For the purpose of the BCAC analyses, we included SNPs on the basis of the analysis of the nine GWAS described above. We ranked SNPs on the basis of the results from five analyses: an overall 1-degree-of-freedom trend test; a 1-degree-of-freedom trend test giving a weight of 2 to those studies selecting cases for a positive family history (UK2, BBCS, DFBBCS and GC-HBOC); a 2-degrees-of-freedom genotype test; and 1-degree-of-freedom tests based on cases diagnosed before the ages of 40 years or 50 years compared with all controls. We also defined lists based on 1-degree-of-freedom trend tests restricted to data from each of the nine component studies. SNPs were also selected from analyses of cases with ER-negative disease, but these are not reported here.
