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. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology |
| Vol/bind | 26 |
| Udgave nummer | 1 |
| Sider (fra-til) | 126-135 |
| Antal sider | 10 |
| ISSN | 1055-9965 |
| DOI | |
| Status | Udgivet - jan. 2017 |
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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 C; Vincent, Daniel; Bacot, François; Van Den Berg, David J; Nelson, Stefanie; Demetriades, Stephen; Goldgar, David E; Couch, Fergus J; Forman, Judith L; Giles, Graham; Conti, David V; Bickeböller, Heike; Risch, Angela; Waldenberger, Melanie; Brüske-Hohlfeld, Irene; Hicks, Belynda D; Ling, Hua; McGuffog, Lesley; Lee, Andrew; Kuchenbaecker, Karoline B; Soucy, Penny; Manz, Judith; Cunningham, Julie M; Butterbach, Katja; Kote-Jarai, Zsofia; Kraft, Peter; Fitzgerald, Liesel; Lindström, 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 L; Amin Al Olama, Ali; Peters, Ulrike; Eeles, Rosalind A; Seldin, Michael F; Gillanders, Elizabeth; Seminara, Daniela; Antoniou, Antonis C; Pharoah, Paul P D; Chenevix-Trench, Georgia; Chanock, Stephen J; Simard, Jacques; Easton, Douglas F.
I: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, Bind 26, Nr. 1, 01.2017, s. 126-135.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
}
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 C
AU - Vincent, Daniel
AU - Bacot, François
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
AU - Conti, David V
AU - Bickeböller, Heike
AU - Risch, Angela
AU - Waldenberger, Melanie
AU - Brüske-Hohlfeld, Irene
AU - Hicks, Belynda D
AU - Ling, Hua
AU - McGuffog, Lesley
AU - Lee, Andrew
AU - Kuchenbaecker, Karoline B
AU - Soucy, Penny
AU - Manz, Judith
AU - Cunningham, Julie M
AU - Butterbach, Katja
AU - Kote-Jarai, Zsofia
AU - Kraft, Peter
AU - Fitzgerald, Liesel
AU - Lindström, 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 L
AU - Amin Al Olama, Ali
AU - Peters, Ulrike
AU - Eeles, Rosalind A
AU - Seldin, Michael F
AU - Gillanders, Elizabeth
AU - Seminara, Daniela
AU - Antoniou, Antonis C
AU - Pharoah, Paul P D
AU - Chenevix-Trench, Georgia
AU - Chanock, Stephen J
AU - Simard, Jacques
AU - Easton, Douglas F
N1 - ©2016 American Association for Cancer Research.
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 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. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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 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. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
KW - Journal Article
U2 - 10.1158/1055-9965.EPI-16-0106
DO - 10.1158/1055-9965.EPI-16-0106
M3 - Journal article
C2 - 27697780
VL - 26
SP - 126
EP - 135
JO - Cancer Epidemiology, Biomarkers & Prevention
JF - Cancer Epidemiology, Biomarkers & Prevention
SN - 1055-9965
IS - 1
ER -