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. Coetzee & 73 others Dennis 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 journalArticle

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 1 2017

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Single Nucleotide Polymorphism
Neoplasms
Quality Control
Pharmacogenetics
Genetic Models
Principal Component Analysis
Causality
Life Style
Research Personnel
Genome
Technology

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

Amos, C. I., Dennis, J., Wang, Z., Byun, J., Schumacher, F. R., Gayther, S. A., ... Easton, D. F. (2017). The oncoarray consortium: A network for understanding the genetic architecture of common cancers. Cancer Epidemiology Biomarkers and Prevention, 26(1), 126-135. https://doi.org/10.1158/1055-9965.EPI-16-0106

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

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 26, No. 1, 01.01.2017, p. 126-135.

Research output: Contribution to journalArticle

Amos, CI, Dennis, J, Wang, Z, Byun, J, Schumacher, FR, Gayther, SA, Casey, G, Hunter, DJ, Sellers, TA, Gruber, SB, Dunning, AM, Michailidou, K, Fachal, L, Doheny, K, Spurdle, AB, Li, Y, Xiao, X, Romm, J, Pugh, E, Coetzee, GA, Hazelett, DJ, Bojesen, SE, Caga-Anan, C, Haiman, CA, Kamal, A, Luccarini, C, Tessier, D, Vincent, D, Bacot, F, Van Den Berg, DJ, Nelson, S, Demetriades, S, Goldgar, DE, Couch, FJ, Forman, JL, Giles, GG, Conti, DV, Bickeboller, H, Risch, A, Waldenberger, M, Bruske-Hohlfeld, I, Hicks, BD, Ling, H, McGuffog, L, Lee, A, Kuchenbaecker, K, Soucy, P, Manz, J, Cunningham, JM, Butterbach, K, Kote-Jarai, Z, Kraft, P, FitzGerald, L, Lindstrom, S, Adams, M, McKay, JD, Phelan, CM, Benlloch, S, Kelemen, LE, Brennan, P, Riggan, M, O'Mara, TA, Shen, H, Shi, Y, Thompson, DJ, Goodman, MT, Nielsen, SF, Berchuck, A, Laboissiere, S, Schmit, SL, Shelford, T, Edlund, CK, Taylor, JA, Field, JK, Park, SK, Offit, K, Thomassen, M, Schmutzler, R, Ottini, L, Hung, RJ, Marchini, J, Olama, AAA, Peters, U, Eeles, RA, Seldin, MF, Gillanders, E, Seminara, D, Antoniou, AC, Pharoah, PDP, Chenevix-Trench, G, Chanock, SJ, Simard, J & Easton, DF 2017, 'The oncoarray consortium: A network for understanding the genetic architecture of common cancers', Cancer Epidemiology Biomarkers and Prevention, vol. 26, no. 1, pp. 126-135. https://doi.org/10.1158/1055-9965.EPI-16-0106
Amos, Christopher I. ; Dennis, Joe ; Wang, Zhaoming ; Byun, Jinyoung ; Schumacher, Fredrick R. ; Gayther, Simon A. ; Casey, Graham ; Hunter, David J. ; Sellers, Thomas A. ; Gruber, Stephen B. ; Dunning, Alison M. ; Michailidou, Kyriaki ; Fachal, Laura ; Doheny, Kimberly ; Spurdle, Amanda B. ; Li, Yafang ; Xiao, Xiangjun ; Romm, Jane ; Pugh, Elizabeth ; Coetzee, Gerhard A. ; Hazelett, Dennis J. ; Bojesen, Stig E. ; Caga-Anan, Charlisse ; Haiman, Christopher A. ; Kamal, Ahsan ; Luccarini, Craig ; Tessier, Daniel ; Vincent, Daniel ; Bacot, Francois ; Van Den Berg, David J. ; Nelson, Stefanie ; Demetriades, Stephen ; Goldgar, David E. ; Couch, Fergus J. ; Forman, Judith L. ; Giles, Graham G. ; Conti, David V. ; Bickeboller, Heike ; Risch, Angela ; Waldenberger, Melanie ; Bruske-Hohlfeld, Irene ; Hicks, Belynda D. ; Ling, Hua ; McGuffog, Lesley ; Lee, Andrew ; Kuchenbaecker, Karoline ; Soucy, Penny ; Manz, Judith ; Cunningham, Julie M. ; Butterbach, Katja ; Kote-Jarai, Zsofia ; Kraft, Peter ; FitzGerald, Liesel ; Lindstrom, Sara ; Adams, Marcia ; McKay, James D. ; Phelan, Catherine M. ; Benlloch, Sara ; Kelemen, Linda E. ; Brennan, Paul ; Riggan, Marjorie ; O'Mara, Tracy A. ; Shen, Hongbing ; Shi, Yongyong ; Thompson, Deborah J. ; Goodman, Marc T. ; Nielsen, Sune F. ; Berchuck, Andrew ; Laboissiere, Sylvie ; Schmit, Stephanie L. ; Shelford, Tameka ; Edlund, Christopher K. ; Taylor, Jack A. ; Field, John K. ; Park, Sue K. ; Offit, Kenneth ; Thomassen, Mads ; Schmutzler, Rita ; Ottini, Laura ; Hung, Rayjean J. ; Marchini, Jonathan ; Olama, Ali Amin Al ; Peters, Ulrike ; Eeles, Rosalind A. ; Seldin, Michael F. ; Gillanders, Elizabeth ; Seminara, Daniela ; Antoniou, Antonis C. ; Pharoah, Paul D P ; Chenevix-Trench, Georgia ; Chanock, Stephen J. ; Simard, Jacques ; Easton, Douglas F. / The oncoarray consortium : A network for understanding the genetic architecture of common cancers. In: Cancer Epidemiology Biomarkers and Prevention. 2017 ; Vol. 26, No. 1. pp. 126-135.
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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.",
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TY - JOUR

T1 - The oncoarray consortium

T2 - A network for understanding the genetic architecture of common cancers

AU - Amos, Christopher I.

AU - Dennis, Joe

AU - Wang, Zhaoming

AU - Byun, Jinyoung

AU - Schumacher, Fredrick R.

AU - Gayther, Simon A.

AU - Casey, Graham

AU - Hunter, David J.

AU - Sellers, Thomas A.

AU - Gruber, Stephen B.

AU - Dunning, Alison M.

AU - Michailidou, Kyriaki

AU - Fachal, Laura

AU - Doheny, Kimberly

AU - Spurdle, Amanda B.

AU - Li, Yafang

AU - Xiao, Xiangjun

AU - Romm, Jane

AU - Pugh, Elizabeth

AU - Coetzee, Gerhard A.

AU - Hazelett, Dennis J.

AU - Bojesen, Stig E.

AU - Caga-Anan, Charlisse

AU - Haiman, Christopher A.

AU - Kamal, Ahsan

AU - Luccarini, Craig

AU - Tessier, Daniel

AU - Vincent, Daniel

AU - Bacot, Francois

AU - Van Den Berg, David J.

AU - Nelson, Stefanie

AU - Demetriades, Stephen

AU - Goldgar, David E.

AU - Couch, Fergus J.

AU - Forman, Judith L.

AU - Giles, Graham G.

AU - Conti, David V.

AU - Bickeboller, Heike

AU - Risch, Angela

AU - Waldenberger, Melanie

AU - Bruske-Hohlfeld, Irene

AU - Hicks, Belynda D.

AU - Ling, Hua

AU - McGuffog, Lesley

AU - Lee, Andrew

AU - Kuchenbaecker, Karoline

AU - Soucy, Penny

AU - Manz, Judith

AU - Cunningham, Julie M.

AU - Butterbach, Katja

AU - Kote-Jarai, Zsofia

AU - Kraft, Peter

AU - FitzGerald, Liesel

AU - Lindstrom, Sara

AU - Adams, Marcia

AU - McKay, James D.

AU - Phelan, Catherine M.

AU - Benlloch, Sara

AU - Kelemen, Linda E.

AU - Brennan, Paul

AU - Riggan, Marjorie

AU - O'Mara, Tracy A.

AU - Shen, Hongbing

AU - Shi, Yongyong

AU - Thompson, Deborah J.

AU - Goodman, Marc T.

AU - Nielsen, Sune F.

AU - Berchuck, Andrew

AU - Laboissiere, Sylvie

AU - Schmit, Stephanie L.

AU - Shelford, Tameka

AU - Edlund, Christopher K.

AU - Taylor, Jack A.

AU - Field, John K.

AU - Park, Sue K.

AU - Offit, Kenneth

AU - Thomassen, Mads

AU - Schmutzler, Rita

AU - Ottini, Laura

AU - Hung, Rayjean J.

AU - Marchini, Jonathan

AU - Olama, Ali Amin Al

AU - Peters, Ulrike

AU - Eeles, Rosalind A.

AU - Seldin, Michael F.

AU - Gillanders, Elizabeth

AU - Seminara, Daniela

AU - Antoniou, Antonis C.

AU - Pharoah, Paul D P

AU - Chenevix-Trench, Georgia

AU - Chanock, Stephen J.

AU - Simard, Jacques

AU - Easton, Douglas F.

PY - 2017/1/1

Y1 - 2017/1/1

N2 - 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.

AB - 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.

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