Large Genomic Rearrangements of BRCA1 and BRCA2 among Patients Referred for Genetic Analysis in Galicia (NW Spain): Delimitation and Mechanism of Three Novel BRCA1 Rearrangements

Abstract

In the Iberian Peninsula, which includes mainly Spain and Portugal, large genomic rearrangements (LGRs) of BRCA1 and BRCA2 have respectively been found in up to 2.33% and 8.4% of families with hereditary breast and/or ovarian cancer (HBOC) that lack point mutations and small indels. In Galicia (Northwest Spain), the spectrum and frequency of BRCA1/BRCA2 point mutations differs from the rest of the Iberian populations. However, to date there are no Galician frequency reports of BRCA1/BRCA2 LGRs. Here we used multiplex ligation-dependent probe amplification (MLPA) to screen 651 Galician index cases (out of the 830 individuals referred for genetic analysis) without point mutations or small indels. We identified three different BRCA1 LGRs in four families. Two of them have been previously classified as pathogenic LGRs: the complete deletion of BRCA1 (identified in two unrelated families) and the deletion of exons 1 to 13. We also identified the duplication of exons 1 and 2 that is a LGR with unknown pathogenicity. Determination of the breakpoints of the BRCA1 LGRs using CNV/SNP arrays and sequencing identified them as NG_005905.2:g.70536_180359del, NG_005905.2:g.90012_97270dup, and NC_000017.10:g.41230935_41399840delinsAluSx1, respectively; previous observations of BRCA1 exon1-24del, exon1-2dup, and exon1-13del LGRs have not characterized them in such detail. All the BRCA1 LGRs arose from unequal homologous recombination events involving Alu elements. We also detected, by sequencing, one BRCA2 LGR, the Portuguese founder mutation c.156_157insAluYa5. The low frequency of BRCA1 LGRs within BRCA1 mutation carriers in Galicia (2.34%, 95% CI: 0.61–7.22) seems to differ from the Spanish population (9.93%, 95% CI: 6.76–14.27, P-value = 0.013) and from the rest of the Iberian population (9.76%, 95% CI: 6.69–13.94, P-value = 0.014).

The importance of analysis of long-range rearrangement of BRCA1 and BRCA2 in genetic diagnosis of familial breast cancer

“…The drawback of MLPA is that it does not identify LGR breakpoints, which are essential for the recognition of recurrent rearrangements. Other strategies, such as NGS, should be applied to identify the breakpoint (23,24). The relative high frequency of…”

“…Criteria for the inclusion of BART testing at no additional charge as part of the BRACAnalysis are listed in Table 3. Wenstrup et al (23) reported on Myriad's BART clinical assay for LGRs. A total of 1,035 high-risk patients initially underwent a comprehensive BRACAnalysis, which included BRCA1 and BRCA2 full gene sequencing plus five common recurrent BRCA1 LGR mutations.…”

Hereditary cancer syndromes in Latino populations: genetic characterization and surveillance guidelines

“…)del (exon deletion)1–13c. (?_-48)_(4357 + 1_4358-1)del (exon deletion)20c.5213_5277 + 3182delinsT (exon deletion)Fachal L et al 2014 [29]Spain (Galicia)6511-2c. (?_-48)_(80 + 1_81-1)del (exon deletion)1–24c.…”

5-Fluorouracil induces apoptosis of colorectal cancer cells

“…LGR (Siyar Ekinci et al, 2015) is a Wnt signal transduction pathway receptor (Fachal et al, 2014) and belongs to the RS5-PO family (Haack et al, 2015). LGR participates in the occurrence and development of breast cancer.…”

“…According to the established protocol (Yan et al, 2015), HCT116 cells were collected for the quantification of the LGR4 protein level (Fachal et al, 2014). Cells were first lysed in buffer for 30 min on ice and were centrifuged to collect proteins.…”