Background: Large rearrangements account for 8% to 15% of deleterious BRCA mutations, although none have been characterized previously in individuals of Mexican ancestry. Methods: DNA from 106 Hispanic patients without an identifiable BRCA mutation by exonic sequence analysis was subjected to multiplexed quantitative differential PCR. One case of Native American and African American ancestry was identified via multiplex ligation-dependent probe amplification. Long-range PCR was used to confirm deletion events and to clone and sequence genomic breakpoints. Splicing patterns were derived by sequencing cDNA from reverse transcription-PCR of lymphoblastoid cell line RNA. Haplotype analysis was conducted for recurrent mutations. Results: The same deletion of BRCA1 exons 9 through 12 was identified in five unrelated families. Long-range PCR and sequencing indicated a deletion event of 14.7 kb. A 3-primer PCR assay was designed based on the deletion breakpoints, identified within an AluSp element in intron 8 and an AluSx element in intron 12. Haplotype analysis confirmed common ancestry. Analysis of cDNA showed direct splicing of exons 8 to 13, resulting in a frameshift mutation and predicted truncation of the BRCA1 protein. Conclusions: We identified and characterized a novel large BRCA1 deletion in five unrelated families - four of Mexican ancestry and one of African and Native American ancestry, suggesting the possibility of founder effect of Amerindian or Mestizo origin. This BRCA1 rearrangement was detected in 3.8% (4 of 106) of BRCA sequence-negative Hispanic families. An assay for this mutation should be considered for sequence-negative high-risk Hispanic patients.
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