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The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.

Publication ,  Journal Article
Amos, CI; Dennis, J; Wang, Z; Byun, J; Schumacher, FR; Gayther, SA; Casey, G; Hunter, DJ; Sellers, TA; Gruber, SB; Dunning, AM; Michailidou, K ...
Published in: Cancer Epidemiol Biomarkers Prev
January 2017

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.

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Published In

Cancer Epidemiol Biomarkers Prev

DOI

EISSN

1538-7755

Publication Date

January 2017

Volume

26

Issue

1

Start / End Page

126 / 135

Location

United States

Related Subject Headings

  • Selection, Genetic
  • Risk Assessment
  • Prognosis
  • Prevalence
  • Polymorphism, Single Nucleotide
  • Neoplasms
  • Male
  • Humans
  • Genotype
  • Genome-Wide Association Study
 

Citation

APA
Chicago
ICMJE
MLA
NLM
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 Epidemiol Biomarkers Prev, 26(1), 126–135. https://doi.org/10.1158/1055-9965.EPI-16-0106
Amos, Christopher I., Joe Dennis, Zhaoming Wang, Jinyoung Byun, Fredrick R. Schumacher, Simon A. Gayther, Graham Casey, et al. “The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.Cancer Epidemiol Biomarkers Prev 26, no. 1 (January 2017): 126–35. https://doi.org/10.1158/1055-9965.EPI-16-0106.
Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, et al. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):126–35.
Amos, Christopher I., et al. “The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.Cancer Epidemiol Biomarkers Prev, vol. 26, no. 1, Jan. 2017, pp. 126–35. Pubmed, doi: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, Bickeböller H, Risch A, Waldenberger M, Brüske-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, Lindström 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, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):126–135.

Published In

Cancer Epidemiol Biomarkers Prev

DOI

EISSN

1538-7755

Publication Date

January 2017

Volume

26

Issue

1

Start / End Page

126 / 135

Location

United States

Related Subject Headings

  • Selection, Genetic
  • Risk Assessment
  • Prognosis
  • Prevalence
  • Polymorphism, Single Nucleotide
  • Neoplasms
  • Male
  • Humans
  • Genotype
  • Genome-Wide Association Study