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The OncoArray Consortium: a network for understanding the genetic architecture of common cancers

Citation

Amos, CI and Dennis, J and Wang, Z and Byun, J and Schumacher, FR and Gayther, SA and Casey, G and Hunter, DJ and Sellers, TA and Gruber, SB and Dunning, AM and Michailidou, K and Fachal, L and Doheny, K and Spurdle, AB and Li, Y and Xiao, X and Romm, J and Pugh, E and Coetzee, GA and Hazelett, DJ and Bojesen, SE and Caga-Anan, C and Haiman, CA and Kamal, A and Luccarini, C and Tessier, D and Vincent, D and Bacot, F and Van Den Berg, DJ and Nelson, S and Demetriades, S and Goldgar, DE and Couch, FJ and Forman, JL and Giles, GG and Conti, DV and Bickeboller, H and Risch, A and Waldenberger, M and Bruske-Hohlfeld, I and Hicks, BD and Ling, H and McGuffog, L and Lee, A and Kuchenbaecker, K and Soucy, P and Manz, J and Cunningham, JM and Butterbach, K and Kote-Jarai, Z and Kraft, P and Fitzgerald, L and Lindstrom, S and Adams, M and McKay, JD and Phelan, CM and Benlloch, S and Kelemen, LE and Brennan, P and Riggan, M and O'Mara, TA and Shen, H and Shi, Y and Thompson, DJ and Goodman, MT and Nielsen, SF and Berchuck, A and Laboissiere, S and Schmit, SL and Shelford, T and Edlund, CK and Taylor, JA and Field, JK and Park, SK and Offit, K and Thomassen, M and Schmutzler, R and Ottini, L and Hung, RJ and Marchini, J and Amin Al Olama, A and Peters, U and Eeles, RA and Seldin, MF and Gillanders, E and Seminara, D and Antoniou, AC and Pharoah, PDP and Chenevix-Trench, G and Chanock, SJ and Simard, J and Easton, DF, The OncoArray Consortium: a network for understanding the genetic architecture of common cancers, Cancer Epidemiology, Biomarkers and Prevention, 26, (1) pp. 126-135. ISSN 1055-9965 (2017) [Refereed Article]

Copyright Statement

Copyright 2016 2016 American Association for Cancer Research

DOI: doi:10.1158/1055-9965.EPI-16-0106

Abstract

BACKGROUND: Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers and cancer related traits.

METHODS: The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background.

RESULTS: The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis.

CONCLUSIONS: Results from these analyses will enable researchers to identify new susceptibility loci, perform fine mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental and lifestyle related exposures.

IMPACT: Ongoing analyses will shed light on etiology and risk assessment for many types of cancer.

Item Details

Item Type:Refereed Article
Keywords:OncoArray, genome-wide association study, cancer
Research Division:Medical and Health Sciences
Research Group:Oncology and Carcinogenesis
Research Field:Cancer Genetics
Objective Division:Health
Objective Group:Clinical Health (Organs, Diseases and Abnormal Conditions)
Objective Field:Cancer and Related Disorders
Author:Fitzgerald, L (Dr Liesel Fitzgerald)
ID Code:113109
Year Published:2017 (online first 2016)
Web of Science® Times Cited:6
Deposited By:Menzies Institute for Medical Research
Deposited On:2016-12-13
Last Modified:2017-04-10
Downloads:0

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