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Julián-Serrano S, Yuan F, Wheeler W, Benyamin B, Machiela MJ, Arslan AA, Beane-Freeman LE, Bracci PM, Duell EJ, Du M, Gallinger S, Giles GG, Goodman PJ, Kooperberg C, Marchand LL, Neale RE, Shu XO, Van Den Eeden SK, Visvanathan K, Zheng W, Albanes D, Andreotti G, Ardanaz E, Babic A, Berndt SI, Brais LK, Brennan P, Bueno-de-Mesquita B, Buring JE, Chanock SJ, Childs EJ, Chung CC, Fabiánová E, Foretová L, Fuchs CS, Gaziano JM, Gentiluomo M, Giovannucci EL, Goggins MG, Hackert T, Hartge P, Hassan MM, Holcátová I, Holly EA, Hung RI, Janout V, Kurtz RC, Lee IM, Malats N, McKean D, Milne RL, Newton CC, Oberg AL, Perdomo S, Peters U, Porta M, Rothman N, Schulze MB, Sesso HD, Silverman DT, Thompson IM, Wactawski-Wende J, Weiderpass E, Wenstzensen N, White E, Wilkens LR, Yu H, Zeleniuch-Jacquotte A, Zhong J, Kraft P, Li D, Campbell PT, Petersen GM, Wolpin BM, Risch HA, Amundadottir LT, Klein AP, Yu K, Stolzenberg-Solomon RZ. Hepcidin-regulating iron metabolism genes and pancreatic ductal adenocarcinoma: a pathway analysis of genome-wide association studies. Am J Clin Nutr 2021; 114:1408-1417. [PMID: 34258619 PMCID: PMC8488877 DOI: 10.1093/ajcn/nqab217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/14/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epidemiological studies have suggested positive associations for iron and red meat intake with risk of pancreatic ductal adenocarcinoma (PDAC). Inherited pathogenic variants in genes involved in the hepcidin-regulating iron metabolism pathway are known to cause iron overload and hemochromatosis. OBJECTIVES The objective of this study was to determine whether common genetic variation in the hepcidin-regulating iron metabolism pathway is associated with PDAC. METHODS We conducted a pathway analysis of the hepcidin-regulating genes using single nucleotide polymorphism (SNP) summary statistics generated from 4 genome-wide association studies in 2 large consortium studies using the summary data-based adaptive rank truncated product method. Our population consisted of 9253 PDAC cases and 12,525 controls of European descent. Our analysis included 11 hepcidin-regulating genes [bone morphogenetic protein 2 (BMP2), bone morphogenetic protein 6 (BMP6), ferritin heavy chain 1 (FTH1), ferritin light chain (FTL), hepcidin (HAMP), homeostatic iron regulator (HFE), hemojuvelin (HJV), nuclear factor erythroid 2-related factor 2 (NRF2), ferroportin 1 (SLC40A1), transferrin receptor 1 (TFR1), and transferrin receptor 2 (TFR2)] and their surrounding genomic regions (±20 kb) for a total of 412 SNPs. RESULTS The hepcidin-regulating gene pathway was significantly associated with PDAC (P = 0.002), with the HJV, TFR2, TFR1, BMP6, and HAMP genes contributing the most to the association. CONCLUSIONS Our results support that genetic susceptibility related to the hepcidin-regulating gene pathway is associated with PDAC risk and suggest a potential role of iron metabolism in pancreatic carcinogenesis. Further studies are needed to evaluate effect modification by intake of iron-rich foods on this association.
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Affiliation(s)
| | - Fangcheng Yuan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Beben Benyamin
- Australian Centre for Precision Health, Allied Health and Human Performance, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, USA
| | - Laura E Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric J Duell
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven Gallinger
- Lunenfeld–Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Loic Le Marchand
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt–Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt–Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eva Ardanaz
- Navarra Public Health Institute, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Ana Babic
- Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lauren K Brais
- Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Erica J Childs
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eleonora Fabiánová
- Specialized Institute of Hygiene and Epidemiology, Banska Bystrica, Slovakia
| | - Lenka Foretová
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Charles S Fuchs
- Yale Cancer Center and Smilow Cancer Hospital, New Haven, CT, USA
| | | | - Manuel Gentiluomo
- Department of Biology, University of Pisa, Italy
- Genomic Epidemiology Group, German Cancer Research Center, (DKFZ), Heidelberg, Germany
| | | | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Manal M Hassan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ivana Holcátová
- Institute of Public Health and Preventive Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Rayjean I Hung
- Lunenfeld–Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Vladimir Janout
- Faculty of Health Sciences, University of Olomouc, Olomouc, Czech Republic
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - I-Min Lee
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - David McKean
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Christina C Newton
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Sandra Perdomo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miquel Porta
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital–Medical Center, San Antonio, TX, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Elisabete Weiderpass
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicolas Wenstzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lynne R Wilkens
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Herbert Yu
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health and Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Jun Zhong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Dounghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter T Campbell
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alison P Klein
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Blackford AL, Childs EJ, Porter N, Petersen G, Rabe K, Gallinger S, Borgida A, Syngal S, Schwartz A, Cote M, Hruban R, Goggins M, Klein AP, Parmigiani G. Abstract 885: A risk prediction tool for individuals with a family history of breast, ovarian, or pancreatic cancer: BRCAPANCPRO. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-885] [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
Introduction: Identifying families with an underlying inherited cancer predisposition is a major goal of cancer prevention efforts. Mendelian risk models have been developed to better predict the risk associated with a pathogenic variant of developing breast/ovarian cancer (with BRCAPRO), and the risk of developing pancreatic cancer (PANCPRO). Given that pathogenic variants involving BRCA2 and BRCA1 predispose to all three of these cancers, we developed a joint risk model to capture shared susceptibility.
Methods: We expanded the existing framework for PANCPRO and BRCAPRO to model underlying risk of pancreatic, breast, and ovarian cancer. We then validated this model on three datasets each reflecting the target populations for these models, including patients referred to a high-risk genetics clinic, patients with multiple family members with pancreatic cancer who underwent genetic testing for BRCA1/2, as well as a prospective registry of pancreatic cancer families. The new model is designated BRCAPANCPRO.
Results: BRCAPANCPRO yielded good discrimination for differentiating BRCA1 and BRCA2 carriers from non-carriers (AUC = 0.84, 95% CI: 0.78, 0.87) and was reasonably well-calibrated for predicting future risk of pancreatic cancer (observed-to-expected (O/E) ratio = 0.82 [0.69, 0.94]). In these families, BRCAPANCPRO outperformed both the prior BRCAPRO and PANCPRO models.
Discussion: The BRCAPANCPRO model improves the identification of families with a pathogenic variant in BRCA2 or BRCA1, particularly for families where there is the co-occurrence of pancreatic cancer in addition to breast and/or ovarian cancer. The model also improves the prediction of pancreatic cancer among families with a pancreatic cancer family history, with or without breast and/or ovarian cancer.
Citation Format: Amanda L. Blackford, Erica J. Childs, Nancy Porter, Gloria Petersen, Kari Rabe, Steven Gallinger, Ayelet Borgida, Sapna Syngal, Ann Schwartz, Michele Cote, Ralph Hruban, Michael Goggins, Alison P. Klein, Giovanni Parmigiani. A risk prediction tool for individuals with a family history of breast, ovarian, or pancreatic cancer: BRCAPANCPRO [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 885.
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3
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Mocci E, Kundu P, Wheeler W, Arslan AA, Beane-Freeman LE, Bracci PM, Brennan P, Canzian F, Du M, Gallinger S, Giles GG, Goodman PJ, Kooperberg C, Le Marchand L, Neale RE, Shu XO, Visvanathan K, White E, Zheng W, Albanes D, Andreotti G, Babic A, Bamlet WR, Berndt SI, Blackford AL, Bueno-de-Mesquita B, Buring JE, Campa D, Chanock SJ, Childs EJ, Duell EJ, Fuchs CS, Gaziano JM, Giovannucci EL, Goggins MG, Hartge P, Hassan MM, Holly EA, Hoover RN, Hung RJ, Kurtz RC, Lee IM, Malats N, Milne RL, Ng K, Oberg AL, Panico S, Peters U, Porta M, Rabe KG, Riboli E, Rothman N, Scelo G, Sesso HD, Silverman DT, Stevens VL, Strobel O, Thompson IM, Tjonneland A, Trichopoulou A, Van Den Eeden SK, Wactawski-Wende J, Wentzensen N, Wilkens LR, Yu H, Yuan F, Zeleniuch-Jacquotte A, Amundadottir LT, Li D, Jacobs EJ, Petersen GM, Wolpin BM, Risch HA, Kraft P, Chatterjee N, Klein AP, Stolzenberg-Solomon R. Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3. Cancer Res 2021; 81:3134-3143. [PMID: 33574088 PMCID: PMC8178175 DOI: 10.1158/0008-5472.can-20-3267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/01/2020] [Revised: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 11/16/2022]
Abstract
Germline variation and smoking are independently associated with pancreatic ductal adenocarcinoma (PDAC). We conducted genome-wide smoking interaction analysis of PDAC using genotype data from four previous genome-wide association studies in individuals of European ancestry (7,937 cases and 11,774 controls). Examination of expression quantitative trait loci data from the Genotype-Tissue Expression Project followed by colocalization analysis was conducted to determine whether there was support for common SNP(s) underlying the observed associations. Statistical tests were two sided and P < 5 × 10-8 was considered statistically significant. Genome-wide significant evidence of qualitative interaction was identified on chr2q21.3 in intron 5 of the transmembrane protein 163 (TMEM163) and upstream of the cyclin T2 (CCNT2). The most significant SNP using the Empirical Bayes method, in this region that included 45 significantly associated SNPs, was rs1818613 [per allele OR in never smokers 0.87, 95% confidence interval (CI), 0.82-0.93; former smokers 1.00, 95% CI, 0.91-1.07; current smokers 1.25, 95% CI 1.12-1.40, P interaction = 3.08 × 10-9). Examination of the Genotype-Tissue Expression Project data demonstrated an expression quantitative trait locus in this region for TMEM163 and CCNT2 in several tissue types. Colocalization analysis supported a shared SNP, rs842357, in high linkage disequilibrium with rs1818613 (r 2 = 0. 94) driving both the observed interaction and the expression quantitative trait loci signals. Future studies are needed to confirm and understand the differential biologic mechanisms by smoking status that contribute to our PDAC findings. SIGNIFICANCE: This large genome-wide interaction study identifies a susceptibility locus on 2q21.3 that significantly modified PDAC risk by smoking status, providing insight into smoking-associated PDAC, with implications for prevention.
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Affiliation(s)
- Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Prosenjit Kundu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - William Wheeler
- Information Management Services, Inc., Silver Spring, Maryland
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, New York
- Department of Population Health, New York University School of Medicine, New York, New York
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
| | | | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Rachel E Neale
- Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kala Visvanathan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Emily White
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | | | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Amanda L Blackford
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, the Netherlands
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie E Buring
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Charles S Fuchs
- Yale Cancer Center, New Haven, Connecticut
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut
- Smilow Cancer Hospital, New Haven, Connecticut
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Boston Veteran Affairs Healthcare System, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Manal M Hassan
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Ontario, Canada
| | - Robert C Kurtz
- Gastroenterology, Hepatology, and Nutrition Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - I-Min Lee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Ulrike Peters
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | | | - Howard D Sesso
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Ian M Thompson
- CHRISTUS Santa Rosa Hospital - Medical Center, San Antonio, Texas
| | - Anne Tjonneland
- Department of Public Health, University of Copenhagen and Danish Cancer Society Research Center Diet, Genes and Environment, Copenhagen, Denmark
| | - Antonia Trichopoulou
- Hellenic Health Foundation, World Health Organization Collaborating Center of Nutrition, Medical School, University of Athens, Greece
| | | | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University of Buffalo, Buffalo, New York
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Fangcheng Yuan
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, New York
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
| | | | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eric J Jacobs
- Department of Public Health, University of Copenhagen and Danish Cancer Society Research Center Diet, Genes and Environment, Copenhagen, Denmark
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
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4
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Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt S, Borgida A, Bracci PM, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Canzian F, Childs EJ, Cotterchio M, Du M, Duell EJ, Fuchs C, Gallinger S, Gaziano JM, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Holly EA, Klein EA, Kogevinas M, Kurtz RJ, LeMarchand L, Malats N, Männistö S, Milne R, Neale RE, Ng K, Obazee O, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Rothman N, Scelo G, Sesso HD, Severi G, Sieri S, Silverman D, Sund M, Tjønneland A, Thornquist MD, Tobias GS, Trichopoulou A, Van Den Eeden SK, Visvanathan K, Wactawski-Wende J, Wentzensen N, White E, Yu H, Yuan C, Zeleniuch-Jacquotte A, Hoover R, Brown K, Kooperberg C, Risch HA, Jacobs EJ, Li D, Yu K, Shu XO, Chanock SJ, Wolpin BM, Stolzenberg-Solomon RZ, Chatterjee N, Klein AP, Smith JP, Kraft P, Shi J, Petersen GM, Zheng W, Amundadottir LT. A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. J Natl Cancer Inst 2020; 112:1003-1012. [PMID: 31917448 PMCID: PMC7566474 DOI: 10.1093/jnci/djz246] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. METHODS To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples). RESULTS We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction. CONCLUSIONS By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.
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Affiliation(s)
- Jun Zhong
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- US Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
- Division of Molecular Genetics and Pathology, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, USA
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, CA, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment, BA, Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michelle Cotterchio
- Cancer Care Ontario, University of Toronto, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute, Catalan Institute of Oncology, Barcelona, Spain
| | | | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Aging, Brigham and Women’s Hospital, Boston, MA, USA
- Boston VA Healthcare System, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Edward Giovannucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Manal Hasan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathy J Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Robert J Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic LeMarchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Roger Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, Lyon, France
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Debra Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Hellenic Health Foundation, Athens, Greece
| | - Mark D Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rachael Z Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jill P Smith
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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5
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Chen F, Childs EJ, Mocci E, Bracci P, Gallinger S, Li D, Neale RE, Olson SH, Scelo G, Bamlet WR, Blackford AL, Borges M, Brennan P, Chaffee KG, Duggal P, Hassan MJ, Holly EA, Hung RJ, Goggins MG, Kurtz RC, Oberg AL, Orlow I, Yu H, Petersen GM, Risch HA, Klein AP. Analysis of Heritability and Genetic Architecture of Pancreatic Cancer: A PanC4 Study. Cancer Epidemiol Biomarkers Prev 2019; 28:1238-1245. [PMID: 31015203 PMCID: PMC6606380 DOI: 10.1158/1055-9965.epi-18-1235] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 11/29/2018] [Revised: 02/02/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pancreatic cancer is the fourth-leading cause of cancer death in both men and women in the United States. The currently identified common susceptibility loci account for a small fraction of estimated heritability. We sought to estimate overall heritability of pancreatic cancer and partition the heritability by variant frequencies and functional annotations. METHODS Analysis using the genome-based restricted maximum likelihood method (GREML) was conducted on Pancreatic Cancer Case-Control Consortium (PanC4) genome-wide association study (GWAS) data from 3,568 pancreatic cancer cases and 3,363 controls of European Ancestry. RESULTS Applying linkage disequilibrium- and minor allele frequency-stratified GREML (GREML-LDMS) method to imputed GWAS data, we estimated the overall heritability of pancreatic cancer to be 21.2% (SE = 4.8%). Across the functional groups (intronic, intergenic, coding, and regulatory variants), intronic variants account for most of the estimated heritability (12.4%). Previously identified GWAS loci explained 4.1% of the total phenotypic variation of pancreatic cancer. Mutations in hereditary pancreatic cancer susceptibility genes are present in 4% to 10% of patients with pancreatic cancer, yet our GREML-LDMS results suggested these regions explain only 0.4% of total phenotypic variance for pancreatic cancer. CONCLUSIONS Although higher than previous studies, our estimated 21.2% overall heritability may still be downwardly biased due to the inherent limitation that the contribution of rare variants in genes with a substantive overall impact on disease are not captured when applying these commonly used methods to imputed GWAS data. IMPACT Our work demonstrated the importance of rare and common variants in pancreatic cancer risk.
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Affiliation(s)
- Fei Chen
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rachel E Neale
- Department of Population Health, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Amanda L Blackford
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Michael Borges
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Manal J Hassan
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Herbert Yu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
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6
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Walsh N, Zhang H, Hyland PL, Yang Q, Mocci E, Zhang M, Childs EJ, Collins I, Wang Z, Arslan AA, Beane-Freeman L, Bracci PM, Brennan P, Canzian F, Duell EJ, Gallinger S, Giles GG, Goggins M, Goodman GE, Goodman PJ, Hung RJ, Kooperberg C, Kurtz RC, Malats N, LeMarchand L, Neale RE, Olson SH, Scelo G, Shu XO, Van Den Eeden SK, Visvanathan K, White E, Zheng W, Albanes D, Andreotti G, Babic A, Bamlet WR, Berndt SI, Borgida A, Boutron-Ruault MC, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Chaffee KG, Chanock S, Cleary S, Cotterchio M, Foretova L, Fuchs C, M Gaziano JM, Giovannucci E, Goggins M, Hackert T, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Herman J, Holcatova I, Holly EA, Hoover R, Hung RJ, Janout V, Klein EA, Kurtz RC, Laheru D, Lee IM, Lu L, Malats N, Mannisto S, Milne RL, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Real FX, Rothman N, Sesso HD, Severi G, Silverman D, Strobel O, Sund M, Thornquist MD, Tobias GS, Wactawski-Wende J, Wareham N, Weiderpass E, Wentzensen N, Wheeler W, Yu H, Zeleniuch-Jacquotte A, Kraft P, Li D, Jacobs EJ, Petersen GM, Wolpin BM, Risch HA, Amundadottir LT, Yu K, Klein AP, Stolzenberg-Solomon RZ. Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer. J Natl Cancer Inst 2019; 111:557-567. [PMID: 30541042 PMCID: PMC6579744 DOI: 10.1093/jnci/djy155] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 01/29/2018] [Revised: 06/15/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) identify associations of individual single-nucleotide polymorphisms (SNPs) with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes. METHODS We conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9040 cases and 12 496 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes contributing to the top associated pathways and gene sets. All statistical tests were two-sided. RESULTS We identified 14 pathways and gene sets associated with PDAC at a false discovery rate of less than 0.05. After Bonferroni correction (P ≤ 1.3 × 10-5), the strongest associations were detected in five pathways and gene sets, including maturity-onset diabetes of the young, regulation of beta-cell development, role of epidermal growth factor (EGF) receptor transactivation by G protein-coupled receptors in cardiac hypertrophy pathways, and the Nikolsky breast cancer chr17q11-q21 amplicon and Pujana ATM Pearson correlation coefficient (PCC) network gene sets. We identified and validated rs876493 and three correlating SNPs (PGAP3) and rs3124737 (CASP7) from the Pujana ATM PCC gene set as eQTLs in two normal derived pancreas tissue datasets. CONCLUSION Our agnostic pathway and gene set analysis integrated with functional annotation and eQTL analysis provides insight into genes and pathways that may be biologically relevant for risk of PDAC, including those not previously identified.
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Affiliation(s)
- Naomi Walsh
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Division of Applied Regulatory Science, Office of Translational Science, Center for Drug Evaluation & Research, U.S. Food and Drug Administration, Silver Spring, MD
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Division of Epidemiology II, Office of Surveillance and Epidemiology, Center for Drug Evaluation & Research, U.S. Food and Drug Administration, Silver Spring, MD
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Zhaoming Wang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY
- Department of Environmental Medicine, New York University School of Medicine, New York, NY
- Department of Population Health, New York University School of Medicine, New York, NY
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Steven Gallinger
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Loic LeMarchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Xiao O Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ayelet Borgida
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Marie-Christine Boutron-Ruault
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sean Cleary
- Division of Hepatobiliary and Pancreas Surgery, Mayo Clinic, Rochester, MN
| | - Michelle Cotterchio
- Cancer Care Ontario, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | | | - J Michael M Gaziano
- Division of Aging, Brigham and Women's Hospital, Boston, MA
- Boston VA Healthcare System, Boston, MA
| | - Edward Giovannucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Manal Hasan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kathy J Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joseph Herman
- Department of Radiation Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Vladimir Janout
- Department of Epidemiology and Public Health, Faculty of Medicine, University of Ostrava, Czech Republic
- Faculty of Medicine, University of Olomouc, Olomouc, Czech Republic
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Laheru
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - I-Min Lee
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Satu Mannisto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco X Real
- CIBERONC, Madrid, Spain
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Debra Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Oliver Strobel
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Mark D Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Elisabete Weiderpass
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Genetic Epidemiology Group, Folkhälsan Research Center and Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Herbert Yu
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY
- Department of Biostatistics, Harvard School of Public Health, Boston, MA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
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Walsh N, Zhang H, Hyland PL, Yang Q, Mocci E, Zhang M, Childs EJ, Wang Z, Chanock S, Hartge P, Hoover R, Kraft P, Li D, Jacobs EJ, Petersen GM, Wolpin BM, Risch HA, Amundadottir LT, Yu K, Klein AP, Stolzenberg-Solomon RZ. Abstract 242: Large pathway and gene set analysis of GWAS data identifies novel associations for pancreatic cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-242] [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 Genome-wide association studies (GWAS) identify associations of individual SNPs with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants has been shown for many disorders to be a powerful tool in discovering novel networks of susceptibility genes. Design We have conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product (sARTP) method to identify novel gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDA) in 9,040 cases and 12,495 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes identified in PDA-associated gene sets and pathways. Results We identified 14 gene sets and pathways associated with PDA at FDR < 0.05. Five of the strongest signals (P-value ≤ 1.3x10-5 Bonferroni corrected) were in genes from KEGG maturity onset diabetes of the young, Reactome regulation of beta cell development, Biocarta role of epidermal growth factor (EGF) receptor transactivation by G-protein-coupled receptors in cardiac hypertrophy pathway, Nikolsky breast cancer chr17q11-q21 amplicon gene set, and Pujana ATM Pearson correlation coefficient (PCC) network gene set. We identified and validated rs876493 and three correlated SNPs (PGAP3) and rs3124737 (CASP7) as eQTLs in two normal derived pancreas tissue datasets. Conclusion Our agnostic gene set and pathway analysis integrated with functional annotation and eQTL analysis provides novel insight into genes and pathways that may be biologically relevant for risk of PDA.
Citation Format: Naomi Walsh, Han Zhang, Paula L. Hyland, Qi Yang, Evelina Mocci, Mingfeng Zhang, Erica J. Childs, Zhaoming Wang, Stephen Chanock, Patricia Hartge, Robert Hoover, Peter Kraft, Donghui Li, Eric J. Jacobs, Gloria M. Petersen, Brian M. Wolpin, Harvey A. Risch, Laufey T. Amundadottir, Kai Yu, Alison P. Klein, Rachael Z. Stolzenberg-Solomon. Large pathway and gene set analysis of GWAS data identifies novel associations for pancreatic cancer [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 242.
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Affiliation(s)
| | - Han Zhang
- 2National Cancer Institute, Bethesda, MD
| | | | - Qi Yang
- 2National Cancer Institute, Bethesda, MD
| | - Evelina Mocci
- 4Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | | | - Erica J. Childs
- 4Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | | | | | | | | | - Peter Kraft
- 5Harvard School of Public Health, Boston, MA
| | - Donghui Li
- 6University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Kai Yu
- 2National Cancer Institute, Bethesda, MD
| | - Alison P. Klein
- 4Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
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8
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Klein AP, Wolpin BM, Risch HA, Stolzenberg-Solomon RZ, Mocci E, Zhang M, Canzian F, Childs EJ, Hoskins JW, Jermusyk A, Zhong J, Chen F, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt SI, Blackford A, Borges M, Borgida A, Bracci PM, Brais L, Brennan P, Brenner H, Bueno-de-Mesquita B, Buring J, Campa D, Capurso G, Cavestro GM, Chaffee KG, Chung CC, Cleary S, Cotterchio M, Dijk F, Duell EJ, Foretova L, Fuchs C, Funel N, Gallinger S, M Gaziano JM, Gazouli M, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Hackert T, Haiman C, Hartge P, Hasan M, Hegyi P, Helzlsouer KJ, Herman J, Holcatova I, Holly EA, Hoover R, Hung RJ, Jacobs EJ, Jamroziak K, Janout V, Kaaks R, Khaw KT, Klein EA, Kogevinas M, Kooperberg C, Kulke MH, Kupcinskas J, Kurtz RJ, Laheru D, Landi S, Lawlor RT, Lee IM, LeMarchand L, Lu L, Malats N, Mambrini A, Mannisto S, Milne RL, Mohelníková-Duchoňová B, Neale RE, Neoptolemos JP, Oberg AL, Olson SH, Orlow I, Pasquali C, Patel AV, Peters U, Pezzilli R, Porta M, Real FX, Rothman N, Scelo G, Sesso HD, Severi G, Shu XO, Silverman D, Smith JP, Soucek P, Sund M, Talar-Wojnarowska R, Tavano F, Thornquist MD, Tobias GS, Van Den Eeden SK, Vashist Y, Visvanathan K, Vodicka P, Wactawski-Wende J, Wang Z, Wentzensen N, White E, Yu H, Yu K, Zeleniuch-Jacquotte A, Zheng W, Kraft P, Li D, Chanock S, Obazee O, Petersen GM, Amundadottir LT. Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. Nat Commun 2018; 9:556. [PMID: 29422604 PMCID: PMC5805680 DOI: 10.1038/s41467-018-02942-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [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: 06/13/2017] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10-14), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10-10), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10-8), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10-8). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.
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Affiliation(s)
- Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA.
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Rachael Z Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jun Zhong
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fei Chen
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, 10016, USA
- Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amanda Blackford
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Michael Borges
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, M5G 1×5, Canada
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), 69372, Lyon, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), 3720 BA, Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, 3584 CX, Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, SW7 2AZ, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Julie Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniele Campa
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, 'Sapienza' University of Rome, 00185, Rome, Italy
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sean Cleary
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, M5G 1×5, Canada
| | - Michelle Cotterchio
- Cancer Care Ontario, University of Toronto, Toronto, Ontario, M5G 2L7, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, M5T 3M7, Canada
| | - Frederike Dijk
- Department of Pathology, Academic Medical Center, University of Amsterdam, 1007 MB, Amsterdam, The Netherlands
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), Barcelona, 08908, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, 65653, Brno, Czech Republic
| | | | - Niccola Funel
- Department of Translational Research and The New Technologies in Medicine and Surgery, University of Pisa, 56126, Pisa, Italy
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, M5G 1×5, Canada
| | - J Michael M Gaziano
- Division of Aging, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Boston VA Healthcare System, Boston, MA, 02132, USA
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, 106 79, Athens, Greece
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Edward Giovannucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Manal Hasan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Peter Hegyi
- First Department of Medicine, University of Szeged, 6725, Szeged, Hungary
| | - Kathy J Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joseph Herman
- Department of Radiation Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, 150 06, Prague 5, Czech Republic
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, M5G 1×5, Canada
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30303, USA
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, 02-776, Warsaw, Poland
| | - Vladimir Janout
- Department of Epidemiology and Public Health, Faculty of Medicine, University of Ostrava, 701 03, Ostrava, Czech Republic
- Faculty of Medicine, University of Olomouc, 771 47, Olomouc, Czech Republic
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kay-Tee Khaw
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), 08003, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 08003, Barcelona, Spain
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Matthew H Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, 44307, Kaunas, Lithuania
| | - Robert J Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Daniel Laheru
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231, USA
| | - Stefano Landi
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Rita T Lawlor
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, 37134, Verona, Italy
| | - I-Min Lee
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Loic LeMarchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
- CIBERONC, 28029, Madrid, Spain
| | - Andrea Mambrini
- Oncology Department, ASL1 Massa Carrara, Carrara, 54033, Italy
| | - Satu Mannisto
- Department of Public Health Solutions, National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Beatrice Mohelníková-Duchoňová
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, 775 20, Olomouc, Czech Republic
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, 4029, Australia
| | - John P Neoptolemos
- Department of General Surgery, University of Heidelburg, Heidelberg, Germany
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, 35124, Padua, Italy
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30303, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Raffaele Pezzilli
- Pancreas Unit, Department of Digestive Diseases and Internal Medicine, Sant'Orsola-Malpighi Hospital, 40138, Bologna, Italy
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública (CIBERESP), 08003, Barcelona, Spain
- Hospital del Mar Institute of Medical Research (IMIM), Universitat Autònoma de Barcelona, 08003, Barcelona, Spain
| | - Francisco X Real
- CIBERONC, 28029, Madrid, Spain
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre-CNIO, 28029, Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08002, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), 69372, Lyon, France
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, 94800, Villejuif, France
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Debra Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jill P Smith
- Department of Medicine, Georgetown University, Washington, 20057, USA
| | - Pavel Soucek
- Laboratory for Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00, Pilsen, Czech Republic
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, 901 85, Umeå, Sweden
| | | | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", 71013, San Giovanni Rotondo, FG, Italy
| | - Mark D Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20, Prague 4, Czech Republic
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, 14214, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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9
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Zhang M, Wang Z, Obazee O, Jia J, Childs EJ, Hoskins J, Figlioli G, Mocci E, Collins I, Chung CC, Hautman C, Arslan AA, Beane-Freeman L, Bracci PM, Buring J, Duell EJ, Gallinger S, Giles GG, Goodman GE, Goodman PJ, Kamineni A, Kolonel LN, Kulke MH, Malats N, Olson SH, Sesso HD, Visvanathan K, White E, Zheng W, Abnet CC, Albanes D, Andreotti G, Brais L, Bueno-de-Mesquita HB, Basso D, Berndt SI, Boutron-Ruault MC, Bijlsma MF, Brenner H, Burdette L, Campa D, Caporaso NE, Capurso G, Cavestro GM, Cotterchio M, Costello E, Elena J, Boggi U, Gaziano JM, Gazouli M, Giovannucci EL, Goggins M, Gross M, Haiman CA, Hassan M, Helzlsouer KJ, Hu N, Hunter DJ, Iskierka-Jazdzewska E, Jenab M, Kaaks R, Key TJ, Khaw KT, Klein EA, Kogevinas M, Krogh V, Kupcinskas J, Kurtz RC, Landi MT, Landi S, Marchand LL, Mambrini A, Mannisto S, Milne RL, Neale RE, Oberg AL, Panico S, Patel AV, Peeters PHM, Peters U, Pezzilli R, Porta M, Purdue M, Quiros JR, Riboli E, Rothman N, Scarpa A, Scelo G, Shu XO, Silverman DT, Soucek P, Strobel O, Sund M, Małecka-Panas E, Taylor PR, Tavano F, Travis RC, Thornquist M, Tjønneland A, Tobias GS, Trichopoulos D, Vashist Y, Vodicka P, Wactawski-Wende J, Wentzensen N, Yu H, Yu K, Zeleniuch-Jacquotte A, Kooperberg C, Risch HA, Jacobs EJ, Li D, Fuchs C, Hoover R, Hartge P, Chanock SJ, Petersen GM, Stolzenberg-Solomon RS, Wolpin BM, Kraft P, Klein AP, Canzian F, Amundadottir LT. Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21. Oncotarget 2016; 7:66328-66343. [PMID: 27579533 PMCID: PMC5340084 DOI: 10.18632/oncotarget.11041] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 12/31/1969] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology.
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Affiliation(s)
- Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erica J. Childs
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jason Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gisella Figlioli
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelina Mocci
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles C. Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Christopher Hautman
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alan A. Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, New York, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, USA
- New York University Cancer Institute, New York, New York, USA
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Julie Buring
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric J. Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Gary E. Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Phyllis J. Goodman
- Southwest Oncology Group Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Aruna Kamineni
- Group Health Research Institute, Seattle, Washington, USA
| | - Laurence N. Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Matthew H. Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, CNIO-Spanish National Cancer Research Centre, Madrid, Spain
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Howard D. Sesso
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kala Visvanathan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - H. Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Daniela Basso
- Department of Laboratory Medicine, University Hospital of Padova, Padua, Italy
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marie-Christine Boutron-Ruault
- Inserm, Centre for Research in Epidemiology and Population Health (CESP), U1018, Nutrition, Hormones and Women's Health Team, F-94805, Villejuif, France
- University Paris Sud, UMRS 1018, F-94805, Villejuif, France
- IGR, F-94805, Villejuif, France
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, ‘Sapienza’ University of Rome, Rome, Italy
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Michelle Cotterchio
- Prevention and Cancer Control, Cancer Care Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Eithne Costello
- National Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Liverpool, United Kingdom
| | - Joanne Elena
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ugo Boggi
- Department of Surgery, Unit of Experimental Surgical Pathology, University Hospital of Pisa, Pisa, Italy
| | - J. Michael Gaziano
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Massachusetts Veteran's Epidemiology, Research, and Information Center, Geriatric Research Education and Clinical Center, Veterans Affairs Boston Healthcare System, Boston, Massachusetts, USA
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Edward L. Giovannucci
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Michael Goggins
- Department of Pathology, Sidney Kimmel Cancer Center and Johns Hopkins University, Baltimore, Maryland, USA
- Department of Medicine, Sidney Kimmel Cancer Center and Johns Hopkins University, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Cancer Center and Johns Hopkins University, Baltimore, Maryland, USA
| | - Myron Gross
- Laboratory of Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher A. Haiman
- Preventive Medicine, University of Southern California, Los Angeles, California, USA
| | - Manal Hassan
- Department of Gastrointestinal Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Kathy J. Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David J. Hunter
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Harvard School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mazda Jenab
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Timothy J. Key
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Kay-Tee Khaw
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Manolis Kogevinas
- Centre de Recerca en Epidemiologia Ambiental (CREAL), CIBER Epidemiología y Salud Pública (CIBERESP), Spain
- Hospital del Mar Institute of Medical Research (IMIM), Barcelona, Spain
- National School of Public Health, Athens, Greece
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Juozas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Maria T. Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Le Loic Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Andrea Mambrini
- Oncology Department, ASL1 Massa Carrara, Massa Carrara, Italy
| | - Satu Mannisto
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Helsinki, Finland
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Rachel E. Neale
- Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ann L. Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Salvatore Panico
- Dipartimento di Medicina Clinica E Chirurgia, Federico II Univeristy, Naples, Italy
| | - Alpa V. Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Petra H. M. Peeters
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Raffaele Pezzilli
- Pancreas Unit, Department of Digestive Diseases and Internal Medicine, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Miquel Porta
- Hospital del Mar Institute of Medical Research (IMIM), Barcelona, Spain
- School of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mark Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - J. Ramón Quiros
- Public Health and Participation Directorate, Asturias, Spain
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Aldo Scarpa
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Debra T. Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel Soucek
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Oliver Strobel
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Malin Sund
- Department of Surgical and Peroperative Sciences, Umeå University, Umeå, Sweden
| | - Ewa Małecka-Panas
- Department of Digestive Tract Diseases, Medical University of Łodz, Łodz, Poland
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Ruth C. Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Mark Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anne Tjønneland
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Geoffrey S. Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
- Hellenic Health Foundation, Athens, Greece
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Hamburg-Eppendorf, Hamburg, Germany
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jean Wactawski-Wende
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, New York, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, USA
- New York University Cancer Institute, New York, New York, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Eric J. Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Charles Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gloria M. Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Rachael S. Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Alison P. Klein
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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Childs EJ, Chaffee KG, Gallinger S, Syngal S, Schwartz AG, Cote ML, Bondy ML, Hruban RH, Chanock SJ, Hoover RN, Fuchs CS, Rider DN, Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM, Risch HA, Goggins MG, Petersen GM, Klein AP. Association of Common Susceptibility Variants of Pancreatic Cancer in Higher-Risk Patients: A PACGENE Study. Cancer Epidemiol Biomarkers Prev 2016. [PMID: 27197284 DOI: 10.1158/1055- 9965.epi-15-1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Individuals from pancreatic cancer families are at increased risk, not only of pancreatic cancer, but also of melanoma, breast, ovarian, and colon cancers. While some of the increased risk may be due to mutations in high-penetrance genes (i.e., BRCA2, PALB2, ATM, p16/CDKN2A or DNA mismatch repair genes), common genetic variants may also be involved. In a high-risk population of cases with either a family history of pancreatic cancer or early-onset pancreatic cancer (diagnosis before the age of 50 years), we examined the role of genetic variants previously associated with risk of pancreatic, breast, ovarian, or prostate cancer. We genotyped 985 cases (79 early-onset cases, 906 cases with a family history of pancreatic cancer) and 877 controls for 215,389 SNPs using the iSelect Collaborative Oncological Gene-Environment Study (iCOGS) array with custom content. Logistic regression was performed using a log-linear additive model. We replicated several previously reported pancreatic cancer susceptibility loci, including recently identified variants on 2p13.3 and 7p13 (2p13.3, rs1486134: OR = 1.36; 95% CI, 1.13-1.63; P = 9.29 × 10(-4); 7p13, rs17688601: OR = 0.76; 95% CI, 0.63-0.93; P = 6.59 × 10(-3)). For the replicated loci, the magnitude of association observed in these high-risk patients was similar to that observed in studies of unselected patients. In addition to the established pancreatic cancer loci, we also found suggestive evidence of association (P < 5 × 10(-5)) to pancreatic cancer for SNPs at HDAC9 (7p21.1) and COL6A2 (21q22.3). Even in high-risk populations, common variants influence pancreatic cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 25(7); 1185-91. ©2016 AACR.
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Affiliation(s)
- Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sapna Syngal
- Population Sciences Division, Dana-Farber Cancer Institute, and Gastroenterology Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ann G Schwartz
- Department of Oncology, Karmanos Cancer Institute and Wayne State University, Detroit, Michigan
| | - Michele L Cote
- Department of Oncology, Karmanos Cancer Institute and Wayne State University, Detroit, Michigan
| | - Melissa L Bondy
- Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Ralph H Hruban
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland. Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David N Rider
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland. Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland.
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11
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Childs EJ, Chaffee KG, Gallinger S, Syngal S, Schwartz AG, Cote ML, Bondy ML, Hruban RH, Chanock SJ, Hoover RN, Fuchs CS, Rider DN, Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM, Risch HA, Goggins MG, Petersen GM, Klein AP. Association of Common Susceptibility Variants of Pancreatic Cancer in Higher-Risk Patients: A PACGENE Study. Cancer Epidemiol Biomarkers Prev 2016; 25:1185-91. [PMID: 27197284 DOI: 10.1158/1055-9965.epi-15-1217] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/14/2016] [Indexed: 12/15/2022] Open
Abstract
Individuals from pancreatic cancer families are at increased risk, not only of pancreatic cancer, but also of melanoma, breast, ovarian, and colon cancers. While some of the increased risk may be due to mutations in high-penetrance genes (i.e., BRCA2, PALB2, ATM, p16/CDKN2A or DNA mismatch repair genes), common genetic variants may also be involved. In a high-risk population of cases with either a family history of pancreatic cancer or early-onset pancreatic cancer (diagnosis before the age of 50 years), we examined the role of genetic variants previously associated with risk of pancreatic, breast, ovarian, or prostate cancer. We genotyped 985 cases (79 early-onset cases, 906 cases with a family history of pancreatic cancer) and 877 controls for 215,389 SNPs using the iSelect Collaborative Oncological Gene-Environment Study (iCOGS) array with custom content. Logistic regression was performed using a log-linear additive model. We replicated several previously reported pancreatic cancer susceptibility loci, including recently identified variants on 2p13.3 and 7p13 (2p13.3, rs1486134: OR = 1.36; 95% CI, 1.13-1.63; P = 9.29 × 10(-4); 7p13, rs17688601: OR = 0.76; 95% CI, 0.63-0.93; P = 6.59 × 10(-3)). For the replicated loci, the magnitude of association observed in these high-risk patients was similar to that observed in studies of unselected patients. In addition to the established pancreatic cancer loci, we also found suggestive evidence of association (P < 5 × 10(-5)) to pancreatic cancer for SNPs at HDAC9 (7p21.1) and COL6A2 (21q22.3). Even in high-risk populations, common variants influence pancreatic cancer susceptibility. Cancer Epidemiol Biomarkers Prev; 25(7); 1185-91. ©2016 AACR.
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Affiliation(s)
- Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sapna Syngal
- Population Sciences Division, Dana-Farber Cancer Institute, and Gastroenterology Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ann G Schwartz
- Department of Oncology, Karmanos Cancer Institute and Wayne State University, Detroit, Michigan
| | - Michele L Cote
- Department of Oncology, Karmanos Cancer Institute and Wayne State University, Detroit, Michigan
| | - Melissa L Bondy
- Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Ralph H Hruban
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland. Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David N Rider
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Michael G Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland. Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland.
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12
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Roberts NJ, Norris AL, Petersen GM, Bondy ML, Brand R, Gallinger S, Kurtz RC, Olson SH, Rustgi AK, Schwartz AG, Stoffel E, Syngal S, Zogopoulos G, Ali SZ, Axilbund J, Chaffee KG, Chen YC, Cote ML, Childs EJ, Douville C, Goes FS, Herman JM, Iacobuzio-Donahue C, Kramer M, Makohon-Moore A, McCombie RW, McMahon KW, Niknafs N, Parla J, Pirooznia M, Potash JB, Rhim AD, Smith AL, Wang Y, Wolfgang CL, Wood LD, Zandi PP, Goggins M, Karchin R, Eshleman JR, Papadopoulos N, Kinzler KW, Vogelstein B, Hruban RH, Klein AP. Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer. Cancer Discov 2015; 6:166-75. [PMID: 26658419 DOI: 10.1158/2159-8290.cd-15-0402] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/02/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED Pancreatic cancer is projected to become the second leading cause of cancer-related death in the United States by 2020. A familial aggregation of pancreatic cancer has been established, but the cause of this aggregation in most families is unknown. To determine the genetic basis of susceptibility in these families, we sequenced the germline genomes of 638 patients with familial pancreatic cancer and the tumor exomes of 39 familial pancreatic adenocarcinomas. Our analyses support the role of previously identified familial pancreatic cancer susceptibility genes such as BRCA2, CDKN2A, and ATM, and identify novel candidate genes harboring rare, deleterious germline variants for further characterization. We also show how somatic point mutations that occur during hematopoiesis can affect the interpretation of genome-wide studies of hereditary traits. Our observations have important implications for the etiology of pancreatic cancer and for the identification of susceptibility genes in other common cancer types. SIGNIFICANCE The genetic basis of disease susceptibility in the majority of patients with familial pancreatic cancer is unknown. We whole genome sequenced 638 patients with familial pancreatic cancer and demonstrate that the genetic underpinning of inherited pancreatic cancer is highly heterogeneous. This has significant implications for the management of patients with familial pancreatic cancer.
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Affiliation(s)
- Nicholas J Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
| | - Alexis L Norris
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Melissa L Bondy
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Randall Brand
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Pancreatic Cancer Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Elena Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Sapna Syngal
- Population Sciences Division, Dana-Farber Cancer Institute, and Gastroenterology Division, Brigham and Women's Hospital, Boston, Massachusetts
| | - George Zogopoulos
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada. Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Syed Z Ali
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jennifer Axilbund
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Yun-Ching Chen
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Michele L Cote
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Erica J Childs
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Christopher Douville
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Joseph M Herman
- Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | | | - Melissa Kramer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Alvin Makohon-Moore
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Richard W McCombie
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - K Wyatt McMahon
- Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Noushin Niknafs
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Jennifer Parla
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. inGenious Targeting Laboratory, Ronkonkoma, New York
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - James B Potash
- Department of Psychiatry, University of Iowa, Iowa City, Iowa
| | - Andrew D Rhim
- Division of Gastroenterology, Departments of Medicine and Genetics, Pancreatic Cancer Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. Department of Medicine, University of Michigan, Ann Arbor, Michigan
| | - Alyssa L Smith
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada. Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Yuxuan Wang
- Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Christopher L Wolfgang
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Medicine, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Kenneth W Kinzler
- Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
| | - Bert Vogelstein
- Ludwig Center and the Howard Hughes Medical Institute, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
| | - Alison P Klein
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland. Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
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13
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Childs EJ, Mocci E, Campa D, Bracci PM, Gallinger S, Goggins M, Li D, Neale RE, Olson SH, Scelo G, Amundadottir LT, Bamlet WR, Bijlsma MF, Blackford A, Borges M, Brennan P, Brenner H, Bueno-de-Mesquita HB, Canzian F, Capurso G, Cavestro GM, Chaffee KG, Chanock SJ, Cleary SP, Cotterchio M, Foretova L, Fuchs C, Funel N, Gazouli M, Hassan M, Herman JM, Holcatova I, Holly EA, Hoover RN, Hung RJ, Janout V, Key TJ, Kupcinskas J, Kurtz RC, Landi S, Lu L, Malecka-Panas E, Mambrini A, Mohelnikova-Duchonova B, Neoptolemos JP, Oberg AL, Orlow I, Pasquali C, Pezzilli R, Rizzato C, Saldia A, Scarpa A, Stolzenberg-Solomon RZ, Strobel O, Tavano F, Vashist YK, Vodicka P, Wolpin BM, Yu H, Petersen GM, Risch HA, Klein AP. Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer. Nat Genet 2015; 47:911-6. [PMID: 26098869 PMCID: PMC4520746 DOI: 10.1038/ng.3341] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [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: 11/20/2014] [Accepted: 05/27/2015] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is the fourth leading cause of cancer death in the developed world. Both inherited high-penetrance mutations in BRCA2 (ref. 2), ATM, PALB2 (ref. 4), BRCA1 (ref. 5), STK11 (ref. 6), CDKN2A and mismatch-repair genes and low-penetrance loci are associated with increased risk. To identify new risk loci, we performed a genome-wide association study on 9,925 pancreatic cancer cases and 11,569 controls, including 4,164 newly genotyped cases and 3,792 controls in 9 studies from North America, Central Europe and Australia. We identified three newly associated regions: 17q25.1 (LINC00673, rs11655237, odds ratio (OR) = 1.26, 95% confidence interval (CI) = 1.19-1.34, P = 1.42 × 10(-14)), 7p13 (SUGCT, rs17688601, OR = 0.88, 95% CI = 0.84-0.92, P = 1.41 × 10(-8)) and 3q29 (TP63, rs9854771, OR = 0.89, 95% CI = 0.85-0.93, P = 2.35 × 10(-8)). We detected significant association at 2p13.3 (ETAA1, rs1486134, OR = 1.14, 95% CI = 1.09-1.19, P = 3.36 × 10(-9)), a region with previous suggestive evidence in Han Chinese. We replicated previously reported associations at 9q34.2 (ABO), 13q22.1 (KLF5), 5p15.33 (TERT and CLPTM1), 13q12.2 (PDX1), 1q32.1 (NR5A2), 7q32.3 (LINC-PINT), 16q23.1 (BCAR1) and 22q12.1 (ZNRF3). Our study identifies new loci associated with pancreatic cancer risk.
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Affiliation(s)
- Erica J Childs
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Daniele Campa
- 1] Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Department of Biology, University of Pisa, Pisa, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rachel E Neale
- Department of Population Health, QIMR Berghofer Medical Research Institute, Kelvin Grove,Queensland, Australia
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Amanda Blackford
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Michael Borges
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - H Bas Bueno-de-Mesquita
- 1] Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands. [2] Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, the Netherlands. [3] Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK. [4] Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, 'Sapienza' University of Rome, Rome, Italy
| | - Giulia M Cavestro
- Università Vita Salute San Raffaele and Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, Italy
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Sean P Cleary
- 1] Department of Surgery, University Health Network, University of Toronto, Toronto, Ontario, Canada. [2] Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Michelle Cotterchio
- 1] Cancer Care Ontario, University of Toronto, Toronto, Ontario, Canada. [2] Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and Medical Faculty Masaryk University, Brno, Czech Republic
| | - Charles Fuchs
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Niccola Funel
- Department of Surgery, Unit of Experimental Surgical Pathology, University Hospital of Pisa, Pisa, Italy
| | - Maria Gazouli
- Department of Medical Sciences, Laboratory of Biology, School of Medicine, University of Athens, Athens, Greece
| | - Manal Hassan
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joseph M Herman
- Department of Radiation Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ivana Holcatova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
| | - Timothy J Key
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Juozas Kupcinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stefano Landi
- Department of Biology, Section of Genetics, University of Pisa, Pisa, Italy
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Ewa Malecka-Panas
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Andrea Mambrini
- Department of Oncology, Azienda USL 1 Massa Carrara, Massa Carrara, Italy
| | | | - John P Neoptolemos
- National Institute for Health Research (NIHR) Pancreas Biomedical Research Unit, Liverpool Clinical Trials Unit and Cancer Research UK Clinical Trials Unit, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Claudio Pasquali
- Department of Surgery, Gastroenterology and Oncology, University of Padua, Padua, Italy
| | - Raffaele Pezzilli
- Pancreas Unit, Department of Digestive Diseases, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Cosmeri Rizzato
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amethyst Saldia
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aldo Scarpa
- ARC-NET-Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Rachael Z Stolzenberg-Solomon
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, Rockville, Maryland, USA
| | - Oliver Strobel
- Department of General Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo, Italy
| | - Yogesh K Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Sciences, Prague, Czech Republic
| | - Brian M Wolpin
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Herbert Yu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Alison P Klein
- 1] Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA. [2] Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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14
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Bailey-Wilson JE, Childs EJ, Cropp CD, Schaid DJ, Xu J, Camp NJ, Cannon-Albright LA, Farnham JM, George A, Powell I, Carpten JD, Giles GG, Hopper JL, Severi G, English DR, Foulkes WD, Mæhle L, Møller P, Eeles R, Easton D, Guy M, Edwards S, Badzioch MD, Whittemore AS, Oakley-Girvan I, Hsieh CL, Dimitrov L, Stanford JL, Karyadi DM, Deutsch K, McIntosh L, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Thibodeau SN, McDonnell SK, Hebbring S, Lange EM, Cooney KA, Tammela TLJ, Schleutker J, Maier C, Bochum S, Hoegel J, Grönberg H, Wiklund F, Emanuelsson M, Cancel-Tassin G, Valeri A, Cussenot O, Isaacs WB. Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families. BMC Med Genet 2012; 13:46. [PMID: 22712434 PMCID: PMC3495053 DOI: 10.1186/1471-2350-13-46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 04/30/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. METHODS Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. RESULTS Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. CONCLUSIONS Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.
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Affiliation(s)
- Joan E Bailey-Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- University of Tampere ICPCG Group, Tampere, Finland
| | - Erica J Childs
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cheryl D Cropp
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jianfeng Xu
- Data Coordinating Center for the ICPCG and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Nicola J Camp
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Lisa A Cannon-Albright
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - James M Farnham
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Asha George
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Isaac Powell
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - John D Carpten
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Translational Genomics Research Institute, Genetic Basis of Human Disease Research Division, Phoenix, AZ, USA
| | - Graham G Giles
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - John L Hopper
- ACTANE consortium
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - Gianluca Severi
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - Dallas R English
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - William D Foulkes
- ACTANE consortium
- Program in Cancer Genetics, McGill University, Montreal, QC, Canada
| | - Lovise Mæhle
- ACTANE consortium
- Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo,Norway
| | - Pål Møller
- ACTANE consortium
- Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo,Norway
| | - Rosalind Eeles
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Douglas Easton
- ACTANE consortium
- Cancer Research UK Genetic Epidemiology Unit, Cambridge, UK
| | - Michelle Guy
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Steve Edwards
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Michael D Badzioch
- ACTANE consortium
- Division of Medical Genetics, University of Washington Medical Center, Seattle, WA, USA
| | - Alice S Whittemore
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Ingrid Oakley-Girvan
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
- Cancer Prevention Institute of California
| | - Chih-Lin Hsieh
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Urology and Department of Biochemistry and Molecular Biology, University of Southern California, Los Ageles, CA, USA
| | - Latchezar Dimitrov
- Data Coordinating Center for the ICPCG and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Janet L Stanford
- FHCRC ICPCG Group, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Danielle M Karyadi
- FHCRC ICPCG Group, Seattle, WA, USA
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Deutsch
- FHCRC ICPCG Group, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Laura McIntosh
- FHCRC ICPCG Group, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Elaine A Ostrander
- FHCRC ICPCG Group, Seattle, WA, USA
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen E Wiley
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Sarah D Isaacs
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Patrick C Walsh
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | | | - Ethan M Lange
- University of Michigan ICPCG Group, Ann Arbor, MI, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kathleen A Cooney
- University of Michigan ICPCG Group, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Teuvo LJ Tammela
- University of Tampere ICPCG Group, Tampere, Finland
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- Centre for Laboratory Medicine and Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Johanna Schleutker
- University of Tampere ICPCG Group, Tampere, Finland
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- Centre for Laboratory Medicine and Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Christiane Maier
- University of Ulm ICPCG Group, Ulm, Germany
- Dept of Urology, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Sylvia Bochum
- University of Ulm ICPCG Group, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Josef Hoegel
- University of Ulm ICPCG Group, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Olivier Cussenot
- CeRePP ICPCG Group, 75020, Paris, France
- Hopital Tenon, Assistance Publique-Hopitaux de Paris, 75020, Paris, France
| | - William B Isaacs
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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15
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Childs EJ, Sobel EM, Palmer CGS, Sinsheimer JS. Detection of intergenerational genetic effects with application to HLA-B matching as a risk factor for schizophrenia. Hum Hered 2011; 72:161-72. [PMID: 22004985 DOI: 10.1159/000332051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/23/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND METHODS Association studies using unrelated individuals cannot detect intergenerational genetic effects contributing to disease. To detect these effects, we improve the extended maternal-fetal genotype (EMFG) incompatibility test to estimate any combination of maternal effects, offspring effects, and their interactions at polymorphic loci or multiple SNPs, using any size pedigrees. We explore the advantages of using extended pedigrees rather than nuclear families. We apply our methods to schizophrenia pedigrees to investigate whether the previously associated mother-daughter HLA-B matching is a genuine risk or the result of bias. RESULTS Simulations demonstrate that using the EMFG test with extended pedigrees increases power and precision, while partitioning extended pedigrees into nuclear families can underestimate intergenerational effects. Application to actual data demonstrates that mother-daughter HLA-B matching remains a schizophrenia risk factor. Furthermore, ascertainment and mate selection biases cannot by themselves explain the observed HLA-B matching and schizophrenia association. CONCLUSIONS Our results demonstrate the power of the EMFG test to examine intergenerational genetic effects, highlight the importance of pedigree rather than case/control or case-mother/control-mother designs, illustrate that pedigrees provide a means to examine alternative, non-causal mechanisms, and they strongly support the hypothesis that HLA-B matching is causally involved in the etiology of schizophrenia in females.
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Affiliation(s)
- Erica J Childs
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
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Abstract
Maternal-fetal genotype (MFG) incompatibility is an interaction between the genes of a mother and offspring at a particular locus that adversely affects the developing fetus, thereby increasing susceptibility to disease. Statistical methods for examining MFG incompatibility as a disease risk factor have been developed for nuclear families. Because families collected as part of a study can be large and complex, containing multiple generations and marriage loops, we create the Extended-MFG (EMFG) Test, a model-based likelihood approach, to allow for arbitrary family structures. We modify the MFG test by replacing the nuclear-family based "mating type" approach with Ott's representation of a pedigree likelihood and calculating MFG incompatibility along with the Mendelian transmission probability. In order to allow for extension to arbitrary family structures, we make a slightly more stringent assumption of random mating with respect to the locus of interest. Simulations show that the EMFG test has appropriate type-I error rate, power, and precise parameter estimation when random mating holds. Our simulations and real data example illustrate that the chief advantages of the EMFG test over the earlier nuclear family version of the MFG test are improved accuracy of parameter estimation and power gains in the presence of missing genotypes.
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Affiliation(s)
- Erica J Childs
- Department of Biostatistics, University of California, Los Angeles, California, USA
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17
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Barczak CA, Barnett RI, Childs EJ, Bosley LM. Fourth national pressure ulcer prevalence survey. Adv Wound Care 1997; 10:18-26. [PMID: 9306782] [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: 02/05/2023]
Abstract
The fourth national pressure ulcer prevalence survey was conducted on November 9, 1995, with stuff at 265 acute-care hospitals surveying 39,874 patients for the presence of pressure ulcers. Data were collected on patient demographics, ulcer site, ulcer stage, and support surface. The goal was to determine the aggregate prevalence of pressure ulcers and to compare the results to those of the previous three surveys. The overall prevalence was 10.1% (range 1.4% to 36.4%), with the sacrum and heels the most common pressure ulcer sites. The predominant age group of patients with pressure ulcers was 71 to 80 years. Seventy-four percent of pressure ulcers were superficial (i.e., Stages I and II). The national pressure ulcer prevalence has remained relatively constant throughout the four surveys, despite the many changes in health care over the past 7 years.
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18
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Alvarez OM, Childs EJ. Pressure ulcers. Physical, supportive, and local aspects of management. Clin Podiatr Med Surg 1991; 8:869-90. [PMID: 1933737] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Pressure ulcers are a common and serious problem predominately among elderly persons who are confined to bed or chair. Additional factors associated with pressure ulcer development include cerebrovascular accident, impaired nutritional intake, urinary or fecal incontinence, hypoalbuminemia, and previous fracture. Implementation of preventive measures, such as an in-depth assessment for mobility, a pressure-relieving device combined with adequate repositioning, and thorough evaluation for nutritional status and urinary incontinence, significantly reduce pressure ulcer incidence. If the pressure ulcer is a partial thickness (stage II) wound, the causative factors are probably friction or moisture. If the ulcer is full thickness (stage III and IV), it is secondary to pressure or shearing forces. The development of wound infection is the most common complication in the management approach. Osteomyelitis is not an uncommon occurrence and must be initially ruled out in all full thickness pressure ulcers. Surgical debridement of necrotic tissue is necessary prior to further treatment and assessments. Antibiotic therapy is indicated only upon evidence of infection (cellulitis, osteomyelitis, leukocytosis, bandemia, or fever). Topical pharmacologic agents may be used to prevent or treat infection but must be carefully controlled to avoid such adverse effects as toxicity to the wound, allergic reaction, and development of resistant pathogens. Proper use of occlusive dressings increase patient comfort, enhance healing, decrease the possibility of infection, save time, and reduce costs. A patient presenting an ulcer that fails to improve or, because of its size, will take a great deal of time to heal should be evaluated for surgical closure.
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Affiliation(s)
- O M Alvarez
- University Wound Healing Clinic, New Brunswick, New Jersey
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