iCOGS chip


iCOGS is a custom Illumina iSelect genotyping array, designed as part of the Collaborative Oncological Gene-Environment Study (COGS). It was devised to test genetic variants associated with three hormone related cancers: breast, ovarian and prostate. 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). Genotyping funding originated from multiple sources, with the largest contributors being the European Union Seventh Framework and Cancer Research UK.

The array includes SNPs associated with: the risk of these cancers in genome-wide association studies (GWAS); breast or ovarian cancer risk in BRCA1 or BRCA2 carriers; subsets of disease (for example, ER-negative breast cancer, serous ovarian cancer and aggressive prostate cancer); survival after diagnosis, a dense set of SNPs across more than 50 regions known to harbour susceptibility variants for one of the target diseases; related quantitative traits (e.g. age at menarche, breast density); functional candidate variants, including rare variants in known cancer susceptibility loci (e.g. BRCA1, PALB2). A more detailed description of the composition of the chip can be found here.

A complete list of all SNPs on the array can be downloaded here. If you wish to purchase iCOGS arrays from Illumina, please complete and return this form for approval by the COGS steering committee.

Nature Genetics has generated an iCOGS Focus comprising a collection of 13 papers from COGS. These represent significant advances in our understanding of genetic susceptibility to three hormone-related cancers: breast, ovarian and prostate.


PRACTICAL contributed with ~70,000 SNPs and ~50,000 samples.

PRACTICAL iCOGS has led to the identification of 23 new prostate cancer susceptibility loci. Details can be found on Eeles RA, Olama AA, Benlloch S, et al., Nature Genetics, Nat Genet. 2013 Apr;45(4):385-91.

Further papers have been published with data generated from PRACTICAL iCOGS, and many manuscripts produced from ~100 proposals of analysis which are currently being undertaken. For the most up to date published papers, please visit the Publications link.

Detailed clinical and epidemiological data has been collected for the samples included in this project. For further information please follow theĀ PRACTICAL iCOGS Inventory link.