The oncoarray consortium: A network for understanding the genetic architecture of common cancers

Christopher I. Amos, Joe Dennis, Zhaoming Wang, Jinyoung Byun, Fredrick R. Schumacher, Simon A. Gayther, Graham Casey, David J. Hunter, Thomas A. Sellers, Stephen B. Gruber, Alison M. Dunning, Kyriaki Michailidou, Laura Fachal, Kimberly Doheny, Amanda B. Spurdle, Yafang Li, Xiangjun Xiao, Jane Romm, Elizabeth Pugh, Gerhard A. CoetzeeDennis J. Hazelett, Stig E. Bojesen, Charlisse Caga-Anan, Christopher A. Haiman, Ahsan Kamal, Craig Luccarini, Daniel Tessier, Daniel Vincent, Francois Bacot, David J. Van Den Berg, Stefanie Nelson, Stephen Demetriades, David E. Goldgar, Fergus J. Couch, Judith L. Forman, Graham G. Giles, David V. Conti, Heike Bickeboller, Angela Risch, Melanie Waldenberger, Irene Bruske-Hohlfeld, Belynda D. Hicks, Hua Ling, Lesley McGuffog, Andrew Lee, Karoline Kuchenbaecker, Penny Soucy, Judith Manz, Julie M. Cunningham, Katja Butterbach, Zsofia Kote-Jarai, Peter Kraft, Liesel FitzGerald, Sara Lindstrom, Marcia Adams, James D. McKay, Catherine M. Phelan, Sara Benlloch, Linda E. Kelemen, Paul Brennan, Marjorie Riggan, Tracy A. O'Mara, Hongbing Shen, Yongyong Shi, Deborah J. Thompson, Marc T. Goodman, Sune F. Nielsen, Andrew Berchuck, Sylvie Laboissiere, Stephanie L. Schmit, Tameka Shelford, Christopher K. Edlund, Jack A. Taylor, John K. Field, Sue K. Park, Kenneth Offit, Mads Thomassen, Rita Schmutzler, Laura Ottini, Rayjean J. Hung, Jonathan Marchini, Ali Amin Al Olama, Ulrike Peters, Rosalind A. Eeles, Michael F. Seldin, Elizabeth Gillanders, Daniela Seminara, Antonis C. Antoniou, Paul D.P. Pharoah, Georgia Chenevix-Trench, Stephen J. Chanock, Jacques Simard, Douglas F. Easton

Research output: Contribution to journalArticlepeer-review

124 Scopus citations

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 diseasespecific 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.

Original languageEnglish (US)
Pages (from-to)126-135
Number of pages10
JournalCancer Epidemiology Biomarkers and Prevention
Volume26
Issue number1
DOIs
StatePublished - Jan 2017

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Fingerprint Dive into the research topics of 'The oncoarray consortium: A network for understanding the genetic architecture of common cancers'. Together they form a unique fingerprint.

Cite this