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; 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

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

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

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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.

Original language	English (US)
Pages (from-to)	126-135
Number of pages	10
Journal	Cancer Epidemiology Biomarkers and Prevention
Volume	26
Issue number	1
DOIs	https://doi.org/10.1158/1055-9965.EPI-16-0106
State	Published - Jan 2017

ASJC Scopus subject areas

General Medicine

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Amos, C. I., Dennis, J., Wang, Z., Byun, J., Schumacher, F. R., Gayther, S. A., Casey, G., Hunter, D. J., Sellers, T. A., Gruber, S. B., Dunning, A. M., Michailidou, K., Fachal, L., Doheny, K., Spurdle, A. B., Li, Y., Xiao, X., Romm, J., Pugh, E., ... 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

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

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title = "The oncoarray consortium: A network for understanding the genetic architecture of common cancers",

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.",

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

note = "Publisher Copyright: {\textcopyright} 2016 American Association for Cancer Research.",

year = "2017",

month = jan,

doi = "10.1158/1055-9965.EPI-16-0106",

language = "English (US)",

volume = "26",

pages = "126--135",

journal = "Cancer Epidemiology Biomarkers and Prevention",

issn = "1055-9965",

publisher = "American Association for Cancer Research Inc.",

number = "1",

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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

Y1 - 2017/1

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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JO - Cancer Epidemiology Biomarkers and Prevention

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

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