The comparison of SNP frequency between CIMBA cases and BCAC cases (case-only analyses), or between unaffected CIMBA subjects and BCAC controls (control-only analyses), was performed using logistic regression adjusted for age at BC diagnosis in the case-only analyses and for age at interview for BCAC controls or at censure for CIMBA unaffected subjects in the control-only analyses, as well as for country and principal components (PCs) to account for population structure. Separate analyses were carried out for BRCA1 and BRCA2 mutation carriers. To define the number of PC for inclusion in the models, the principal component analysis was carried out using 35,858 uncorrelated genotyped SNPs on the OncoArray and purpose-written software (http://ccge.medschl.cam.ac.uk/software/pccalc/). The inflation statistic was calculated and converted to an equivalent statistic for a study of 1,000 subjects for each outcome (λ1,000) by adjusting for effective study size:

where n and m are the numbers of BCAC and CIMBA subjects respectively. The models were adjusted with the first four PCs (λ1,000 with and without PCs in the model = 1.03 and 1.21, respectively) since additional PCs did not result in further reduction in the inflation of the test statistics.

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