The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers
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, co...
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| Vydáno v: | Cancer epidemiology, biomarkers & prevention Ročník 26; číslo 1; s. 126 - 135 |
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| Médium: | Journal Article |
| Jazyk: | angličtina |
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United States
01.01.2017
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| ISSN: | 1538-7755 |
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| Abstract | 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.
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.
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.
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.
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. |
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| AbstractList | 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.
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.
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.
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.
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. BACKGROUNDCommon 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.METHODSThe 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.RESULTSThe 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.CONCLUSIONSResults 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.IMPACTOngoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR. |
| Author | Butterbach, Katja Hung, Rayjean J Dennis, Joe Park, Sue K Kote-Jarai, Zsofia Couch, Fergus J Hicks, Belynda D Coetzee, Gerhard A O'Mara, Tracy A Amos, Christopher I Luccarini, Craig Phelan, Catherine M Shi, Yongyong Kelemen, Linda E Adams, Marcia Sellers, Thomas A Michailidou, Kyriaki Bacot, François Chenevix-Trench, Georgia Byun, Jinyoung Amin Al Olama, Ali Risch, Angela Easton, Douglas F Kuchenbaecker, Karoline Spurdle, Amanda B Edlund, Christopher K Waldenberger, Melanie Schmit, Stephanie L Conti, David V Benlloch, Sara Romm, Jane Li, Yafang Caga-Anan, Charlisse Antoniou, Antonis C Kamal, Ahsan Doheny, Kimberly Kraft, Peter Thompson, Deborah J Van Den Berg, David J Nielsen, Sune F Wang, Zhaoming Manz, Judith Cunningham, Julie M FitzGerald, Liesel Tessier, Daniel Schumacher, Fredrick R Hazelett, Dennis J Haiman, Christopher A Pugh, Elizabeth Offit, Kenneth Bojesen, Stig E Demetriades, Stephen Shen, Hongbing Seldin, Michael F Fachal, Laura Vincent, Daniel McKay, James D Forman, Judith L Ling, Hua Field, John K Xiao, Xiangjun Peters, Ulrike Ottin |
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| Snippet | Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from... BACKGROUNDCommon cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding... |
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| SubjectTerms | Female Genetic Predisposition to Disease - epidemiology Genetic Variation - genetics Genome-Wide Association Study - methods Genotype Humans Male Neoplasms - epidemiology Neoplasms - genetics Neoplasms - physiopathology Polymorphism, Single Nucleotide - genetics Prevalence Prognosis Risk Assessment Selection, Genetic |
| Title | The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers |
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