Complex germline rearrangement of BRCA1 associated with breast and ovarian cancer

Germline mutations in BRCA1 predispose to breast and ovarian cancer. Most germline BRCA1 mutations are small insertions, deletions, or single base pair (bp) substitutions. These mutation classes are rarely found as somatic mutations in BRCA1. On the other hand, somatic deletions of multiple mega-base pairs (Mb) including BRCA1, as reflected by loss of heterozygosity, occur frequently in both inherited and sporadic breast and ovarian cancers. To determine whether deletions or rearrangements of hundreds to thousands of bps might contribute to inherited mutation in BRCA1, we developed a Long PCR strategy for screening the entire genomic BRCA1 locus in high-risk families. We evaluated genomic DNA from one high-risk family of European ancestry with BRCA1-linked cancer in which no genomic mutations had been detected using conventional methods. Long PCR revealed a complex mutation, g.12977 ins10 del1039 (based on GenBank L78833), comprising an inverted duplication and deletion in BRCA1 that removes portions of exon 3 and intron 3, including the 5' splice site for intron 3. As a result of the deletion, exon 3 is skipped, leading to a truncated protein and disease predisposition. Unlike previously reported large germline deletions in BRCA1, neither breakpoint resides within an Alu element. The g.12977 ins10 del1039 mutation was not detected among 11 other breast cancer families, nor among 406 breast cancer patients unselected for family history.