Journal article

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer

Stephanie A Bien, Yu-Ru Su, David V Conti, Tabitha A Harrison, Conghui Qu, Xingyi Guo, Yingchang Lu, Demetrius Albanes, Paul L Auer, Barbara L Banbury, Sonja I Berndt, Stephane Bezieau, Hermann Brenner, Daniel D Buchanan, Bette J Caan, Peter T Campbell, Christopher S Carlson, Andrew T Chan, Jenny Chang-Claude, Sai Chen Show all

HUMAN GENETICS | SPRINGER | Published : 2019

Grants

Awarded by National Institutes of Health


Awarded by United States Department of Health and Human Services


Awarded by University Hospital Center of Nantes


Awarded by United States Public Health Service from the National Cancer Institute, Department of Health and Human Services


Awarded by Colon CFR


Awarded by Surveillance, Epidemiology and End Results Program of the National Cancer Institute


Awarded by California Department of Public Health


Awarded by National Institutes of Environmental Health Sciences, National Institutes of Health


Awarded by World Cancer Research Fund International Regular Grant Programme


Awarded by Dutch Cancer Society


Awarded by German Research Council [Deutsche Forschungsgemeinschaft]


Awarded by German Federal Ministry of Education and Research


Awarded by Health Research Fund (FIS) (Spain)


Awarded by ISCIII RETIC (Spain)


Awarded by Cancer Research UK (United Kingdom)


Awarded by Medical Research Council (United Kingdom)


Awarded by FIS Intrasalud


Awarded by Australian NHMRC grants


Awarded by Florida Department of Health Bankhead-Coley Grant


Awarded by Tissue Core at the H. Lee Moffitt Cancer Center & Research Institute, a National Cancer Institute-designated Comprehensive Cancer Center


Awarded by ZonMW investment grant


Awarded by PREVIEW, the project PRE-Vention of diabetes through lifestyle intervention and population studies in Europe and around the World (PREVIEW) project from the European Union Seventh Framework Programme (FP7/2007-2013)


Awarded by National Institutes of Health, Genes, Environment and Health Initiative


Awarded by Cancer Research UK


Awarded by FEDER funds-a way to build Europe


Awarded by Catalan Government DURSI


Awarded by Junta de Castilla y Leon


Awarded by FEDER funds. a way to build Europe


Awarded by Swedish research council


Awarded by SAIC-Frederick, Inc. (SAIC-F)


Awarded by SAIC-F subcontract


Awarded by Brain Bank



Funding Acknowledgements

GECCO: This work was supported by the National Cancer Institute; National Institutes of Health; and the United States Department of Health and Human Services (U01 CA137088, R01 CA059045, U01 CA164930, R01 CA201407, R01 CA206279). Genotyping/Sequencing services were provided by the Center for Inherited Disease Research and is supported by a federal contract from the National Institutes of Health to The Johns Hopkins University (HHSN268201200008I). ASTERISK: a Hospital Clinical Research Program (PHRC-BRD09/C) from the University Hospital Center of Nantes and supported by the Regional Council of Pays de la Loire, the Groupement des Entreprises Francaises dans la Lutte contre le Cancer; the Association Anne de Bretagne Genetique; and the Ligue Regionale Contre le Cancer. ATBC: The ATBC Study is supported by the Intramural Research Program of the United States National Cancer Institute; National Institutes of Health; and by United States Public Health Service (HHSN261201500005C) from the National Cancer Institute, Department of Health and Human Services. COLO2&3: National Institutes of Health (R01 CA60987). CCFR: Illumina GWAS was supported by funding from the National Cancer Institute; and the National Institutes of Health (U01 CA122839, R01 CA143247). The Colon CFR/CORECT Affymetrix Axiom GWAS and OncoArray GWAS were supported by funding from the National Cancer Institute; and National Institutes of Health (U19 CA148107 to S.B.G.). The Colon CFR participant recruitment and collection of data and biospecimens used in this study were supported by the National Cancer Institute; and National Institutes of Health (UM1 CA167551) and through cooperative agreements between multiple Colon CFR centers: (U01 CA074778, U01/U24 CA097735 to Australasian Colorectal Cancer Family Registry, U01/U24 CA074799 to USC Consortium Colorectal Cancer Family Registry, U01/U24 CA074800 to Mayo Clinic Cooperative Family Registry for Colon Cancer Studies, U01/U24 CA074783 to Ontario Familial Colorectal Cancer Registry, U01/U24 CA074794 to Seattle Colorectal Cancer Family Registry, U01/U24 CA074806 to University of Hawaii Colorectal Cancer Family Registry). Additional support for case ascertainment was provided from the Surveillance, Epidemiology and End Results Program of the National Cancer Institute (N01-CN-67009, N01-PC-35142, HHSN2612013000121 to Fred Hutchinson Cancer Research Center), the Hawaii Department of Health (N01-PC-67001 and N01-PC-35137, HHSN26120100037C), and the California Department of Public Health (HHSN261201000035C to the University of Southern California), and the following state cancer registries: AZ, CO, MN, NC, NH, and by the Victoria Cancer Registry and Ontario Cancer Registry. CORECT: The CORECT Study was supported by the National Cancer Institute; National Institutes of Health; and the United States Department of Health and Human Services (U19 CA148107, R01 CA81488 to S.B.G., P30 CA014089, R01 CA197350 to S.B.G., P01 CA196569, R01 CA201407); and National Institutes of Environmental Health Sciences, National Institutes of Health (T32 ES013678). CPSII: The Cancer Prevention Study-II Nutrition Cohort is supported by the American Cancer Society. COLON: The COLON study is sponsored by Wereld Kanker Onderzoek Fonds, including funds from grant 2014/1179 as part of the World Cancer Research Fund International Regular Grant Programme, by Alpe d'Huzes and the Dutch Cancer Society (UM 2012-5653, UW 2013-5927, UW2015-7946), and by TRANSCAN (JTC2012-MetaboCCC, JTC2013-FOCUS).ColoCare: This work was supported by the National Institutes of Health (R01 CA189184, U01 CA206110, 2P30CA015704-40 to Gilliland]; the Matthias Lackas-Foundation; the German Consortium for Translational Cancer Research; and the EU TRANSCAN initiative. DACHS: This work is supported by the German Research Council [Deutsche Forschungsgemeinschaft, BR 1704/6-1, BR 1704/6-3, BR 1704/6-4 and CH 117/1-1); and the German Federal Ministry of Education and Research (01KH0404 and 01ER0814). DALS: This work is supported by the National Institutes of Health (R01 CA48998 to M. L. S.) EPIC: The coordination of EPIC is financially supported by the European Commission (DG-SANCO) and the International Agency for Research on Cancer. The national cohorts are supported by Danish Cancer Society (Denmark); Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Generale de l'Education Nationale, Institut National de la Sante et de la Recherche Medicale (INSERM) (France); German Cancer Aid, German Cancer Research Center (DKFZ), Federal Ministry of Education and Research (BMBF), Deutsche Krebshilfe, Deutsches Krebsforschungszentrum and Federal Ministry of Education and Research (Germany); the Hellenic Health Foundation (Greece); Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy and National Research Council (Italy); Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF), Statistics Netherlands (The Netherlands); ERC-2009-AdG 232997 and Nordforsk, Nordic Centre of Excellence programme on Food, Nutrition and Health (Norway); Health Research Fund (FIS), PI13/00061 to Granada, PI13/01162 to EPIC-Murcia, Regional Governments of Andalucia, Asturias, Basque Country, Murcia and Navarra, ISCIII RETIC (RD06/0020) (Spain); Swedish Cancer Society, Swedish Research Council and County Councils of Skane and Vasterbotten (Sweden); Cancer Research UK (14136 to EPIC-Norfolk; C570/A16491 and C8221/A19170 to EPIC-Oxford), Medical Research Council (1000143 to EPIC-Norfolk, MR/M012190/1 to EPIC-Oxford) (United Kingdom). ESTHER/VERDI: This work was supported by grants from the Baden-Wurttemberg Ministry of Science, Research and Arts, and the German Cancer Aid. HPFS: This work is supported by the National Institutes of Health (P01 CA055075, UM1 CA167552, R01 CA137178, R01 CA151993, R35 CA197735, K07 CA190673, P50 CA127003); NHS is supported by the National Institutes of Health (R01 CA137178, P01 CA087969, UM1 CA186107, R01 CA151993, R35 CA197735, K07 CA190673, and P50 CA127003); and PHS by the National Institutes of Health (R01 CA042182). MEC: This work is supported by the National Institutes of Health (R37 CA54281, P01 CA033619, R01 CA063464). MCCS: Cohort recruitment was supported by VicHealth and Cancer Council Victoria. GALEON: FIS Intrasalud (PI13/01136). The MCCS was further supported by Australian NHMRC grants (509348, 209057, 251553, 504711), and by infrastructure provided by the Cancer Council Victoria. Cases and their vital status were ascertained through the Victorian Cancer Registry and the Australian Institute of Health and Welfare, including the National Death Index and the Australian Cancer Database. MSKCC: The work at Sloan Kettering in New York was supported by the Robert and Kate Niehaus Center for Inherited Cancer Genomics and the Romeo Milio Foundation.Moffitt: This work was supported by the National Institutes of Health (R01 CA189184, P30 CA076292); Florida Department of Health Bankhead-Coley Grant (09BN-13); and the University of South Florida Oehler Foundation. Moffitt contributions were supported in part by the Total Cancer Care Initiative; Collaborative Data Services Core; and Tissue Core at the H. Lee Moffitt Cancer Center & Research Institute, a National Cancer Institute-designated Comprehensive Cancer Center (P30 CA076292). NQplus: The NQplus study is sponsored by a ZonMW investment grant (98-10030); by PREVIEW, the project PRE-Vention of diabetes through lifestyle intervention and population studies in Europe and around the World (PREVIEW) project which received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant no. 312057; by funds from TI Food and Nutrition (cardiovascular health theme), a public-private partnership on pre-competitive research in food and nutrition; and by FOODBALL, the Food Biomarker Alliance, a project from JPI Healthy Diet for a Healthy Life. OFCCR: As subset of ARCTIC, OFCCR is supported by a GL2 grant from the Ontario Research Fund; the Canadian Institutes of Health Research; and the Cancer Risk Evaluation Program grant from the Canadian Cancer Society Research Institute. This work is supported by the Ontario Institute for Cancer Research, through generous support from the Ontario Ministry of Research and Innovation (Senior Investigator Awards to T.J.H. and B.W.Z.) PLCO: This work is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and the Division of Cancer Prevention, National Cancer Institute DHHS. Additionally, a subset of control samples were genotyped as part of the Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer GWAS (Yeager, M et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007 May;39[5]:645-9), CGEMS pancreatic cancer scan [PanScan] (Amundadottir, L et al. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat Genet. 2009 Sep; 41[9]:986-90, and Petersen, GM et al. A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat Genet. 2010 Mar;42[3]:224-8), and the Lung Cancer and Smoking study (Landi MT, et al. A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009 Nov;85[5]:679-91). The prostate and PanScan study datasets were accessed with appropriate approval through the dbGaP online resource [http://cgems.cancer.gov/data/] accession numbers phs000207.v1.p1 and phs000206.v3.p2, respectively, and the lung datasets were accessed from the dbGaP website (http://www.ncbi.nlm.nih.gov/gap) through accession number phs000093.v2.p2. Funding for the Lung Cancer and Smoking studywas provided by National Institutes of Health, Genes, Environment and Health Initiative (Z01 CP 010200, NIH U01 HG004446, and NIH GEI U01 HG 004438). For the lung study, the GENEVA Coordinating Center provided assistance with genotype cleaning and general study coordination, and the Johns Hopkins University Center for Inherited Disease Research conducted genotyping. SEARCH: Cancer Research UK (C490/A16561).The Spanish study was supported by Instituto de Salud Carlos III, co-funded by FEDER funds-a way to build Europe(PI14-613, PI09-1286); Catalan Government DURSI (2014SGR647); and Junta de Castilla y Leon (LE22A10-2). Spain: Catalan Government DURSI (2014SGR647); and Instituto de Salud Carlos III, co-funded by FEDER funds. a way to build Europe (PI14-00613). The Swedish Low-risk Colorectal Cancer Study: The study was supported by the Swedish research council (K2015-55X-22674-01-4, K2008-55X-20157-03-3, K2006-72X-20157-01-2); and the Stockholm County Council (ALF project). VITAL: This work is supported by the National Institutes of Health (K05 CA154337). WHI: The WHI program is supported by the National Heart, Lung, and Blood Institute; National Institutes of Health; United States Department of Health and Human Services through contracts (HHSN268201100046C, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C, HHSN271201100004C) The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. Additional funds were provided by the National Cancer Institute, National Human Genome Research Institute, National Human Lung and Blood Institute, National Institute of Drug Abuse, National Institute of Mental Health, and National Institute of Neurological Disorders and Stroke. Donors were enrolled at Biospecimen Source Sites supported by the National Cancer Institute and SAIC-Frederick, Inc. (SAIC-F) subcontracts to the National Disease Research Interchange (10XS170), Roswell Park Cancer Institute (10XS171), and Science Care, Inc. (X10S172). The Laboratory, Data Analysis, and Coordinating Center was supported by a contract (HHSN268201000029C to The Broad Institute, Inc). Biorepository operations were funded through an SAIC-F subcontract to Van Andel Institute (10ST1035). Additional data repository and project management were provided by SAIC-F (HHSN261200800001E). The Brain Bank was supported by a supplement to University of Miami (DA006227, DA033684, N01MH000028). Statistical Methods development grants were made to the University of Geneva (MH090941 & MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina -Chapel Hill (MH090936, MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822). The data used for the analyses described in this manuscript were obtained from the GTEx Portal on 10/19/2016.