Abstract
Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.
Highlights
Germline pathogenic single nucleotide variations (SNVs) and small indels of the BRCA1 and BRCA2 genes are well-studied genetic changes in hereditary breast and ovarian cancers [1]
large genomic rearrangements (LGRs) of BRCA1 accounted for approximately 10% of the overall BRCA1 mutations, whereas BRCA2 LGRs took up ≤0.5% of the total BRCA2 mutations
According to the statistics based on next-generation sequencing (NGS) data of our laboratory, BRCA1 LGRs take up approx. 10% of the overall BRCA1 mutations in Hungary
Summary
Germline pathogenic single nucleotide variations (SNVs) and small indels of the BRCA1 and BRCA2 genes are well-studied genetic changes in hereditary breast and ovarian cancers [1]. LGRs in BRCA1 are responsible for between 0% and 27% of all BRCA1 disease-causing mutations identified in numerous populations. Such alterations are far less common in the BRCA2 gene [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17]. These chromosomal changes are not readily detectable by conventional sequencing, but require copy-number sensitive methods, such as multiplex ligation-dependent probe amplification (MLPA) [18], quantitative multiplex PCR of short fluorescent fragments (QMPSF) [19], or comparing the relative numbers of the aligned reads yielded by next-generation sequencing (NGS) [20]
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