COGS update June 28, 2010
- Created on Monday, 28 June 2010 06:43
- Last Updated on Saturday, 20 October 2012 12:49
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The first year has now passed and we have met all the deliverables in due time. The first annual report is about to be submitted within days.
The final SNP list for the creation of the chip named iCOGS was sent to Illumina 11 June. The iCOGS is a custom SNP Illumina Custom Infinium genotyping array specifically designed to evaluate genetic variants for association with the risk of with breast, ovarian and prostate cancer. Specific objectives are to replicate potential associations arising through GWAS in these diseases and obtain precise estimates of genotype-specific risk, to evaluate potential loci for subsets of disease (e.g. ER-negative breast cancer), to evaluate variants for associations with disease survival, to conduct dense genotyping of SNPs across known associated regions, to facilitate fine-mapping, to evaluate variants selected as functional candidates and to genotype SNPs associated with related quantitative traits (e.g. age at menarche). iCOGS is comprising ≈200,000 SNPs.
COGS is built on a multistep procedure and it is essential that each step is completed before the next steps can be initiated. The first year has also been a year of data collection and preparation. DNA has been extracted and normalised from samples provided by a large number of COGS groups. The samples have been sent to the genotyping facilities that are conducting the analyses. In parallel, information on life style factors, clinical information and tumour characteristics has been collected, “normalised” and stored in specially designed databases. Fine-mapping of regions of the genome has begun, to search for the casual variants behind cancer associations in established susceptibility loci. In the coming two years an enormous amount of data will be generated and we will be well prepared to study and estimate the health care, societal and ethical challenges these results will generate.