Journal article

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data

Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stephane Bezieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister Show all

PLOS ONE | PUBLIC LIBRARY SCIENCE | Published : 2017

Grants

Awarded by National Institutes of Health


Awarded by National Cancer Institute


Awarded by Australasian Colorectal Cancer Family Registry


Awarded by Mayo Clinic Cooperative Family Registry for Colon Cancer Studies


Awarded by Ontario Familial Colorectal Cancer Registry


Awarded by Seattle Colorectal Cancer Family Registry


Awarded by University of Hawaii Colorectal Cancer Family Registry


Awarded by USC Consortium Colorectal Cancer Family Registry


Awarded by National Cancer Institute, National Institutes of Health


Awarded by German Research Council (Deutsche Forschungsgemeinschaft)


Awarded by German Federal Ministry of Education and Research


Awarded by National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services


Awarded by NHS by the National Institutes of Health


Awarded by PHS by the National Institutes of Health


Awarded by National Institutes of Health (NIH), Genes, Environment and Health Initiative (GEI)


Awarded by National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services


Funding Acknowledgements

ASTERISK: a Hospital Clinical Research Program (PHRC) and supported by the Regional Council of Pays de la Loire, the Groupement des Entreprises Francaises dans la Lutte contre le Cancer (GEFLUC), the Association Anne de Bretagne Genetique and the Ligue Regionale Contre le Cancer (LRCC). COLO2&3: National Institutes of Health (R01 CA60987). CCFR: This work was supported by grant UM1 CM 67551 from the National Cancer Institute and through cooperative agreements with the following CCFR centers: Australasian Colorectal Cancer Family Registry (U01 CA074778 and U01/U24 CA097735), Mayo Clinic Cooperative Family Registry for Colon Cancer Studies (U01/U24 CA074800), Ontario Familial Colorectal Cancer Registry (U01/U24 CA074783), Seattle Colorectal Cancer Family Registry (U01/U24 CA074794), University of Hawaii Colorectal Cancer Family Registry (U01/U24 CA074806), and USC Consortium Colorectal Cancer Family Registry U01/U24 CA074799). The Colon CFR GWAS was supported by funding from the National Cancer Institute, National Institutes of Health (U01 CM 22839 and R01 CA143237 to Graham Casey). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Colon Cancer Family Registry (CCFR), nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government or the CCFR. DACHS: 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: National Institutes of Health (R01 CA48998 to M.L. Slattery). GECCO: National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services (U01 CM 37088; R01 CA059045; R01 CM 20582; U01 CM 64930). HPFS is supported by the National Institutes of Health (P01 CA 055075, UM1 CM 67552, R01 137178, R01 CA151993 and P50 CA127003), NHS by the National Institutes of Health (UM1 CM 86107, R01 CM 37178, P01 CA87969, R01 CM 51993 and P50 CM 27003) and PHS by the National Institutes of Health (R01 CA042182). MEC: National Institutes of Health (R37 CA54281, P01 CA033619, and R01 CA63464). OFCCR: National Institutes of Health, through funding allocated to the Ontario Registry for Studies of Familial Colorectal Cancer (U01 CA074783); see CCFR section above. Additional funding toward genetic analyses of OFCCR includes the Ontario Research Fund, the Canadian Institutes of Health Research, and the Ontario Institute for Cancer Research, through generous support from the Ontario Ministry of Research and Innovation. PLCO: Intramural Research Program of the Division of Cancer Epidemiology and Genetics and supported by contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, 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), Colon 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.r 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 study was provided by National Institutes of Health (NIH), Genes, Environment and Health Initiative (GEI) 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. PMH: National Institutes of Health (R01 CA076366). VITAL: National Institutes of Health (K05 CA154337). WHI: The WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through contracts HHSN268201100046C, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C, and HHSN271201100004C.