Validated copy number variations.

Abbreviations: CI = confidence interval; na = not available; OR = odds ratio.aAccording to the NCBI Genome Build 36.1 (hg 18). Exact start and end positions of the CNVs are provided in Table S1.bSize reported in HBOC individuals analysed in the SNP array (may vary between individuals).cCombined frequencies of original cohort of 81 HBOC individuals (analysed in the SNP array) and cohort of 20 additional HBOC individuals (genotyped by TaqMan® Copy Number Assays). CNVs in the 2q34, 5q15, 8p23.2, and 17q21.31 regions were not observed in additional cohort of 20 HBOC individuals. Heterozygous deletion (copy number 1) in the 3p11.1 region was also identified in 4 out of the 20 additional HBOC individuals (File S2). Heterozygous duplication (copy number 3) in the 19q13.41 region was also identified in 3 out of the 20 additional HBOC individuals (File S2). Homozygous duplication (copy number 4) in the 19q13.41 region was identified in 1 out of the 20 additional HBOC individuals (File S2).dThirty-five controls were first analyzed in the SNP array. CNVs were also screened in additional controls by TaqMan® Copy Number Assays (excluding BRCA1 affecting CNV since large deletions in BRCA1 coding regions are known to associate with breast and ovarian cancer susceptibility).eSearch against the Database of Genomic Variants (DGV).fDeletion in the 5q15 region was homozygous (copy number 0) in 1 out of the 101 (0.010) HBOC individuals and in 1 out of the 899 (0.001) controls and heterozygous (copy number 1) in 4 out of the 101 (0.040) HBOC individuals and in 56 out of the 899 (0.062) controls.gDuplication in the 19q13.41 region was homozygous (copy number 4) in 4 out of the 101 (0.040) HBOC individuals and in 3 out of the 334 (0.009) controls and heterozygous (copy number 3) in 7 out of the 101 (0.069) HBOC individuals and in 31 out of the 334 (0.093) controls.