iCOGS is a custom Illumina iSelect genotyping array, designed to test, in a cost-effective manner, genetic variants related to three hormone related cancers: breast, ovary and prostate. It was designed as part of the Collaborative Oncological Gene-Environment Study (COGS). It has been genotyped on more than 250,000 subjects, principally in studies participating in the Breast Cancer Association Consortium (BCAC), the Ovarian Cancer Association Consortium (OCAC), the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) and The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Funding for the genotyping has come from multiple sources, with the largest contributors being the European Union Seventh Framework and Cancer Research UK
The array includes SNPs putatively associated with the risk of these cancers in genome-wide association studies (GWAS), SNPs associated with breast or ovarian cancer risk in BRCA1 or BRCA2 carriers, SNPs associated with subsets of disease (for example, ER-negative breast cancer, serous ovarian cancer and aggressive prostate cancer), SNPs associated with survival after diagnosis, a dense set of SNPs across more than 50 regions known to harbour susceptibility variants for one of the target diseases, SNPs associated with related quantitative traits (e.g. age at menarche, breast density), and functional candidate variants, including rare variants in known cancer susceptibility loci (e.g. BRCA1, PALB2). A detailed description of the composition of the chip may be found here.
A complete list of all SNPs on the array can be downloaded here: icogs_snp_list (13 MB CSV file)
If you wish to purchase iCOGS arrays from Illumina, please complete and return this form for approval by the COGS steering committee.