.e1-313.e8. [PMID: 33836872 PMCID: PMC8036238 DOI: 10.1016/j.jtct.2021.01.013] [Citation(s) in RCA: 4] [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: 10/08/2020] [Revised: 01/13/2021] [Indexed: 01/17/2023]
Abstract
Cellular aging in hematopoietic cell transplantation (HCT) is important in the context of immune reconstitution and age-related complications. Recently, several DNA-methylation (DNAm)-based biomarkers of aging known as "epigenetic clocks" have been introduced as novel tools to predict cellular age. Here, we used Cox proportional hazards models to assess the possible associations of donor pre-HCT DNAm age, and its post-HCT changes, using the recently published lifespan-associated epigenetic clock known as "DNAm-GrimAge," with outcomes among patients with severe aplastic anemia (SAA). The study included 732 SAA patients from the Transplant Outcomes in Aplastic Anemia project, who underwent unrelated donor HCT and for whom a donor pre-HCT blood DNA sample was available; 41 also had a post-HCT sample collected at day 100. In multivariable analyses, we found similar associations for donor chronological age and pre-HCT DNAm-GrimAge with post-HCT survival (hazard ratio [HR] per decade = 1.13; 95% confidence interval [CI], 0.99-1.28; P = .07 and HR = 1.14; 95% CI, 0.99-1.28; P = .06, respectively). In donors with 10+ years of GrimAge acceleration (ie, deviation from expected DNAm age for chronological age), elevated risks of chronic graft versus host disease (HR = 2.4; 95% CI, 1.21-4.65; P = .01) and possibly post-HCT mortality (HR = 1.79; 95% CI, 0.96-3.33; P = .07) were observed. In the subset with post-HCT samples, we observed a significant increase in DNAm-GrimAge in the first 100 days after HCT (median change 12.5 years, range 1.4 to 26.4). Higher DNAm-GrimAge after HCT was associated with inferior survival (HR per year = 1.11; 95% CI, 1.02-1.21; P = .01), predominantly within the first year after HCT. This study highlights the possible role cellular aging may play in HCT outcomes.
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Affiliation(s)
- Rotana Alsaggaf
- Clinical Genetics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Shilpa Katta
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - 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
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Steve Horvath
- David Geffen School of Medicine, University of California, Los Angeles, California
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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14
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Mirabello L, Zhu B, Koster R, Karlins E, Dean M, Yeager M, Gianferante M, Spector LG, Morton LM, Karyadi D, Robison LL, Armstrong GT, Bhatia S, Song L, Pankratz N, Pinheiro M, Gastier-Foster JM, Gorlick R, de Toledo SRC, Petrilli AS, Patino-Garcia A, Lecanda F, Gutierrez-Jimeno M, Serra M, Hattinger C, Picci P, Scotlandi K, Flanagan AM, Tirabosco R, Amary MF, Kurucu N, Ilhan IE, Ballinger ML, Thomas DM, Barkauskas DA, Mejia-Baltodano G, Valverde P, Hicks BD, Zhu B, Wang M, Hutchinson AA, Tucker M, Sampson J, Landi MT, Freedman ND, Gapstur S, Carter B, Hoover RN, Chanock SJ, Savage SA. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in Patients With Osteosarcoma. JAMA Oncol 2021; 6:724-734. [PMID: 32191290 DOI: 10.1001/jamaoncol.2020.0197] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Importance Osteosarcoma, the most common malignant bone tumor in children and adolescents, occurs in a high number of cancer predisposition syndromes that are defined by highly penetrant germline mutations. The germline genetic susceptibility to osteosarcoma outside of familial cancer syndromes remains unclear. Objective To investigate the germline genetic architecture of 1244 patients with osteosarcoma. Design, Setting, and Participants Whole-exome sequencing (n = 1104) or targeted sequencing (n = 140) of the DNA of 1244 patients with osteosarcoma from 10 participating international centers or studies was conducted from April 21, 2014, to September 1, 2017. The results were compared with the DNA of 1062 individuals without cancer assembled internally from 4 participating studies who underwent comparable whole-exome sequencing and 27 173 individuals of non-Finnish European ancestry who were identified through the Exome Aggregation Consortium (ExAC) database. In the analysis, 238 high-interest cancer-susceptibility genes were assessed followed by testing of the mutational burden across 736 additional candidate genes. Principal component analyses were used to identify 732 European patients with osteosarcoma and 994 European individuals without cancer, with outliers removed for patient-control group comparisons. Patients were subsequently compared with individuals in the ExAC group. All data were analyzed from June 1, 2017, to July 1, 2019. Main Outcomes and Measures The frequency of rare pathogenic or likely pathogenic genetic variants. Results Among 1244 patients with osteosarcoma (mean [SD] age at diagnosis, 16 [8.9] years [range, 2-80 years]; 684 patients [55.0%] were male), an analysis restricted to individuals with European ancestry indicated a significantly higher pathogenic or likely pathogenic variant burden in 238 high-interest cancer-susceptibility genes among patients with osteosarcoma compared with the control group (732 vs 994, respectively; P = 1.3 × 10-18). A pathogenic or likely pathogenic cancer-susceptibility gene variant was identified in 281 of 1004 patients with osteosarcoma (28.0%), of which nearly three-quarters had a variant that mapped to an autosomal-dominant gene or a known osteosarcoma-associated cancer predisposition syndrome gene. The frequency of a pathogenic or likely pathogenic cancer-susceptibility gene variant was 128 of 1062 individuals (12.1%) in the control group and 2527 of 27 173 individuals (9.3%) in the ExAC group. A higher than expected frequency of pathogenic or likely pathogenic variants was observed in genes not previously linked to osteosarcoma (eg, CDKN2A, MEN1, VHL, POT1, APC, MSH2, and ATRX) and in the Li-Fraumeni syndrome-associated gene, TP53. Conclusions and Relevance In this study, approximately one-fourth of patients with osteosarcoma unselected for family history had a highly penetrant germline mutation requiring additional follow-up analysis and possible genetic counseling with cascade testing.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Roelof Koster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eric Karlins
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Matthew Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Logan G Spector
- Department of Pediatrics, University of Minnesota, Minneapolis
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Danielle Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Pediatrics, University of Minnesota, Minneapolis
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Julie M Gastier-Foster
- Department of Pathology and Pediatrics, Nationwide Children's Hospital, The Ohio State University, Columbus
| | - Richard Gorlick
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston
| | - Silvia Regina Caminada de Toledo
- Laboratorio de Genetica, Instituto de Oncologia Pediatrica, Grupo de Apoio ao Adolescente e a Crianca com Cancer/Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Antonio S Petrilli
- Laboratorio de Genetica, Instituto de Oncologia Pediatrica, Grupo de Apoio ao Adolescente e a Crianca com Cancer/Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Ana Patino-Garcia
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain.,Center for Applied Medical Research, University of Navarra, Instituto de Investigacion Sanitaria de Navarra, and Centro de Investigacion Biomedica en Red Cancer, Pamplona, Spain
| | - Fernando Lecanda
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain.,Center for Applied Medical Research, University of Navarra, Instituto de Investigacion Sanitaria de Navarra, and Centro de Investigacion Biomedica en Red Cancer, Pamplona, Spain
| | - Miriam Gutierrez-Jimeno
- Solid Tumor Division, Department of Pediatrics, University Clinic of Navarra and Center for Applied Medical Research, Navarra Institute for Health Research, Pamplona, Spain
| | - Massimo Serra
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Piero Picci
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Adrienne M Flanagan
- Research Department of Pathology, UCL Cancer Institute, London, United Kingdom.,Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Maria Fernanda Amary
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, United Kingdom
| | - Nilgün Kurucu
- Department of Pediatric Oncology, A.Y. Ankara Oncology Training and Research Hospital, Yenimahalle, Ankara, Turkey
| | - Inci Ergurhan Ilhan
- Department of Pediatric Oncology, A.Y. Ankara Oncology Training and Research Hospital, Yenimahalle, Ankara, Turkey
| | - Mandy L Ballinger
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Donald A Barkauskas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles
| | | | | | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Susan Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Brian Carter
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Morton LM, Karyadi DM, Hartley SW, Frone MN, Sampson JN, Howell RM, Neglia JP, Arnold MA, Hicks BD, Jones K, Zhu B, Dagnall CL, Karlins E, Yeager MS, Leisenring WM, Yasui Y, Turcotte LM, Smith SA, Weathers RE, Miller J, Sigel BS, Merino DM, Berrington de Gonzalez A, Bhatia S, Robison LL, Tucker MA, Armstrong GT, Chanock SJ. Subsequent Neoplasm Risk Associated With Rare Variants in DNA Damage Response and Clinical Radiation Sensitivity Syndrome Genes in the Childhood Cancer Survivor Study. JCO Precis Oncol 2020; 4:2000141. [PMID: 32923912 DOI: 10.1200/po.20.00141] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Radiotherapy for childhood cancer is associated with elevated subsequent neoplasm (SN) risk, but the contribution of rare variants in DNA damage response and radiation sensitivity genes to SN risk is unknown. PATIENTS AND METHODS We conducted whole-exome sequencing in a cohort of childhood cancer survivors originally diagnosed during 1970 to 1986 (mean follow-up, 32.7 years), with reconstruction of doses to body regions from radiotherapy records. We identified patients who developed SN types previously reported to be related to radiotherapy (RT-SNs; eg, basal cell carcinoma [BCC], breast cancer, meningioma, thyroid cancer, sarcoma) and matched controls (sex, childhood cancer type/diagnosis, age, SN location, radiation dose, survival). Conditional logistic regression assessed SN risk associated with potentially protein-damaging rare variants (SnpEff, ClinVar) in 476 DNA damage response or radiation sensitivity genes with exact permutation-based P values using a Bonferroni-corrected significance threshold of P < 8.06 × 10-5. RESULTS Among 5,105 childhood cancer survivors of European descent, 1,108 (21.7%) developed at least 1 RT-SN. Out-of-field RT-SN risk, excluding BCC, was associated with homologous recombination repair (HRR) gene variants (patient cases, 23.2%; controls, 10.8%; odds ratio [OR], 2.6; 95% CI, 1.7 to 3.9; P = 4.79 × 10-5), most notably but nonsignificantly for FANCM (patient cases, 4.0%; matched controls, 0.6%; P = 9.64 × 10-5). HRR variants were not associated with likely in/near-field RT-SNs, excluding BCC (patient cases, 12.7%; matched controls, 12.9%; P = .92). Irrespective of radiation dose, risk for RT-SNs was also associated with EXO1 variants (patient cases, 1.8%; controls, 0.4%; P = 3.31 × 10-5), another gene implicated in DNA double-strand break repair. CONCLUSION In this large-scale discovery study, we identified novel associations between RT-SN risk after childhood cancer and potentially protein-damaging rare variants in genes involved in DNA double-strand break repair, particularly HRR. With replication, these results could affect screening recommendations for 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
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Megan N 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, National Institutes of Health, Bethesda, MD
| | - Rebecca M Howell
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Joseph P Neglia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Michael A Arnold
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH.,Department of Pathology, Wexner Medical Center, Ohio State University, Columbus, OH
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Meredith S Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Lucie M Turcotte
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Susan A Smith
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rita E Weathers
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Byron S Sigel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Diana M Merino
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Amy Berrington de Gonzalez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Vogtmann E, Hua X, Yu G, Hullings A, Wan Y, Dagnall CL, Jones K, Hicks BD, Hutchinson A, Suman S, Zhu B, Graubard B, Gail MH, Caporaso JG, Wheeler W, Sandler D, Freeman LEB, Liao L, Freedman ND, Caporaso N, Sinha R, Shi J, Abnet CC. Abstract A39: The human oral microbiota and risk of lung cancer: An analysis of three prospective cohort studies. Cancer Res 2020. [DOI: 10.1158/1538-7445.mvc2020-a39] [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: The oral microbiota may be associated with lung cancer risk through direct mechanisms, including infection, immune responses, and periodontal disease, and through indirect mechanisms such as the modification of the oral microbiota by tobacco. We conducted a case-cohort study nested within three US prospective cohort studies to evaluate the association between oral microbiota ascertained years before a cancer diagnosis and risk of lung cancer.
Methods: Incident lung cancer cases within the Agricultural Health Study (AHS; N=244), NIH-AARP Diet and Health Study (N=376), and the Prostate, Lung, Colorectum, and Ovarian Cancer Screening Trial (PLCO; N=700) who provided an oral wash sample were identified. The median time between oral sample collection and diagnosis was approximately 6.6 years, 3.4 years, and 4.5 years for AHS, NIH-AARP, and PLCO, respectively. A referent subcohort was randomly selected by strata of age, sex, and cigarette smoking history. We extracted DNA using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using the MiSeq. The sequencing data were processed using QIIME2 with the DADA2 plugin and we generated alpha and beta diversity metrics. Cox proportional hazards models were used to evaluate the hazard ratios (HR) and 95% confidence intervals (CI) for the association between the oral microbial measures and the risk of lung cancer with adjustment for known lung cancer risk factors, and estimates from the three cohorts were meta-analyzed.
Results: Increased alpha diversity was associated with decreased lung cancer risk, although only the association with the Shannon Index reached statistical significance (HR for 5th quintile versus 1st quintile 0.74; 95% CI 0.60, 0.92) with no evidence of between-study heterogeneity (p = 0.5968). Specific principal coordinate vectors from the beta diversity matrices were also significantly associated with lung cancer risk, suggesting differing bacterial communities between future lung cancer cases. When stratified by histologic subtypes, the inverse association with alpha diversity was restricted to squamous cell carcinoma, with all alpha diversity metrics reaching statistical significance (e.g., Faith’s phylogenetic diversity HR for 5th quintile versus 1st quintile 0.57; 95% CI: 0.37, 0.87). Similarly, when stratified by smoking history, the inverse association with alpha diversity was restricted to former smokers (e.g., observed species HR for 5th quintile versus 1st quintile 0.63; 95% CI: 0.44, 0.89).
Conclusions: In oral wash samples collected years before diagnosis, we found significant associations between both alpha and beta diversity metrics of the oral microbial communities and risk of lung cancer. Additional work is required to understand the associations by histologic subtype and smoking history.
Citation Format: Emily Vogtmann, Xing Hua, Guoqin Yu, Autumn Hullings, Yunhu Wan, Casey L Dagnall, Kristine Jones, Belynda D. Hicks, Amy Hutchinson, Shalabh Suman, Bin Zhu, Barry Graubard, Mitchell H. Gail, J. Gregory Caporaso, William Wheeler, Dale Sandler, Laura E. Beane Freeman, Linda Liao, Neal D. Freedman, Neil Caporaso, Rashmi Sinha, Jianxin Shi, Christian C Abnet. The human oral microbiota and risk of lung cancer: An analysis of three prospective cohort studies [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A39.
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Affiliation(s)
| | | | - Guoqin Yu
- 2University of Kansas Medical Center, Kansas City, KS,
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17
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Sapkota Y, Turcotte LM, Ehrhardt MJ, Howell RM, Arnold MA, Wilson CL, Leisenring W, Wang Z, Sampson J, Dagnall CL, Karlins E, Li SA, Hicks BD, Weathers R, Smith SA, Shelton K, Liu Q, Tucker MA, Chanock SJ, Zhang J, Hudson MM, Neglia JP, Armstrong GT, Robison LL, Morton LM, Bhatia S, Yasui Y. Genome-Wide Association Study in Irradiated Childhood Cancer Survivors Identifies HTR2A for Subsequent Basal Cell Carcinoma. J Invest Dermatol 2019; 139:2042-2045.e8. [PMID: 30910758 DOI: 10.1016/j.jid.2019.02.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
| | - Lucie M Turcotte
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Matthew J Ehrhardt
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rebecca M Howell
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Arnold
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA; Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wendy Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Shengchao Alfred Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rita Weathers
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Susan A Smith
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyla Shelton
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Qi Liu
- School of Public Health, University of Alberta, Alberta, Canada
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Joseph P Neglia
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Public Health, University of Alberta, Alberta, Canada
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Gianferante DM, Rotunno M, Dean M, Zhou W, Hicks BD, Wyatt K, Jones K, Wang M, Zhu B, Goldstein AM, Mirabello L. Whole-exome sequencing of nevoid basal cell carcinoma syndrome families and review of Human Gene Mutation Database PTCH1 mutation data. Mol Genet Genomic Med 2018; 6:1168-1180. [PMID: 30411536 PMCID: PMC6305672 DOI: 10.1002/mgg3.498] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 06/25/2018] [Revised: 09/05/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Background Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder with variable expression and nearly complete penetrance. PTCH1 is the major susceptibility locus and has no known hot spots or genotype–phenotype relationships. Methods We evaluated 18 NBCCS National Cancer Institute (NCI) families plus PTCH1 data on 333 NBCCS disease‐causing mutations (DM) reported in the Human Gene Mutation Database (HGMD). National Cancer Institute families underwent comprehensive genomic evaluation, and clinical data were extracted from NCI and HGMD cases. Genotype–phenotype relationships were analyzed using Fisher's exact tests focusing on mutation type and PTCH1 domains. Results PTCH1 pathogenic mutations were identified in 16 of 18 NCI families, including three previously mutation‐negative families. PTCH1 mutations were spread across the gene with no hot spot. After adjustment for multiple tests, a statistically significant genotype–phenotype association was observed for developmental delay and gross deletion–insertions (p = 9.0 × 10−6), and suggestive associations between falx cerebri calcification and all transmembrane domains (p = 0.002) and severe outcomes and gross deletion–insertions (p = 4.0 × 10−4). Conclusion Overall, 89% of our NCI families had a pathogenic PTCH1 mutation. The identification of PTCH1 mutations in previously mutation‐negative families underscores the importance of repeated testing when new technologies become available. Additional clinical information linked to mutation databases would enhance follow‐up and future studies of genotype–phenotype relationships.
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Affiliation(s)
- D Matthew Gianferante
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Melissa Rotunno
- Division of Cancer Control and Population Science, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kathleen Wyatt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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McMaster ML, Berndt SI, Zhang J, Slager SL, Li SA, Vajdic CM, Smedby KE, Yan H, Birmann BM, Brown EE, Smith A, Kleinstern G, Fansler MM, Mayr C, Zhu B, Chung CC, Park JH, Burdette L, Hicks BD, Hutchinson A, Teras LR, Adami HO, Bracci PM, McKay J, Monnereau A, Link BK, Vermeulen RCH, Ansell SM, Maria A, Diver WR, Melbye M, Ojesina AI, Kraft P, Boffetta P, Clavel J, Giovannucci E, Besson CM, Canzian F, Travis RC, Vineis P, Weiderpass E, Montalvan R, Wang Z, Yeager M, Becker N, Benavente Y, Brennan P, Foretova L, Maynadie M, Nieters A, de Sanjose S, Staines A, Conde L, Riby J, Glimelius B, Hjalgrim H, Pradhan N, Feldman AL, Novak AJ, Lawrence C, Bassig BA, Lan Q, Zheng T, North KE, Tinker LF, Cozen W, Severson RK, Hofmann JN, Zhang Y, Jackson RD, Morton LM, Purdue MP, Chatterjee N, Offit K, Cerhan JR, Chanock SJ, Rothman N, Vijai J, Goldin LR, Skibola CF, Caporaso NE. Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia. Nat Commun 2018; 9:4182. [PMID: 30305637 PMCID: PMC6180091 DOI: 10.1038/s41467-018-06541-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 11/17/2017] [Accepted: 09/04/2018] [Indexed: 01/07/2023] Open
Abstract
Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P = 1.36 × 10-54) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 × 10-19). Both risk alleles are observed at a low frequency among controls (~2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.
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Affiliation(s)
- Mary L McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Jianqing Zhang
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Shengchao Alfred Li
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Claire M Vajdic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Karin E Smedby
- Department of Medicine, Solna Karolinska Institutet, Stockholm, 17176, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, 17176, Sweden
| | - Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Alex Smith
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, 10021, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Charles C Chung
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Ju-Hyun Park
- Department of Statistics, Dongguk University, Seoul, 100-715, Republic of Korea
| | - Laurie Burdette
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Lauren R Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, 30303, GA, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, NO-0316, Norway
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, 94118, CA, USA
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, 69372, France
| | - Alain Monnereau
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, F-94807, France
- Université Paris Descartes, Paris, 75006, France
- Registry of Hematological Malignancies in Gironde, Institut Bergonié, University of Bordeaux, Inserm, Team EPICENE, UMR 1219, Bordeaux, 33000, France
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, 52242, IA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, 3508 TD, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, 55905, MN, USA
| | - Ann Maria
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, 30303, GA, USA
| | - Mads Melbye
- Division of Health Surveillance and Research, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, 2300, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Akinyemi I Ojesina
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Paolo Boffetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Jacqueline Clavel
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, F-94807, France
- Université Paris Descartes, Paris, 75006, France
| | - Edward Giovannucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Caroline M Besson
- Service d'hématologie et Oncologie, Centre Hospitalier de Versailles, Le Chesnay, Inserm U1018, Centre pour la Recherche en Epidémiologie et Santé des Populations (CESP), Villejuif, 78157, France
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, OX3 7LF, UK
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, UK
- Human Genetics Foundation, Turin, 10126, Italy
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, 9019, Norway
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, 0379, Norway
- Genetic Epidemiology Group, Folkhälsan Research Center and University of Helsinki, Helsinki, 00250, Finland
| | | | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, 38105, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20877, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Lab for Cancer Research, Frederick, 20877, MD, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Baden-Württemberg, Germany
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, 69372, France
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and MF MU, Brno, 65653, Czech Republic
| | - Marc Maynadie
- EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, 21070, France
| | - Alexandra Nieters
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, 79108, Baden-Württemberg, Germany
| | - Silvia de Sanjose
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, 28029, Spain
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin, 9, Ireland
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, 35233, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, 94720, CA, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75105, Sweden
| | - Henrik Hjalgrim
- Division of Health Surveillance and Research, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, 2300, Denmark
- Department of Hematology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Nisha Pradhan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, 55905, MN, USA
| | | | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, 02903, RI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, 27599, NC, USA
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, 98117, WA, USA
| | - Wendy Cozen
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
- Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, 48201, MI, USA
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, 06520, CT, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, 43210, OH, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
- Ontario Health Study, Toronto, M5S 1C6, ON, Canada
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, 21205, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, 21205, MD, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Lynn R Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, 30322, GA, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, 20892, MD, USA
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20
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Lupo PJ, Morimoto L, Karlins E, Shao X, Morton LM, Scheurer ME, Bhatia S, Robison LL, Armstrong GT, Hettmer S, Khan J, Chanock SJ, Freedman ND, Wyatt K, Hicks BD, Yeager M, Dagnall CL, Li SA, Skapek SX, Hawkins DS, Metayer C, Mirabello L. Abstract 2966: A genome-wide scan identifies a new locus associated with pediatric rhabdomyosarcoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2966] [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: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and has one of the poorest survival rates among all pediatric cancers. The two major histologic subtypes of RMS are embryonal (eRMS) and alveolar (aRMS), which display differences in terms of age-incidence patterns and somatic mutations. Approximately 10% of RMS cases are associated with germline mutations in known cancer predisposition genes (e.g., TP53, NF1), but very little is known about the genetic susceptibility to the ~90% of RMS cases that are sporadic. We conducted the first multi-institutional genome-wide association study (GWAS) of RMS in 727 cases and 3,384 controls.
Methods: Phase 1 of the GWAS included 421 RMS cases from Children's Oncology Group clinical trials, Texas Children's Hospital, and the Universidad de Navarra. Controls (n=2,763) were cancer-free individuals included in previous studies at the National Cancer Institute (NCI). Phase 2 included 306 cases from the Childhood Cancer Survivor Study and 621 independent controls from NCI. Genotypes were generated using the Illumina OmniExpress or the HumanOmni5Exome array and imputed based on the 1000 Genomes Project. Analyses were restricted to those of European (EUR) ancestry, and controls were matched to the cases based on principal components and genotype platform. Assuming an additive genetic model in SNPTEST, we used multivariable logistic regression models to estimate the odds ratio (OR), 95% confidence interval (CI), and P value for each variant on RMS overall and by two RMS subtypes: eRMS and aRMS.
Results: After quality control filtering and assessment of population substructure, there were 555 combined EUR RMS cases and 1,561 controls, which included: 1) 278 cases and 1,112 controls in phase 1; and 2) 277 cases and 449 controls in phase 2. In the combined set, we identified a new locus at chromosome 11p15.2 that was strongly associated with an increased risk of aRMS and significant at the genome-wide level (OR=2.3, P=2.2x10-8). Results were consistent across studies: phase 1 OR=2.3, 95% CI 1.7-3.2; and phase 2 OR=2.3, 95% CI 1.2-4.5. The top variant, rs12785926, mapped to an intron in the PSMA1 (proteasome subunit alpha 1) gene. Based on data from GTEx, rs12785926 is significantly associated with RRAS2 expression across multiple tissues. RRAS2 is involved in cell proliferation and is somatically mutated in several tumors. When evaluating eRMS and RMS overall in the combined set, there were no variants significant at the genome-wide level.
Conclusion: In the first GWAS of pediatric RMS, we identified a susceptibility locus associated with the more aggressive aRMS subtype that has a poorer prognosis. Additional replication analyses are underway using DNA obtained from archived newborn blood spots linked to population-based cancer registries, as well as other institutional cohorts. Further investigation will advance understanding of RMS etiology and biology.
Citation Format: Philip J. Lupo, Libby Morimoto, Eric Karlins, Xiaorong Shao, Lindsay M. Morton, Michael E. Scheurer, Smita Bhatia, Leslie L. Robison, Gregory T. Armstrong, Simone Hettmer, Javed Khan, Stephen J. Chanock, Neal D. Freedman, Kathleen Wyatt, Belynda D. Hicks, Meredith Yeager, Casey L. Dagnall, Shengchao A. Li, Stephen X. Skapek, Douglas S. Hawkins, Catherine Metayer, Lisa Mirabello. A genome-wide scan identifies a new locus associated with pediatric rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2966.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Javed Khan
- 3National Cancer Institute, Bethesda, MD
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21
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Koster R, Panagiotou OA, Wheeler WA, Karlins E, Gastier-Foster JM, de Toledo SRC, Petrilli AS, Flanagan AM, Tirabosco R, Andrulis IL, Wunder JS, Gokgoz N, Patiño-Garcia A, Lecanda F, Serra M, Hattinger C, Picci P, Scotlandi K, Thomas DM, Ballinger ML, Gorlick R, Barkauskas DA, Spector LG, Tucker M, Hicks BD, Yeager M, Hoover RN, Wacholder S, Chanock SJ, Savage SA, Mirabello L. Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients. Int J Cancer 2018; 142:1594-1601. [PMID: 29210060 PMCID: PMC5814322 DOI: 10.1002/ijc.31195] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 09/20/2017] [Accepted: 11/13/2017] [Indexed: 12/31/2022]
Abstract
Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. We conducted a multi-institutional genome-wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma, including 523 patients of European ancestry and 109 from Brazil. We conducted a time-to-event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease. The results were combined across the European and Brazilian case sets using a random-effects meta-analysis. The strongest association after meta-analysis was for rs3765555 at 9p24.1, which was inversely associated with overall survival (HR = 1.76; 95% CI 1.41-2.18, p = 4.84 × 10-7 ). After imputation across this region, the combined analysis identified two SNPs that reached genome-wide significance. The strongest single association was with rs55933544 (HR = 1.9; 95% CI 1.5-2.4; p = 1.3 × 10-8 ), which localizes to the GLDC gene, adjacent to the IL33 gene and was consistent across both the European and Brazilian case sets. Using publicly available data, the risk allele was associated with lower expression of IL33 and low expression of IL33 was associated with poor survival in an independent set of patients with osteosarcoma. In conclusion, we have identified the GLDC/IL33 locus on chromosome 9p24.1 as associated with overall survival in patients with osteosarcoma. Further studies are needed to confirm this association and shed light on the biological underpinnings of this susceptibility locus.
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Affiliation(s)
- Roelof Koster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Orestis A. Panagiotou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Julie M. Gastier-Foster
- Nationwide Children’s Hospital, and The Ohio State University Department of Pathology and Pediatrics, Columbus, OH, USA
| | | | - Antonio S. Petrilli
- Laboratorio de Genética, Pediatric Oncology Institute, GRAACC/UNIFESP, São Paulo, Brazil
| | - Adrienne M. Flanagan
- UCL Cancer Institute, Huntley Street, London, UK
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Irene L. Andrulis
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jay S. Wunder
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ana Patiño-Garcia
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Fernando Lecanda
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Massimo Serra
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Piero Picci
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - David M. Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mandy L. Ballinger
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard Gorlick
- Albert Einstein College of Medicine, The Children’s Hospital at Montefiore, New York, NY, USA
| | - Donald A. Barkauskas
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota Minneapolis, MN, 55455, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 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, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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22
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Dagnall CL, Morton LM, Hicks BD, Li S, Zhou W, Karlins E, Teshome K, Chowdhury S, Lashley KS, Sampson JN, Robison LL, Armstrong GT, Bhatia S, Radloff GA, Davies SM, Tucker MA, Yeager M, Chanock SJ. Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays. BMC Genomics 2018; 19:182. [PMID: 29510662 PMCID: PMC5838969 DOI: 10.1186/s12864-018-4572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 10/03/2017] [Accepted: 03/01/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. RESULTS Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. CONCLUSIONS Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.
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Affiliation(s)
- Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA. .,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shengchao Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedest Teshome
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Salma Chowdhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kerrie S Lashley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Department of Population Sciences, City of Hope, Duarte, CA, USA.,Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gretchen A Radloff
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stella M Davies
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
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23
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Vogtmann E, Hua X, Zhou L, Wan Y, Suman S, Zhu B, Dagnall CL, Hutchinson A, Jones K, Hicks BD, Sinha R, Shi J, Abnet CC. Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies. Cancer Epidemiol Biomarkers Prev 2018; 27:594-600. [PMID: 29475969 DOI: 10.1158/1055-9965.epi-17-1004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/22/2017] [Accepted: 02/09/2018] [Indexed: 01/01/2023] Open
Abstract
Background: Few studies have prospectively evaluated the association between oral microbiota and health outcomes. Precise estimates of the intrasubject microbial metric stability will allow better study planning. Therefore, we conducted a study to evaluate the temporal variability of oral microbiota.Methods: Forty individuals provided six oral samples using the OMNIgene ORAL kit and Scope mouthwash oral rinses approximately every two months over 10 months. DNA was extracted using the QIAsymphony and the V4 region of the 16S rRNA gene was amplified and sequenced using the MiSeq. To estimate temporal variation, we calculated intraclass correlation coefficients (ICCs) for a variety of metrics and examined stability after clustering samples into distinct community types using Dirichlet multinomial models (DMMs).Results: The ICCs for the alpha diversity measures were high, including for number of observed bacterial species [0.74; 95% confidence interval (CI): 0.65-0.82 and 0.79; 95% CI: 0.75-0.94] from OMNIgene ORAL and Scope mouthwash, respectively. The ICCs for the relative abundance of the top four phyla and beta diversity matrices were lower. Three clusters provided the best model fit for the DMM from the OMNIgene ORAL samples, and the probability of remaining in a specific cluster was high (59.5%-80.7%).Conclusions: The oral microbiota appears to be stable over time for multiple metrics, but some measures, particularly relative abundance, were less stable.Impact: We used this information to calculate stability-adjusted power calculations that will inform future field study protocols and experimental analytic designs. Cancer Epidemiol Biomarkers Prev; 27(5); 594-600. ©2018 AACR.
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Affiliation(s)
- Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Xing Hua
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
| | - Liang Zhou
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
| | - Yunhu Wan
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
| | - Shalabh Suman
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland.,Leidos Biomedical Research Laboratory, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
| | - Christian C Abnet
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland
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24
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Morton LM, Sampson JN, Armstrong GT, Chen TH, Hudson MM, Karlins E, Dagnall CL, Li SA, Wilson CL, Srivastava DK, Liu W, Kang G, Oeffinger KC, Henderson TO, Moskowitz CS, Gibson TM, Merino DM, Wong JR, Hammond S, Neglia JP, Turcotte LM, Miller J, Bowen L, Wheeler WA, Leisenring WM, Whitton JA, Burdette L, Chung C, Hicks BD, Jones K, Machiela MJ, Vogt A, Wang Z, Yeager M, Neale G, Lear M, Strong LC, Yasui Y, Stovall M, Weathers RE, Smith SA, Howell R, Davies SM, Radloff GA, Onel K, Berrington de González A, Inskip PD, Rajaraman P, Fraumeni JF, Bhatia S, Chanock SJ, Tucker MA, Robison LL. Genome-Wide Association Study to Identify Susceptibility Loci That Modify Radiation-Related Risk for Breast Cancer After Childhood Cancer. J Natl Cancer Inst 2017; 109:3855140. [PMID: 29059430 DOI: 10.1093/jnci/djx058] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/08/2017] [Indexed: 12/28/2022] Open
Abstract
Background Childhood cancer survivors treated with chest-directed radiotherapy have substantially elevated risk for developing breast cancer. Although genetic susceptibility to breast cancer in the general population is well studied, large-scale evaluation of breast cancer susceptibility after chest-directed radiotherapy for childhood cancer is lacking. Methods We conducted a genome-wide association study of breast cancer in female survivors of childhood cancer, pooling two cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. The study population comprised 207 survivors who developed breast cancer and 2774 who had not developed any subsequent neoplasm as of last follow-up. Genotyping and subsequent imputation yielded 16 958 466 high-quality variants for analysis. We tested associations in the overall population and in subgroups stratified by receipt of lower than 10 and 10 or higher gray breast radiation exposure. We report P values and pooled per-allele risk estimates from Cox proportional hazards regression models. All statistical tests were two-sided. Results Among survivors who received 10 or higher gray breast radiation exposure, a locus on 1q41 was associated with subsequent breast cancer risk (rs4342822, nearest gene PROX1 , risk allele frequency in control subjects [RAF controls ] = 0.46, hazard ratio = 1.92, 95% confidence interval = 1.49 to 2.44, P = 7.09 × 10 -9 ). Two rare variants also showed potentially promising associations (breast radiation ≥10 gray: rs74949440, 11q23, TAGLN , RAF controls = 0.02, P = 5.84 × 10 -8 ; <10 gray: rs17020562, 1q32.3, RPS6KC1 , RAF controls = 0.0005, P = 6.68 × 10 -8 ). Associations were restricted to these dose subgroups, with consistent findings in the two survivor cohorts. Conclusions Our study provides strong evidence that germline genetics outside high-risk syndromes could modify the effect of radiation exposure on breast cancer risk after childhood cancer.
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Affiliation(s)
- Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Gregory T Armstrong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Ting-Huei Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Melissa M Hudson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Shengchao Alfred Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Carmen L Wilson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Deo Kumar Srivastava
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Wei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Guolian Kang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Kevin C Oeffinger
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Tara O Henderson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Chaya S Moskowitz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Todd M Gibson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Diana M Merino
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Jeannette R Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Sue Hammond
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Joseph P Neglia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Lucie M Turcotte
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Jeremy Miller
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Laura Bowen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - William A Wheeler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy M Leisenring
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - John A Whitton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Charles Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Geoffrey Neale
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Matthew Lear
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Louise C Strong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Yutaka Yasui
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Marilyn Stovall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Rita E Weathers
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Susan A Smith
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Rebecca Howell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Stella M Davies
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Gretchen A Radloff
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Kenan Onel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Amy Berrington de González
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Peter D Inskip
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Smita Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Leslie L Robison
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD; Department of Epidemiology and Cancer Control, Division of Cancer Survivorship, Department of Oncology, Department of Biostatistics, Hartwell Center for Bioinformatics and Biotechnology, and Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; Departments of Medicine, Pediatrics, and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY; Section of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Chicago, IL; Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH; Department of Pediatrics, University of Minnesota, Minneapolis, MN; Information Management Services, Inc., Calverton, MD; Cancer Prevention and Clinical Statistics Programs and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Genetics and Department of Radiation Physics, The University of Texas at MD Anderson Cancer Center, Houston, TX; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
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25
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Mirabello L, Khincha PP, Ellis SR, Giri N, Brodie S, Chandrasekharappa SC, Donovan FX, Zhou W, Hicks BD, Boland JF, Yeager M, Jones K, Zhu B, Wang M, Alter BP, Savage SA. Novel and known ribosomal causes of Diamond-Blackfan anaemia identified through comprehensive genomic characterisation. J Med Genet 2017; 54:417-425. [PMID: 28280134 DOI: 10.1136/jmedgenet-2016-104346] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [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: 10/04/2016] [Revised: 02/08/2017] [Accepted: 02/16/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND Diamond-Blackfan anaemia (DBA) is an inherited bone marrow failure syndrome (IBMFS) characterised by erythroid hypoplasia. It is associated with congenital anomalies and a high risk of developing specific cancers. DBA is caused predominantly by autosomal dominant pathogenic variants in at least 15 genes affecting ribosomal biogenesis and function. Two X-linked recessive genes have been identified. OBJECTIVES We aim to identify the genetic aetiology of DBA. METHODS Of 87 families with DBA enrolled in an institutional review board-approved cohort study (ClinicalTrials.gov Identifier:NCT00027274), 61 had genetic testing information available. Thirty-five families did not have a known genetic cause and thus underwent comprehensive genomic evaluation with whole exome sequencing, deletion and CNV analyses to identify their disease-associated pathogenic variant. Controls for functional studies were healthy mutation-negative individuals enrolled in the same study. RESULTS Our analyses uncovered heterozygous pathogenic variants in two previously undescribed genes in two families. One family had a non-synonymous variant (p.K77N) in RPL35; the second family had a non-synonymous variant (p. L51S) in RPL18. Both of these variants result in pre-rRNA processing defects. We identified heterozygous pathogenic variants in previously known DBA genes in 16 of 35 families. Seventeen families who underwent genetic analyses are yet to have a genetic cause of disease identified. CONCLUSIONS Overall, heterozygous pathogenic variants in ribosomal genes were identified in 44 of the 61 families (72%). De novo pathogenic variants were observed in 57% of patients with DBA. Ongoing studies of DBA genomics will be important to understand this complex disorder.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, Kentucky, USA
| | - Neelam Giri
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Seth Brodie
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Blanche P Alter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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26
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Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev 2017; 26:126-135. [PMID: 27697780 PMCID: PMC5224974 DOI: 10.1158/1055-9965.epi-16-0106] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [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: 02/01/2016] [Revised: 06/30/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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Affiliation(s)
- Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - David J Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kimberly Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlisse Caga-Anan
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christopher A Haiman
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Tessier
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Daniel Vincent
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - François Bacot
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Stefanie Nelson
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Stephen Demetriades
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | | | | | - Judith L Forman
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Brüske-Hohlfeld
- Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lesley McGuffog
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karoline Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Katja Butterbach
- Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kraft
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Liesel FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Sara Lindström
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marjorie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew Berchuck
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Sylvie Laboissiere
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jack A Taylor
- Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sue K Park
- College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Hospital, New York, New York
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Rita Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California
- Department of Internal Medicine, University of California at Davis, Davis, California
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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Yang B, Shebl FM, Sternberg LR, Warner AC, Kleiner DE, Edelman DC, Gomez A, Dagnall CL, Hicks BD, Altekruse SF, Hernandez BY, Lynch CF, Meltzer PS, McGlynn KA. Telomere Length and Survival of Patients with Hepatocellular Carcinoma in the United States. PLoS One 2016; 11:e0166828. [PMID: 27880792 PMCID: PMC5120796 DOI: 10.1371/journal.pone.0166828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 09/19/2016] [Accepted: 11/05/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Telomere shortening is an important molecular event in hepatocellular carcinoma (HCC) initiation; however, its role in HCC progression and prognosis is less clear. Our study aimed to examine the association of telomere length with survival of patients with HCC. METHODS We measured telomere length in tumor and adjacent non-tumor tissues from 126 persons with HCC in the United States (U.S.) who were followed for mortality outcomes. Relative telomere length (RTL) was measured by a monochrome multiplex quantitative polymerase chain reaction assay. Multivariable Cox proportional hazards modeling was used to calculate hazard ratios (HRs) and 95% CIs for the association between telomere length and all-cause mortality. We also examined associations between telomere length and patient characteristics using multiple linear regression. RESULTS During a mean follow-up of 6.0 years, 79 deaths occurred among 114 individuals for whom survival data were available. The ratio of RTL in tumor relative to non-tumor tissue was greater for individuals with regional or distant stage tumors (0.97) than localized stage tumors (0.77), and for individuals with grade III or IV tumors (0.95) than grade II (0.88) or grade I (0.67) tumors. An RTL ratio ≥1 was not associated with survival (HR 0.92, 95% CI 0.55, 1.55) compared to a ratio <1, after adjusting for age at diagnosis, sex, tumor stage and tumor size. Similarly, RTL in the tumor and non-tumor tissue, respectively, were not associated with survival. CONCLUSIONS This U.S. based study found that telomeres may be longer in more aggressive HCCs. There was no evidence, however, that telomere length was associated with survival of patients with HCC. Future investigations are warranted to clarify the role of telomere length in HCC prognosis.
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Affiliation(s)
- Baiyu Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Fatma M. Shebl
- Yale University School of Public Health, New Haven, CT, 06520, United States of America
| | - Lawrence R. Sternberg
- Pathology-Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, United States of America
| | - Andrew C. Warner
- Pathology-Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, United States of America
| | - David E. Kleiner
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Daniel C. Edelman
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Allison Gomez
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Casey L. Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, 20892, United States of America
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, 20892, United States of America
| | - Sean F. Altekruse
- Division of Cancer Control & Population Sciences, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Brenda Y. Hernandez
- University of Hawaii Cancer Center, Honolulu, HI, 96813, United States of America
| | - Charles F. Lynch
- University of Iowa College of Public Health, Iowa City, IA, 52242, United States of America
| | - Paul S. Meltzer
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Katherine A. McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, United States of America
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Yang B, Shebl FM, Sternberg LR, Warner AC, Kleiner DE, Edelman DC, Gomez A, Dagnall CL, Hicks BD, Altekruse SF, Hernandez BY, Lynch CF, Meltzer PS, McGlynn KA. Abstract 818: Shortened telomere length in hepatocellular carcinoma in the United States. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-818] [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: Telomeres play an important role in the maintenance of chromosomal stability. It has been previously reported that telomere length is shortened in hepatocellular carcinoma (HCC) compared to paired non-tumor tissue. However, most studies have been conducted in high-risk regions such as Asia. To date, no prior study has examined telomere length and HCC in the United States, a low risk region where HCC etiology may differ from that of high risk regions.
Methods: We measured telomere length in 127 paired tumor and non-tumor tissue samples from persons with HCC in Iowa, Hawaii and Connecticut. Formalin-fixed, paraffin-embedded tissues were collected at the time of diagnosis. Relative telomere length was measured by a monochrome multiplex quantitative PCR assay. The Wilcoxon signed-rank test was used to compare telomere length between tumor and paired non-tumor tissues. Cox proportional hazards modeling was used to estimate the association between telomere length and mortality, adjusting for age at diagnosis, sex, and tumor stage and size at diagnosis.
Results: Of the 127 pairs of samples, telomere length was shorter in the tumor in 88 pairs (69%), longer in the tumor in 33 pairs (26%) and the same length in the tumor and non-tumor tissue in 6 pairs (5%). Overall, the HCC tissues had statistically significantly shorter telomere length than their matched non-tumor tissues (p < 0.01). The proportion of pairs in which the tumor telomere was shorter than non-tumor was higher among those with localized stage tumors (81%) compared to those with regional or distant stage tumors (50%) (p < 0.01 after adjusting for age at diagnosis, sex, and source of the case). In addition, we observed a 119% higher risk of mortality (adjusted relative risk 2.19) among persons whose tumors had shorter telomeres than their non-tumor tissue, compared to persons whose tumors had longer telomeres; however, the confidence interval was relatively wide (0.94-5.12).
Conclusion: Using tissue samples from persons with HCC in the United States, we found that telomere length was shorter in tumor tissue compared to paired non-tumor tissue, especially among localized stage tumors. In addition, there was a suggestion that tumor telomere shortening might be associated with higher risk of mortality. Together, these results may provide insight into the role of biological mechanisms associated with telomere shortening and into the prognosis of HCC in lower risk populations.
Citation Format: Baiyu Yang, Fatma M. Shebl, Lawrence R. Sternberg, Andrew C. Warner, David E. Kleiner, Daniel C. Edelman, Allison Gomez, Casey L. Dagnall, Belynda D. Hicks, Sean F. Altekruse, Brenda Y. Hernandez, Charles F. Lynch, Paul S. Meltzer, Katherine A. McGlynn. Shortened telomere length in hepatocellular carcinoma in the United States. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 818.
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Affiliation(s)
- Baiyu Yang
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | | | | | | | - Casey L. Dagnall
- 3National Cancer Institute/Frederick National Laboratory for Cancer Research, Bethesda/Frederick, MD
| | - Belynda D. Hicks
- 3National Cancer Institute/Frederick National Laboratory for Cancer Research, Bethesda/Frederick, MD
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Morton LM, Sampson JN, Armstrong GT, Chen TH, Hudson M, Karlins E, Dagnall CL, Li S, Wilson CL, Srivastava K, Liu W, Kang G, Oeffinger K, Henderson TO, Moskowitz CS, Gibson TM, Merino DM, Wong JR, Hammond S, Neglia JP, Turcotte LM, Miller J, Bowen L, Wheeler WA, Leisenring WM, Whitton JA, Burdette L, Hicks BD, Machiela MJ, Vogt A, Wang Z, Yeager M, Neale G, Lear M, Strong LC, Yasui Y, Stovall M, Weathers RE, Smith SA, Howell R, Davies SM, Radloff GA, Berrington de González A, Inskip PD, Rajaraman P, Fraumeni JF, Bhatia S, Chanock SJ, Tucker MA, Robison LL. Abstract 2691: Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2691] [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: Childhood cancer survivors treated with chest radiotherapy have substantially elevated risk for developing breast cancer. Although numerous breast cancer susceptibility variants have been established, genetic predisposition for breast cancer after childhood cancer remains poorly understood.
Methods: We conducted the first genome-wide association study of subsequent breast cancer in female childhood cancer survivors within two large-scale cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study [CCSS; 178 breast cancer cases, 2200 controls (survivors without subsequent neoplasm) of European descent] and the St. Jude Lifetime Cohort (SJLIFE; 29 cases, 574 controls). Genotyping on the Illumina HumanOmni5MExome (CCSS) or Affymetrix 6.0 (SJLIFE) array and imputation based on the 1000 Genomes Project yielded >16 million high quality genotyped or imputed variants available in both studies. Assuming an additive genetic model, we used multivariate Cox regression to quantify the effect of each variant in the overall population and stratified by receipt of ≥10 Gray (Gy) or <10 Gy radiation exposure to the chest.
Results: We identified two loci associated with breast cancer risk among children who received ≥10 Gy radiation to the chest (131 cases, 493 controls): one at 1q41 [rs4342822, risk allele frequency (RAF) = 0.46 in controls, pooled per allele hazard ratio (HR) = 1.94, 95% confidence interval (CI) = 1.50-2.51, Pexact = 1.20×10−8] and another at 11q23 (rs74949440, RAF = 0.02 in controls, HR = 3.71, 95%CI = 2.18-6.32, Pexact = 2.00×10−9). Neither locus was associated with breast cancer risk among children who received <10 Gy radiation to the chest (69 cases, 2144 controls; rs4342822: HR = 1.03, 95%CI = 0.75-1.44; rs74949440: HR = 1.21, 0.41-3.54). Results were consistent in the two studies, and the associations did not appear to be related to type of first primary childhood cancer. Both loci fall in or near biologically plausible candidate genes: the variant rs4342822 lies near PROX1, which is amplified in >10% of breast cancers in The Cancer Genome Atlas data. The variant rs74949440 is intronic to TAGLN, whose expression levels have been associated with breast cancer prognosis and altered cell death resistance following irradiation in human carcinoma cell lines.
Conclusion: These findings represent the first evidence outside of identified high-risk cancer susceptibility genes that certain individuals are genetically predisposed to developing breast cancer after radiotherapy and suggest that radiation exposure may interact with germline genetics to modify breast cancer risk.
Citation Format: Lindsay M. Morton, Joshua N. Sampson, Gregory T. Armstrong, Ting-Huei Chen, Melissa Hudson, Eric Karlins, Casey L. Dagnall, Shenchao Li, Carmen L. Wilson, Kumar Srivastava, Wei Liu, Guolian Kang, Kevin Oeffinger, Tara O. Henderson, Chaya S. Moskowitz, Todd M. Gibson, Diana M. Merino, Jeannette R. Wong, Sue Hammond, Joseph P. Neglia, Lucie M. Turcotte, Jeremy Miller, Laura Bowen, William A. Wheeler, Wendy M. Leisenring, John A. Whitton, Laurie Burdette, Belynda D. Hicks, Mitchell J. Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C. Strong, Yutaka Yasui, Marilyn Stovall, Rita E. Weathers, Susan A. Smith, Rebecca Howell, Stella M. Davies, Gretchen A. Radloff, Amy Berrington de González, Peter D. Inskip, Preetha Rajaraman, Joseph F. Fraumeni, Smita Bhatia, Stephen J. Chanock, Margaret A. Tucker, Leslie L. Robison. Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2691.
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Affiliation(s)
- Lindsay M. Morton
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Joshua N. Sampson
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Gregory T. Armstrong
- 2Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
| | - Ting-Huei Chen
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Melissa Hudson
- 3Division of Cancer Survivorship, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Eric Karlins
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Casey L. Dagnall
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Shenchao Li
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Carmen L. Wilson
- 2Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
| | - Kumar Srivastava
- 5Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Wei Liu
- 5Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Guolian Kang
- 5Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Tara O. Henderson
- 7Department of Pediatrics, Section of Hematology, Oncology and Stem Cell Transplantation, University of Chicago, Chicago, IL
| | | | - Todd M. Gibson
- 2Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
| | - Diana M. Merino
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Jeannette R. Wong
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | | | - Joseph P. Neglia
- 9Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | - Jeremy Miller
- 10Information Management Services, Inc., Calverton, MD
| | - Laura Bowen
- 10Information Management Services, Inc., Calverton, MD
| | | | | | | | - Laurie Burdette
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Belynda D. Hicks
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Mitchell J. Machiela
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Aurelie Vogt
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Zhaoming Wang
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Meredith Yeager
- 4Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research & Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Geoffrey Neale
- 12Hartwell Center for Bioinformatics and Biotechnology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Matthew Lear
- 13Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Louise C. Strong
- 14Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yutaka Yasui
- 2Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
| | - Marilyn Stovall
- 15Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rita E. Weathers
- 15Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Susan A. Smith
- 15Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rebecca Howell
- 15Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stella M. Davies
- 16Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Gretchen A. Radloff
- 16Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Peter D. Inskip
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Preetha Rajaraman
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Joseph F. Fraumeni
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Smita Bhatia
- 17School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Stephen J. Chanock
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Margaret A. Tucker
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Leslie L. Robison
- 2Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN
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Mirabello L, Koster R, Moriarity BS, Spector LG, Meltzer PS, Gary J, Machiela MJ, Pankratz N, Panagiotou OA, Largaespada D, Wang Z, Gastier-Foster JM, Gorlick R, Khanna C, de Toledo SRC, Petrilli AS, Patiño-Garcia A, Sierrasesúmaga L, Lecanda F, Andrulis IL, Wunder JS, Gokgoz N, Serra M, Hattinger C, Picci P, Scotlandi K, Flanagan AM, Tirabosco R, Amary MF, Halai D, Ballinger ML, Thomas DM, Davis S, Barkauskas DA, Marina N, Helman L, Otto GM, Becklin KL, Wolf NK, Weg MT, Tucker M, Wacholder S, Fraumeni JF, Caporaso NE, Boland JF, Hicks BD, Vogt A, Burdett L, Yeager M, Hoover RN, Chanock SJ, Savage SA. A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma. Cancer Discov 2015; 5:920-31. [PMID: 26084801 DOI: 10.1158/2159-8290.cd-15-0125] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/11/2015] [Indexed: 02/02/2023]
Abstract
UNLABELLED Metastasis is the leading cause of death in patients with osteosarcoma, the most common pediatric bone malignancy. We conducted a multistage genome-wide association study of osteosarcoma metastasis at diagnosis in 935 osteosarcoma patients to determine whether germline genetic variation contributes to risk of metastasis. We identified an SNP, rs7034162, in NFIB significantly associated with metastasis in European osteosarcoma cases, as well as in cases of African and Brazilian ancestry (meta-analysis of all cases: P = 1.2 × 10(-9); OR, 2.43; 95% confidence interval, 1.83-3.24). The risk allele was significantly associated with lowered NFIB expression, which led to increased osteosarcoma cell migration, proliferation, and colony formation. In addition, a transposon screen in mice identified a significant proportion of osteosarcomas harboring inactivating insertions in Nfib and with lowered NFIB expression. These data suggest that germline genetic variation at rs7034162 is important in osteosarcoma metastasis and that NFIB is an osteosarcoma metastasis susceptibility gene. SIGNIFICANCE Metastasis at diagnosis in osteosarcoma is the leading cause of death in these patients. Here we show data that are supportive for the NFIB locus as associated with metastatic potential in osteosarcoma.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland.
| | - Roelof Koster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota. Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Logan G Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Paul S Meltzer
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Joy Gary
- Laboratory of Cancer Biology and Genetics, NCI, NIH, Bethesda, Maryland; College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Orestis A Panagiotou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - David Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota. Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Zhaoming Wang
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, and The Ohio State University Department of Pathology and Pediatrics, Columbus, Ohio
| | - Richard Gorlick
- Albert Einstein College of Medicine, The Children's Hospital at Montefiore, Bronx, New York
| | - Chand Khanna
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | | | | | - Ana Patiño-Garcia
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Luis Sierrasesúmaga
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Fernando Lecanda
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Irene L Andrulis
- University of Toronto, Litwin Centre for Cancer Genetics, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jay S Wunder
- University of Toronto, Litwin Centre for Cancer Genetics, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- University of Toronto, Litwin Centre for Cancer Genetics, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Massimo Serra
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Piero Picci
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Adrienne M Flanagan
- University College London Cancer Institute, London, United Kingdom. Royal National Orthopaedic Hospital National Health Service Trust, Stanmore, Middlesex, United Kingdom
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital National Health Service Trust, Stanmore, Middlesex, United Kingdom
| | - Maria Fernanda Amary
- Royal National Orthopaedic Hospital National Health Service Trust, Stanmore, Middlesex, United Kingdom
| | - Dina Halai
- Royal National Orthopaedic Hospital National Health Service Trust, Stanmore, Middlesex, United Kingdom
| | | | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Sean Davis
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Donald A Barkauskas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Neyssa Marina
- Stanford University and Lucile Packard Children's Hospital, Palo Alto, California
| | - Lee Helman
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - George M Otto
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Kelsie L Becklin
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Natalie K Wolf
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Madison T Weg
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Joseph F Boland
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Aurelie Vogt
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
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Kocak H, Ballew BJ, Bisht K, Eggebeen R, Hicks BD, Suman S, O'Neil A, Giri N, Maillard I, Alter BP, Keegan CE, Nandakumar J, Savage SA. Hoyeraal-Hreidarsson syndrome caused by a germline mutation in the TEL patch of the telomere protein TPP1. Genes Dev 2014; 28:2090-102. [PMID: 25233904 PMCID: PMC4180972 DOI: 10.1101/gad.248567.114] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [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] [Indexed: 12/30/2022]
Abstract
Germline mutations in telomere biology genes cause dyskeratosis congenita (DC), an inherited bone marrow failure and cancer predisposition syndrome. Hoyeraal-Hreidarsson syndrome (HH) is a clinically severe variant of DC. Using exome sequencing, Kocak et al. identified mutations in ACD (encoding TPP1), a component of the telomeric shelterin complex, in one family affected by HH. Characterization of the mutations revealed that the single-amino-acid deletion affecting the TEL patch surface of the TPP1 protein significantly compromises both telomerase recruitment and processivity. Germline mutations in telomere biology genes cause dyskeratosis congenita (DC), an inherited bone marrow failure and cancer predisposition syndrome. DC is a clinically heterogeneous disorder diagnosed by the triad of dysplastic nails, abnormal skin pigmentation, and oral leukoplakia; Hoyeraal-Hreidarsson syndrome (HH), a clinically severe variant of DC, also includes cerebellar hypoplasia, immunodeficiency, and intrauterine growth retardation. Approximately 70% of DC cases are associated with a germline mutation in one of nine genes, the products of which are all involved in telomere biology. Using exome sequencing, we identified mutations in Adrenocortical Dysplasia Homolog (ACD) (encoding TPP1), a component of the telomeric shelterin complex, in one family affected by HH. The proband inherited a deletion from his father and a missense mutation from his mother, resulting in extremely short telomeres and a severe clinical phenotype. Characterization of the mutations revealed that the single-amino-acid deletion affecting the TEL patch surface of the TPP1 protein significantly compromises both telomerase recruitment and processivity, while the missense mutation in the TIN2-binding region of TPP1 is not as clearly deleterious to TPP1 function. Our results emphasize the critical roles of the TEL patch in proper stem cell function and demonstrate that TPP1 is the second shelterin component (in addition to TIN2) to be implicated in DC.
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Affiliation(s)
- Hande Kocak
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Bari J Ballew
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, Maryland 20850, USA
| | - Kamlesh Bisht
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rebecca Eggebeen
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, NCI-Frederick, Rockville, Maryland 20850, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, NCI-Frederick, Rockville, Maryland 20850, USA
| | - Shalabh Suman
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, NCI-Frederick, Rockville, Maryland 20850, USA
| | - Adri O'Neil
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, NCI-Frederick, Rockville, Maryland 20850, USA
| | - Neelam Giri
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, Maryland 20850, USA
| | | | | | - Ivan Maillard
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA; Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Cell and Developmental Biology, Ann Arbor, Michigan 48109, USA
| | - Blanche P Alter
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, Maryland 20850, USA
| | - Catherine E Keegan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Rockville, Maryland 20850, USA;
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Abstract
Subcomponents of the N200 component of the event-related brain potential believed to be differentially sensitive to involuntary and voluntary cognitive processes were examined. Nonpatients (N = 131) identified initially by the Chapman and Depue research scales and classified later on the basis of diagnostic symptom clusters and family psychiatric history provided converging evidence for an intact mismatch negativity subcomponent. In contrast, the N2b subcomponent distinguished several groups of subjects. Results suggested abnormal voluntary cognitive processing, perhaps reflecting compensatory efforts in subjects at risk for or manifesting psychopathology, particularly those showing negative symptoms.
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Affiliation(s)
- L O Fernandes
- Department of Psychology, University of Illinois at Urbana-Champaign, USA.
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Abstract
Prenatal diagnosis for fragile X syndrome was performed in 34 pregnancies of 33 known carriers, on 22 chorionic villus samples (CVS), and 15 amniocentesis samples. Fetal and maternal DNA were analyzed by the EagI/EcoRI Southern blot of Rousseau et al. [1991: N Engl J Med 325:1673-1681], with detection of full mutations ensured by a second loading with brief electrophoresis. As a supplemental assay for full mutations, cytogenetic induction was performed in 20 cases. Positive cytogenetic results were helpful in confirming full mutations in CVS cases where the fetal DNA was intermediate in appearance, between a large premutation and a small full mutation. Of 8 mothers with full mutations, the fetal results were 5 full, 2 normal, and 1 premutation (whose mother was a full/pre compound heterozygote). Of 26 mothers with premutations, the fetal results were 5 full, 13 normal, 7 premutation, and 1 uninterpretable (maternal contamination). Maternal premutations were sized in kb by Southern blot and in CGG repeat number by PCR; the predicted correlation between maternal length and penetrance was seen. Follow-up studies include 3 full mutations and 2 premutations confirmed by DNA analysis at birth. Maternal contamination of CVS samples was encountered in 3 of 22 cases, illustrating the value of EagI in detecting maternal (lyonized) chromosomes.
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Affiliation(s)
- A Maddalena
- Genetics & IVF Institute, Fairfax, Virginia 22031
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Hicks BD. Canadian aquaculture. Can Vet J 1987; 28:640-2. [PMID: 17422902 PMCID: PMC1680529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
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Desjardins LM, Hicks BD, Hilton JW. Iron catalyzed oxidation of trout diets and its effect on the growth and physiological response of rainbow trout. Fish Physiol Biochem 1987; 3:173-82. [PMID: 24233557 DOI: 10.1007/bf02180278] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Two experiments were conducted to determine 1) the effect of iron supplementation and the quality of fish oils on dietary lipid peroxidation and 2) the concurrent effects of diet rancidity and iron overload on the growth and physiological response of rainbow trout. Semi-purified diets supplemented with graded levels of iron (0-6250 mg/kg diet as ferrous sulphate) were fed to trout for 12-36 weeks. The malonaldehyde (MA) concentration of the test diets increased as the iron levels in the diets increased indicating that iron catalyzed lipid oxidation was occurring. However, when ethoxyquin was added to the oils, the increase in dietary MA level was significantly reduced. Fish oils with an initial high peroxide value were more susceptible to iron-catalyzed lipid oxidation. The concurrent effects of diet rancidity and iron overload (greater than 86 mg/kg) led to the development of unique histopathological signs, poor growth and high mortalities in the trout. In contrast, when diet rancidity was low (less than 10 µg MA/g diet), the toxic level of dietary iron was greater than 1380 mg/kg diet. The concentration of iron in trout tissues, and the hematocrit and hemoglobin concentrations increased as dietary iron levels increased and were not affected by the degree of diet rancidity.
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Affiliation(s)
- L M Desjardins
- Group for Advancement of Fish Studies Department of Nutritional Sciences, College of Biological Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Abstract
Histopathologic, ultrastructural, and negative-staining studies indicated that nodular lesions on the flippers, head, and necks of recently weaned, captive grey seals (Halichoerus grypus) were similar to sealpox lesions reported from several other species of seals. Virions associated with the nodules were characteristic of the parapoxvirus subgroup of pox viruses. Two of the three persons handling the seals developed nodular lesions similar to "milker's nodules," the characteristic lesion in persons infected with parapoxvirus. The clinical course of the parapoxvirus infection in both the grey seals and their handlers is described. It was concluded that although sealpox is transmissible to man, the mild clinical manifestations place it in the nuisance category of zoonotic diseases.
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Abstract
Epidermal growth in two mature female bottlenose dolphins, Tursiops truncatus, was investigated by following the movement of a cohort of tritiated thymidine-labeled epidermal cells for 59 days. The majority of the cells migrated in a cluster which was estimated to reach the skin surface in 73 days. We calculate that the outermost cell layer is sloughed 12 times per day. Turnover time and sloughing rate are estimated to be 1.7 times longer and 8.5 times faster than the respective values for epidermal cell kinetics in humans. This apparent inconsistency of slow transit time and rapid sloughing rate is reconciled by the convoluted structure of the stratum germinativum in the dolphin which results in a ratio of germinatival to superficial cells of 876:1. The stratum germinativum of dolphin epidermis appears to lack morphologically distinct, spatially segregated subpopulations of anchoring and stem cells. Dolphin epidermis has a large capacity for cell population, relatively long turnover time, and rapid sloughing rate. The adaptive advantages of these characteristics are discussed.
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Hicks BD, Geraci JR, Cunningham JC, Arif BM. Effects of red-headed in sawfly, Neodiprion lecontei, nuclear polyhedrosis virus on rainbow trout, Salmo gairdneri, and Daphnia pulex. J Environ Sci Health B 1981; 16:493-509. [PMID: 7026655 DOI: 10.1080/03601238109372274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The effects of a nuclear polyhedrosis virus (NPV) of the red-headed pine sawfly, Neodiprion lecontei, on rainbow trout, Salmo gairdneri, were investigated. The fish were exposed to this virus by intubation and topical application and no ill-effects were observed. Similarly, no ill-effects were detected in Daphnia pulex when the same NPV was added to their culture medium. The materials were lyophilized, NPV-infected sawfly larvae (normally used for insect control), lyophilized, uninfected larvae and purified, polyhedral inclusion bodies. On the basis of these laboratory tests, this virus, when disseminated as a biocontrol agent, should present no hazard to rainbow trout or to the aquatic invertebrate Daphnia pulex, two species frequently used in toxicity tests of chemical pesticides.
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Geraci JR, Hicks BD, St Aubin DJ. Dolphin pox: a skin disease of cetaceans. Can J Comp Med 1979; 43:399-404. [PMID: 232852 PMCID: PMC1320012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poxvirus has been identified morphologically from skin lesions in captive and free-ranging bottlenosed dolphins, Tursiops truncatus and a stranded Atlantic white-sided dolphin, Lagenorhynchus acutus. The lesions, commonly referred to as ring or pinhole lesions, appear as solitary or coalesced circular grey blemishes. Advanced ring lesions may take the form of black punctiform stippled patterns known as "tattoo". Histologically, the stratum externum is thickened, and there is ballooning degeneration and eosinophilic intractyoplasmic inclusions in the stratum intermedium. These includions contain virus particles which exhibit typical poxvirus morphology. Stress, environmental conditions and general health appear to play a major role in the clinical manifestation of dolphin pox.
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