1
|
Darst BF, Saunders E, Dadaev T, Sheng X, Wan P, Pooler L, Xia LY, Chanock S, Berndt SI, Wang Y, Patel AV, Albanes D, Weinstein SJ, Gnanapragasam V, Huff C, Couch FJ, Wolk A, Giles GG, Nguyen-Dumont T, Milne RL, Pomerantz MM, Schmidt JA, Travis RC, Key TJ, Stopsack KH, Mucci LA, Catalona WJ, Marosy B, Hetrick KN, Doheny KF, MacInnis RJ, Southey MC, Eeles RA, Wiklund F, Conti DV, Kote-Jarai Z, Haiman CA. Germline Sequencing Analysis to Inform Clinical Gene Panel Testing for Aggressive Prostate Cancer. JAMA Oncol 2023; 9:1514-1524. [PMID: 37733366 PMCID: PMC10881219 DOI: 10.1001/jamaoncol.2023.3482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/09/2023] [Indexed: 09/22/2023]
Abstract
Importance Germline gene panel testing is recommended for men with advanced prostate cancer (PCa) or a family history of cancer. While evidence is limited for some genes currently included in panel testing, gene panels are also likely to be incomplete and missing genes that influence PCa risk and aggressive disease. Objective To identify genes associated with aggressive PCa. Design, Setting, and Participants A 2-stage exome sequencing case-only genetic association study was conducted including men of European ancestry from 18 international studies. Data analysis was performed from January 2021 to March 2023. Participants were 9185 men with aggressive PCa (including 6033 who died of PCa and 2397 with confirmed metastasis) and 8361 men with nonaggressive PCa. Exposure Sequencing data were evaluated exome-wide and in a focused investigation of 29 DNA repair pathway and cancer susceptibility genes, many of which are included on gene panels. Main Outcomes and Measures The primary study outcomes were aggressive (category T4 or both T3 and Gleason score ≥8 tumors, metastatic PCa, or PCa death) vs nonaggressive PCa (category T1 or T2 and Gleason score ≤6 tumors without known recurrence), and metastatic vs nonaggressive PCa. Results A total of 17 546 men of European ancestry were included in the analyses; mean (SD) age at diagnosis was 65.1 (9.2) years in patients with aggressive PCa and 63.7 (8.0) years in those with nonaggressive disease. The strongest evidence of association with aggressive or metastatic PCa was noted for rare deleterious variants in known PCa risk genes BRCA2 and ATM (P ≤ 1.9 × 10-6), followed by NBN (P = 1.7 × 10-4). This study found nominal evidence (P < .05) of association with rare deleterious variants in MSH2, XRCC2, and MRE11A. Five other genes had evidence of greater risk (OR≥2) but carrier frequency differences between aggressive and nonaggressive PCa were not statistically significant: TP53, RAD51D, BARD1, GEN1, and SLX4. Deleterious variants in these 11 candidate genes were carried by 2.3% of patients with nonaggressive, 5.6% with aggressive, and 7.0% with metastatic PCa. Conclusions and Relevance The findings of this study provide further support for DNA repair and cancer susceptibility genes to better inform disease management in men with PCa and for extending testing to men with nonaggressive disease, as men carrying deleterious alleles in these genes are likely to develop more advanced disease.
Collapse
Affiliation(s)
- Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ed Saunders
- The Institute of Cancer Research, London, United Kingdom
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, United Kingdom
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Lucy Y. Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ying Wang
- Department of Population Science, American Cancer Society, Atlanta, Georgia
| | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, Georgia
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephanie J. Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Vincent Gnanapragasam
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Chad Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston
| | - Fergus J. Couch
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
| | - Roger L. Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | | | - Julie A. Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Department of Clinical Epidemiology, Department of Clinical Medicine, Aarhus University Hospital and Aarhus University, Aarhus N, Denmark
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Timothy J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | | | - Lorelei A. Mucci
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - Beth Marosy
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kurt N. Hetrick
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kimberly F. Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Robert J. MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Melissa C. Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London, United Kingdom
- Royal Marsden NHS Foundation Trust, Fulham Road, London, United Kingdom
| | | | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | | | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| |
Collapse
|
2
|
Zhou YH, Gallins PJ, Pace RG, Dang H, Aksit MA, Blue EE, Buckingham KJ, Collaco JM, Faino AV, Gordon WW, Hetrick KN, Ling H, Liu W, Onchiri FM, Pagel K, Pugh EW, Raraigh KS, Rosenfeld M, Sun Q, Wen J, Li Y, Corvol H, Strug LJ, Bamshad MJ, Blackman SM, Cutting GR, Gibson RL, O’Neal WK, Wright FA, Knowles MR. Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med 2023; 207:1324-1333. [PMID: 36921087 PMCID: PMC10595435 DOI: 10.1164/rccm.202209-1653oc] [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: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.
Collapse
Affiliation(s)
- Yi-Hui Zhou
- Bioinformatics Research Center
- Department of Biological Sciences, and
| | | | - Rhonda G. Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | | | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Medical Genetics, Department of Medicine
| | | | | | - Anna V. Faino
- Children’s Core for Biostatistics, Epidemiology and Analytics in Research and
| | | | - Kurt N. Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | | | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth W. Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | - Margaret Rosenfeld
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Yun Li
- Department of Biostatistics
- Department of Genetics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Paris, France
- Centre de Recherche Saint Antoine, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health
- Department of Statistical Sciences, and
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; and
- Program in Genetics and Genome Biology and
- The Center for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Genetic Medicine, Department of Pediatrics
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Scott M. Blackman
- McKusick-Nathans Department of Genetic Medicine
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ronald L. Gibson
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Fred A. Wright
- Bioinformatics Research Center
- Department of Biological Sciences, and
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | | |
Collapse
|
3
|
Wang A, Xu Y, Yu Y, Nead KT, Kim T, Xu K, Dadaev T, Saunders E, Sheng X, Wan P, Pooler L, Xia LY, Chanock S, Berndt SI, Gapstur SM, Stevens V, Albanes D, Weinstein SJ, Gnanapragasam V, Giles GG, Nguyen-Dumont T, Milne RL, Pomerantz MM, Schmidt JA, Stopsack KH, Mucci LA, Catalona WJ, Hetrick KN, Doheny KF, MacInnis RJ, Southey MC, Eeles RA, Wiklund F, Kote-Jarai Z, de Smith AJ, Conti DV, Huff C, Haiman CA, Darst BF. Clonal hematopoiesis and risk of prostate cancer in large samples of European ancestry men. Hum Mol Genet 2023; 32:489-495. [PMID: 36018819 PMCID: PMC9851740 DOI: 10.1093/hmg/ddac214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/31/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Little is known regarding the potential relationship between clonal hematopoiesis (CH) of indeterminate potential (CHIP), which is the expansion of hematopoietic stem cells with somatic mutations, and risk of prostate cancer, the fifth leading cause of cancer death of men worldwide. We evaluated the association of age-related CHIP with overall and aggressive prostate cancer risk in two large whole-exome sequencing studies of 75 047 European ancestry men, including 7663 prostate cancer cases, 2770 of which had aggressive disease, and 3266 men carrying CHIP variants. We found that CHIP, defined by over 50 CHIP genes individually and in aggregate, was not significantly associated with overall (aggregate HR = 0.93, 95% CI = 0.76-1.13, P = 0.46) or aggressive (aggregate OR = 1.14, 95% CI = 0.92-1.41, P = 0.22) prostate cancer risk. CHIP was weakly associated with genetic risk of overall prostate cancer, measured using a polygenic risk score (OR = 1.05 per unit increase, 95% CI = 1.01-1.10, P = 0.01). CHIP was not significantly associated with carrying pathogenic/likely pathogenic/deleterious variants in DNA repair genes, which have previously been found to be associated with aggressive prostate cancer. While findings from this study suggest that CHIP is likely not a risk factor for prostate cancer, it will be important to investigate other types of CH in association with prostate cancer risk.
Collapse
Affiliation(s)
- Anqi Wang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yili Xu
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Kevin T Nead
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - TaeBeom Kim
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Keren Xu
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ed Saunders
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Xin Sheng
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Loreall Pooler
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lucy Y Xia
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen Chanock
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Demetrius Albanes
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Vincent Gnanapragasam
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | | | - Julie A Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
- Department of Clinical Epidemiology, Department of Clinical Medicine, Aarhus University Hospital and Aarhus University, Aarhus N, DK-8200, Denmark
| | | | - Lorelei A Mucci
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - William J Catalona
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kurt N Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria 3010, Australia
| | - Rosalind A Eeles
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | | | - Adam J de Smith
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chad Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Burcu F Darst
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| |
Collapse
|
4
|
Darst BF, Saunders E, Dadaev T, Sheng X, Wan P, Pooler L, Xia LY, Chanock S, Berndt SI, Gapstur SM, Stevens V, Albanes D, Weinstein SJ, Gnanapragasam V, Giles GG, Nguyen-Dumont T, Milne RL, Pomerantz MM, Schmidt JA, Travis RC, Key TJ, Stopsack KH, Mucci LA, Catalona WJ, Marosy B, Hetrick KN, Doheny KF, MacInnis RJ, Southey MC, Eeles RA, Wiklund F, Kote-Jarai Z, Conti DV, Haiman CA. Abstract 688: Multi-stage exome sequencing study of 17,546 aggressive and non-aggressive prostate cancer cases. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-688] [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
Rare pathogenic variants in DNA repair genes have been found to influence risk of aggressive prostate cancer. We conducted a large case-only exome sequencing study to further understand the role of rare coding variation in aggressive prostate cancer in a study of 9,185 aggressive (prostate cancer death, metastatic disease, T4, or both T3 and Gleason≥8) and 8,361 non-aggressive cases (T1/T2 and Gleason≤6) of European ancestry from 19 international studies. Stage 1 samples (N=5,545) had whole exome-sequencing, and stage 2 samples (N=12,001) had targeted exome sequencing for 1,459 genes selected based on stage 1 results and previous evidence. Logistic regression models were used to evaluate gene-based tests and the aggregate effect of multiple genes to investigate whether carrying pathogenic/likely pathogenic/deleterious (P/LP/D) variants (18,759 identified) was associated with risk of aggressive prostate cancer, prostate cancer death (N=6,033), or metastatic disease (N=1,730) compared to non-aggressive disease. Gene-based tests were meta-analyzed across stages 1 and 2. BRCA2, ATM, and NBN had the most statistically significant gene-based results: BRCA2 P/LP/D variant carriers had 4.3-fold higher odds of aggressive disease (95% CI=3.15-5.86, P=4x10-20), 4.7-fold higher odds of prostate cancer death (95% CI=3.41-6.59, P=2x10-20), and 5.7-fold higher odds of metastatic disease (95% CI=3.71-8.76, P=2x10-15); ATM P/LP/D variant carriers had 2.2-fold higher odds of aggressive disease (95% CI=1.58-2.99, P=2x10-6), 2.2-fold higher odds of prostate cancer death (95% CI=1.52-3.05, P=2x10-5), and 3.0-fold higher odds of metastatic disease (95% CI=1.93-4.61, P=9x10-7); and NBN P/LP/D variant carriers had 5.9-fold higher odds of metastatic disease (95% CI=2.56-13.84, P=3x10-5). Among potentially novel genes with strong but not exome-wide significant statistical evidence were MMP19, involved in reproduction and metastasis, with carriers having 2.8-fold higher odds of prostate cancer death (95% CI=1.53-5.05, P=8x10-4); PKD2L2, involved in fertility, with carriers having 3.5-fold higher odds of prostate cancer death (95% CI=1.76-7.04, P=5x10-4); and SMPD1, involved in converting sphingomyelin to ceramide, with carriers having 5.3-fold higher odds of metastatic disease (95% CI=1.85-14.98, P=0.002). At least one P/LP/D variant within a subset of 24 previously curated candidate prostate cancer DNA repair genes was carried by 12.8% of aggressive cases (OR=1.48, 95% CI=1.34-1.64, P=3x10-14), 12.6% of cases who died due to prostate cancer (OR=1.47, 95% CI=1.31-1.65, P=3x10-11), and 15.1% of metastatic cases (OR=2.16, 95% CI=1.57-2.16, P=5x10-14) compared to 9.4% of non-aggressive cases. These findings support the importance of rare genetic variation in aggressive prostate cancer risk and may have important implications for prostate cancer risk stratification and screening.
Citation Format: Burcu F. Darst, Ed Saunders, Tokhir Dadaev, Xin Sheng, Peggy Wan, Loreall Pooler, Lucy Y. Xia, Stephen Chanock, Sonja I. Berndt, Susan M. Gapstur, Victoria Stevens, Demetrius Albanes, Stephanie J. Weinstein, Vincent Gnanapragasam, Graham G. Giles, Tu Nguyen-Dumont, Roger L. Milne, Mark M. Pomerantz, Julie A. Schmidt, Ruth C. Travis, Timothy J. Key, Konrad H. Stopsack, Lorelei A. Mucci, William J. Catalona, Beth Marosy, Kurt N. Hetrick, Kimberly F. Doheny, Robert J. MacInnis, Melissa C. Southey, Rosalind A. Eeles, Fredrik Wiklund, Zsofia Kote-Jarai, David V. Conti, Christopher A. Haiman. Multi-stage exome sequencing study of 17,546 aggressive and non-aggressive prostate cancer cases [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 688.
Collapse
Affiliation(s)
| | - Ed Saunders
- 2Institute of Cancer Research, London, United Kingdom
| | - Tokhir Dadaev
- 2Institute of Cancer Research, London, United Kingdom
| | - Xin Sheng
- 1University of Southern California, Los Angeles, CA
| | - Peggy Wan
- 1University of Southern California, Los Angeles, CA
| | | | - Lucy Y. Xia
- 1University of Southern California, Los Angeles, CA
| | - Stephen Chanock
- 3National Cancer Institute, National Institute of Health, Bethesda, MD
| | - Sonja I. Berndt
- 3National Cancer Institute, National Institute of Health, Bethesda, MD
| | | | | | - Demetrius Albanes
- 3National Cancer Institute, National Institute of Health, Bethesda, MD
| | | | | | | | | | | | | | - Julie A. Schmidt
- 8Aarhus University Hospital and Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | - Beth Marosy
- 12Center for Inherited Disease Research, Baltimore, MD
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Darst BF, Dadaev T, Saunders E, Sheng X, Wan P, Pooler L, Xia LY, Chanock S, Berndt SI, Gapstur SM, Stevens V, Albanes D, Weinstein SJ, Gnanapragasam V, Giles GG, Nguyen-Dumont T, Milne RL, Pomerantz M, Schmidt JA, Mucci L, Catalona WJ, Hetrick KN, Doheny KF, MacInnis RJ, Southey MC, Eeles RA, Wiklund F, Kote-Jarai Z, Conti DV, Haiman CA. Germline Sequencing DNA Repair Genes in 5545 Men With Aggressive and Nonaggressive Prostate Cancer. J Natl Cancer Inst 2020; 113:616-625. [PMID: 32853339 DOI: 10.1093/jnci/djaa132] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/27/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is an urgent need to identify factors specifically associated with aggressive prostate cancer (PCa) risk. We investigated whether rare pathogenic, likely pathogenic, or deleterious (P/LP/D) germline variants in DNA repair genes are associated with aggressive PCa risk in a case-case study of aggressive vs nonaggressive disease. METHODS Participants were 5545 European-ancestry men, including 2775 nonaggressive and 2770 aggressive PCa cases, which included 467 metastatic cases (16.9%). Samples were assembled from 12 international studies and germline sequenced together. Rare (minor allele frequency < 0.01) P/LP/D variants were analyzed for 155 DNA repair genes. We compared single variant, gene-based, and DNA repair pathway-based burdens by disease aggressiveness. All statistical tests are 2-sided. RESULTS BRCA2 and PALB2 had the most statistically significant gene-based associations, with 2.5% of aggressive and 0.8% of nonaggressive cases carrying P/LP/D BRCA2 alleles (odds ratio [OR] = 3.19, 95% confidence interval [CI] = 1.94 to 5.25, P = 8.58 × 10-7) and 0.65% of aggressive and 0.11% of nonaggressive cases carrying P/LP/D PALB2 alleles (OR = 6.31, 95% CI = 1.83 to 21.68, P = 4.79 × 10-4). ATM had a nominal association, with 1.6% of aggressive and 0.8% of nonaggressive cases carrying P/LP/D ATM alleles (OR = 1.88, 95% CI = 1.10 to 3.22, P = .02). In aggregate, P/LP/D alleles within 24 literature-curated candidate PCa DNA repair genes were more common in aggressive than nonaggressive cases (carrier frequencies = 14.2% vs 10.6%, respectively; P = 5.56 × 10-5). However, this difference was non-statistically significant (P = .18) on excluding BRCA2, PALB2, and ATM. Among these 24 genes, P/LP/D carriers had a 1.06-year younger diagnosis age (95% CI = -1.65 to 0.48, P = 3.71 × 10-4). CONCLUSIONS Risk conveyed by DNA repair genes is largely driven by rare P/LP/D alleles within BRCA2, PALB2, and ATM. These findings support the importance of these genes in both screening and disease management considerations.
Collapse
Affiliation(s)
- Burcu F Darst
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Ed Saunders
- The Institute of Cancer Research, London, UK
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lucy Y Xia
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Chanock
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja I Berndt
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Demetrius Albanes
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Vincent Gnanapragasam
- Department of Surgery and Oncology, Academic Urology Group, University of Cambridge, Cambridge, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | | | | | | | | | - Kurt N Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.,The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - David V Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
6
|
Wang Z, Wei Y, Zhang R, Su L, Gogarten SM, Liu G, Brennan P, Field JK, McKay JD, Lissowska J, Swiatkowska B, Janout V, Bolca C, Kontic M, Scelo G, Zaridze D, Laurie CC, Doheny KF, Pugh EK, Marosy BA, Hetrick KN, Xiao X, Pikielny C, Hung RJ, Amos CI, Lin X, Christiani DC. Multi-Omics Analysis Reveals a HIF Network and Hub Gene EPAS1 Associated with Lung Adenocarcinoma. EBioMedicine 2018; 32:93-101. [PMID: 29859855 PMCID: PMC6021270 DOI: 10.1016/j.ebiom.2018.05.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 02/03/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Recent technological advancements have permitted high-throughput measurement of the human genome, epigenome, metabolome, transcriptome, and proteome at the population level. We hypothesized that subsets of genes identified from omic studies might have closely related biological functions and thus might interact directly at the network level. Therefore, we conducted an integrative analysis of multi-omic datasets of non-small cell lung cancer (NSCLC) to search for association patterns beyond the genome and transcriptome. A large, complex, and robust gene network containing well-known lung cancer-related genes, including EGFR and TERT, was identified from combined gene lists for lung adenocarcinoma. Members of the hypoxia-inducible factor (HIF) gene family were at the center of this network. Subsequent sequencing of network hub genes within a subset of samples from the Transdisciplinary Research in Cancer of the Lung-International Lung Cancer Consortium (TRICL-ILCCO) consortium revealed a SNP (rs12614710) in EPAS1 associated with NSCLC that reached genome-wide significance (OR = 1.50; 95% CI: 1.31-1.72; p = 7.75 × 10-9). Using imputed data, we found that this SNP remained significant in the entire TRICL-ILCCO consortium (p = .03). Additional functional studies are warranted to better understand interrelationships among genetic polymorphisms, DNA methylation status, and EPAS1 expression.
Collapse
Affiliation(s)
- Zhaoxi Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yongyue Wei
- Department of Epidemiology, Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruyang Zhang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephanie M Gogarten
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - Paul Brennan
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James D McKay
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - Vladimir Janout
- Department of Epidemiology and Public Health, University of Ostrava, University of Olomouc, Olomouc, Czech Republic
| | - Ciprian Bolca
- Thoracic Surgery Division, "Marius Nasta" National Institute of Pneumology, Bucharest, Romania
| | - Milica Kontic
- Clinic of Pulmonology, Clinical Center of Serbia (KCS), Belgrade, Serbia
| | - Ghislaine Scelo
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Cathy C Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth K Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Beth A Marosy
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt N Hetrick
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Claudio Pikielny
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Canada
| | - Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
7
|
Marosy BA, Craig BD, Hetrick KN, Witmer PD, Ling H, Griffith SM, Myers B, Ostrander EA, Stanford JL, Brody LC, Doheny KF. Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next-Generation Sequencing. Curr Protoc Hum Genet 2017; 92:18.10.1-18.10.25. [PMID: 28075488 DOI: 10.1002/cphg.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes a technique for generating exome-enriched sequencing libraries using DNA extracted from formalin-fixed paraffin-embedded (FFPE) samples. Utilizing commercially available kits, we present a low-input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in-solution-targeted selection for exons, followed by sequencing using the Illumina next-generation short-read sequencing platform. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Beth A Marosy
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Brian D Craig
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Kurt N Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - P Dane Witmer
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sean M Griffith
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Benjamin Myers
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Janet L Stanford
- Program in Prostate Cancer Research, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lawrence C Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Kimberly F Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
8
|
Minillo RM, Sobreira N, de Faria Soares MDF, Jurgens J, Ling H, Hetrick KN, Doheny KF, Valle D, Brunoni D, Perez ABA. Novel Deletion of SERPINF1 Causes Autosomal Recessive Osteogenesis Imperfecta Type VI in Two Brazilian Families. Mol Syndromol 2014; 5:268-75. [PMID: 25565926 DOI: 10.1159/000369108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2014] [Indexed: 12/17/2022] Open
Abstract
Autosomal recessive osteogenesis imperfecta (OI) accounts for 10% of all OI cases, and, currently, mutations in 10 genes (CRTAP, LEPRE1, PPIB, SERPINH1, FKBP10, SERPINF1, SP7, BMP1, TMEM38B, and WNT1) are known to be responsible for this form of the disease. PEDF is a secreted glycoprotein of the serpin superfamily that maintains bone homeostasis and regulates osteoid mineralization, and it is encoded by SERPINF1, currently associated with OI type VI (MIM 172860). Here, we report a consanguineous Brazilian family in which multiple individuals from at least 4 generations are affected with a severe form of OI, and we also report an unrelated individual from the same small city in Brazil with a similar but more severe phenotype. In both families the same homozygous SERPINF1 19-bp deletion was identified which is not known in the literature yet. We described intra- and interfamilial clinical and radiological phenotypic variability of OI type VI caused by the same homozygous SERPINF1 19-bp deletion and suggest a founder effect. Furthermore, the SERPINF1 genotypes/phenotypes reported so far in the literature are reviewed.
Collapse
Affiliation(s)
| | - Nara Sobreira
- McKusick-Nathan Institute of Genetic Medicine, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | | | - Julie Jurgens
- McKusick-Nathan Institute of Genetic Medicine, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | - Kurt N Hetrick
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | - David Valle
- McKusick-Nathan Institute of Genetic Medicine, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Md., USA
| | - Decio Brunoni
- Center of Medical Genetics, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Ana B Alvarez Perez
- Center of Medical Genetics, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| |
Collapse
|
9
|
Shenje LT, Andersen P, Halushka MK, Lui C, Fernandez L, Collin GB, Amat-Alarcon N, Meschino W, Cutz E, Chang K, Yonescu R, Batista DAS, Chen Y, Chelko S, Crosson JE, Scheel J, Vricella L, Craig BD, Marosy BA, Mohr DW, Hetrick KN, Romm JM, Scott AF, Valle D, Naggert JK, Kwon C, Doheny KF, Judge DP. Mutations in Alström protein impair terminal differentiation of cardiomyocytes. Nat Commun 2014; 5:3416. [PMID: 24595103 PMCID: PMC3992616 DOI: 10.1038/ncomms4416] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/10/2014] [Indexed: 02/08/2023] Open
Abstract
Cardiomyocyte cell division and replication in mammals proceed through embryonic development and abruptly decline soon after birth. The process governing cardiomyocyte cell cycle arrest is poorly understood. Here we carry out whole exome sequencing in an infant with evidence of persistent postnatal cardiomyocyte replication to determine the genetic risk factors. We identify compound heterozygous ALMS1 mutations in the proband, and confirm their presence in her affected sibling, one copy inherited from each heterozygous parent. Next, we recognise homozygous or compound heterozygous truncating mutations in ALMS1 in four other children with high levels of postnatal cardiomyocyte proliferation. Alms1 mRNA knockdown increases multiple markers of proliferation in cardiomyocytes, the percentage of cardiomyocytes in G2/M phases, and the number of cardiomyocytes by 10% in cultured cells. Homozygous Alms1-mutant mice have increased cardiomyocyte proliferation at two weeks postnatal compared to wild-type littermates. We conclude that deficiency of Alström protein impairs postnatal cardiomyocyte cell cycle arrest.
Collapse
Affiliation(s)
- Lincoln T Shenje
- 1] Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2]
| | - Peter Andersen
- 1] Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2]
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Cecillia Lui
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Laviel Fernandez
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | | | - Nuria Amat-Alarcon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Wendy Meschino
- North York General Hospital, Toronto, Ontario, Canada M2K 1E1
| | - Ernest Cutz
- Division of Pathology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Kenneth Chang
- 1] Division of Pathology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8 [2] KK Women's and Children's Hospital and Duke-NUS Graduate Medical School, Singapore 229899, Singapore
| | - Raluca Yonescu
- 1] Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Denise A S Batista
- 1] Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Yan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephen Chelko
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Jane E Crosson
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Janet Scheel
- Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Luca Vricella
- Division of Cardiothoracic Surgery, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brian D Craig
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Beth A Marosy
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - David W Mohr
- 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] High Throughput Sequencing Facility, Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kurt N Hetrick
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Jane M Romm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Alan F Scott
- 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA [2] High Throughput Sequencing Facility, Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | | | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Daniel P Judge
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| |
Collapse
|
10
|
Hoover-Fong J, Sobreira N, Jurgens J, Modaff P, Blout C, Moser A, Kim OH, Cho TJ, Cho SY, Kim SJ, Jin DK, Kitoh H, Park WY, Ling H, Hetrick KN, Doheny KF, Valle D, Pauli RM. Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. Am J Hum Genet 2014; 94:105-12. [PMID: 24387990 DOI: 10.1016/j.ajhg.2013.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 11/22/2013] [Indexed: 12/30/2022] Open
Affiliation(s)
- Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peggy Modaff
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Carrie Blout
- McKusick-Nathans Institute of Genetic Medicine, Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ann Moser
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ok-Hwa Kim
- Department of Radiology, Ajou University Hospital, Suwon, Kyunggi 443-721, Korea
| | - Tae-Joon Cho
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital, Seoul 110-744, Korea
| | - Sung Yoon Cho
- Department of Pediatrics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-Do 471-701, Korea
| | - Sang Jin Kim
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Dong-Kyu Jin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Korea
| | - Hiroshi Kitoh
- Department of Orthopaedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 135-710, Korea; Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
| | - Hua Ling
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kurt N Hetrick
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - David Valle
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard M Pauli
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| |
Collapse
|
11
|
Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am J Hum Genet 2012; 91:839-48. [PMID: 23103226 DOI: 10.1016/j.ajhg.2012.09.004] [Citation(s) in RCA: 302] [Impact Index Per Article: 25.2] [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: 05/06/2012] [Revised: 08/10/2012] [Accepted: 09/07/2012] [Indexed: 11/28/2022] Open
Abstract
DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies.
Collapse
Affiliation(s)
- Goo Jun
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Pankratz N, Dumitriu A, Hetrick KN, Sun M, Latourelle JC, Wilk JB, Halter C, Doheny KF, Gusella JF, Nichols WC, Myers RH, Foroud T, DeStefano AL. Copy number variation in familial Parkinson disease. PLoS One 2011; 6:e20988. [PMID: 21829596 PMCID: PMC3149037 DOI: 10.1371/journal.pone.0020988] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 05/17/2011] [Indexed: 01/28/2023] Open
Abstract
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
Collapse
Affiliation(s)
- Nathan Pankratz
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Abstract
Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish. Availability and Implementation: The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html. Contact:mritchie@wehi.edu.au; rafa@jhu.edu
Collapse
Affiliation(s)
- Matthew E Ritchie
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia.
| | | | | | | | | |
Collapse
|
14
|
Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU, Prokunina-Olsson L, Ding CJ, Swift AJ, Narisu N, Hu T, Pruim R, Xiao R, Li XY, Conneely KN, Riebow NL, Sprau AG, Tong M, White PP, Hetrick KN, Barnhart MW, Bark CW, Goldstein JL, Watkins L, Xiang F, Saramies J, Buchanan TA, Watanabe RM, Valle TT, Kinnunen L, Abecasis GR, Pugh EW, Doheny KF, Bergman RN, Tuomilehto J, Collins FS, Boehnke M. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 2007; 316:1341-5. [PMID: 17463248 PMCID: PMC3214617 DOI: 10.1126/science.1142382] [Citation(s) in RCA: 2018] [Impact Index Per Article: 118.7] [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] [Indexed: 12/11/2022]
Abstract
Identifying the genetic variants that increase the risk of type 2 diabetes (T2D) in humans has been a formidable challenge. Adopting a genome-wide association strategy, we genotyped 1161 Finnish T2D cases and 1174 Finnish normal glucose-tolerant (NGT) controls with >315,000 single-nucleotide polymorphisms (SNPs) and imputed genotypes for an additional >2 million autosomal SNPs. We carried out association analysis with these SNPs to identify genetic variants that predispose to T2D, compared our T2D association results with the results of two similar studies, and genotyped 80 SNPs in an additional 1215 Finnish T2D cases and 1258 Finnish NGT controls. We identify T2D-associated variants in an intergenic region of chromosome 11p12, contribute to the identification of T2D-associated variants near the genes IGF2BP2 and CDKAL1 and the region of CDKN2A and CDKN2B, and confirm that variants near TCF7L2, SLC30A8, HHEX, FTO, PPARG, and KCNJ11 are associated with T2D risk. This brings the number of T2D loci now confidently identified to at least 10.
Collapse
Affiliation(s)
- Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Cristen J. Willer
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yun Li
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - William L. Duren
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael R. Erdos
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chia-Jen Ding
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Tianle Hu
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randall Pruim
- Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI 49546, USA
| | - Rui Xiao
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiao-Yi Li
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen N. Conneely
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nancy L. Riebow
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Andrew G. Sprau
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Maurine Tong
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Peggy P. White
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kurt N. Hetrick
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Michael W. Barnhart
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Craig W. Bark
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Janet L. Goldstein
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Lee Watkins
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Fang Xiang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Thomas A. Buchanan
- Division of Endocrinology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Timo T. Valle
- Diabetes Unit, Department of Epidemiology and Health Promotion, National Public Health Institute, 00300 Helsinki, Finland
| | - Leena Kinnunen
- Diabetes Unit, Department of Epidemiology and Health Promotion, National Public Health Institute, 00300 Helsinki, Finland
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
| | - Gonçalo R. Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth W. Pugh
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Kimberly F. Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Richard N. Bergman
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jaakko Tuomilehto
- Diabetes Unit, Department of Epidemiology and Health Promotion, National Public Health Institute, 00300 Helsinki, Finland
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
- South Ostrobothnia Central Hospital, 60220 Seinäjoki, Finland
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|