660 quad snp array

The POSH (Prospective study of Outcomes in Sporadic vs. Hereditary breast cancer) data were collected from January 2000 to January 2008 from oncology clinics in the United Kingdom (Rafiq et al. 2013 ). The average age of the participants at diagnosis is 35.5 years.
Genotyping of 543 cases was conducted using the Illumina 660-Quad SNP array in two separate batches at two locations: 243 triple negative (ER, PR, and HER2 negative) patients were genotyped at the Mayo Clinic, Rochester, Minnesota (Haiman et al. 2011 (link)) and the rest of the patients were genotyped at the Genome Institute of Singapore. To ensure complete harmonization of the genotype calling, the intensity data available from all locations in form of *.idat files were further combined and used to generate genotypes based on the algorithm available in the genotyping module of Illumina’s Genome Studio software. A GenCall threshold of 0.15 and the HumanHap660 annotation file were used.

The POSH GWS consisted of 536 individuals (236 any-cause deaths; 44%) selected from a consecutively ascertained cohort of early onset cases (diagnosed with invasive breast cancer at the age of 40 or earlier) from the United Kingdom. These cases were enrolled into the Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH) between 2000 and 2008, as previously described [38 (link)]. The POSH GWS material was enriched for cases with poor prognosis by including cases with triple-negative breast cancer (n=401), and cases with particularly short duration of breast cancer survival (<2 years, n=48); additional cases with relatively long survival were then included for contrast (>4 years, n=125) [39 (link)]. These cases were genotyped on the Illumina 660-Quad SNP array; genotyping and quality control was carried out as previously described [39 (link)]. 518 cases (97%) in this data set were treated with adjuvant chemotherapy.