Screening for BRCA1, BRCA2, CHEK2, PALB2, BRIP1, RAD50, and CDH1 mutations in high-risk Finnish BRCA1/2-founder mutation-negative breast and/or ovarian cancer individuals

Abstract

IntroductionTwo major high-penetrance breast cancer genes, BRCA1 and BRCA2, are responsible for approximately 20% of hereditary breast cancer (HBC) cases in Finland. Additionally, rare mutations in several other genes that interact with BRCA1 and BRCA2 increase the risk of HBC. Still, a majority of HBC cases remain unexplained which is challenging for genetic counseling. We aimed to analyze additional mutations in HBC-associated genes and to define the sensitivity of our current BRCA1/2 mutation analysis protocol used in genetic counseling.MethodsEighty-two well-characterized, high-risk hereditary breast and/or ovarian cancer (HBOC) BRCA1/2-founder mutation-negative Finnish individuals, were screened for germline alterations in seven breast cancer susceptibility genes, BRCA1, BRCA2, CHEK2, PALB2, BRIP1, RAD50, and CDH1. BRCA1/2 were analyzed by multiplex ligation-dependent probe amplification (MLPA) and direct sequencing. CHEK2 was analyzed by the high resolution melt (HRM) method and PALB2, RAD50, BRIP1 and CDH1 were analyzed by direct sequencing. Carrier frequencies between 82 (HBOC) BRCA1/2-founder mutation-negative Finnish individuals and 384 healthy Finnish population controls were compared by using Fisher's exact test. In silico prediction for novel missense variants effects was carried out by using Pathogenic-Or-Not -Pipeline (PON-P).ResultsThree previously reported breast cancer-associated variants, BRCA1 c.5095C > T, CHEK2 c.470T > C, and CHEK2 c.1100delC, were observed in eleven (13.4%) individuals. Ten of these individuals (12.2%) had CHEK2 variants, c.470T > C and/or c.1100delC. Fourteen novel sequence alterations and nine individuals with more than one non-synonymous variant were identified. One of the novel variants, BRCA2 c.72A > T (Leu24Phe) was predicted to be likely pathogenic in silico. No large genomic rearrangements were detected in BRCA1/2 by multiplex ligation-dependent probe amplification (MLPA).ConclusionsIn this study, mutations in previously known breast cancer susceptibility genes can explain 13.4% of the analyzed high-risk BRCA1/2-negative HBOC individuals. CHEK2 mutations, c.470T > C and c.1100delC, make a considerable contribution (12.2%) to these high-risk individuals but further segregation analysis is needed to evaluate the clinical significance of these mutations before applying them in clinical use. Additionally, we identified novel variants that warrant additional studies. Our current genetic testing protocol for 28 Finnish BRCA1/2-founder mutations and protein truncation test (PTT) of the largest exons is sensitive enough for clinical use as a primary screening tool.

Whole-exome sequencing of Finnish hereditary breast cancer families

“…Interestingly, in this family, two deleterious CHEK2 variants, c.470T4C and c.1100delC have been reported previously. 10 It can be seen in Figure 3b that the truncating CHEK2 c.1100delC variant is not segregating with the disease in the family, indicating its moderate character. It would be interesting to study further if the EDN3, MAGEF1, and APEX1 variants could be modifiers of the CHEK2 variants.…”

“…Here, exome sequencing failed to detect the CHEK2 c.1100delC variant in a patient 110010 (Figure 2), who is known to carry the two CHEK2 variants c.470T4C and c.1100delC based on previous analyses. 10 The c.1100delC variant is located in a gene region that shows homology with other chromosomal regions; this might be the reason why it was not identified by exome sequencing.…”

“…individuals collected from Tampere University Hospital in which index patients have been screened for variants in BRCA1, BRCA2, CHEK2, PALB2, BRIP1, RAD50, and CDH1 genes and for copy number variations on a genome-wide scale. 10,11 In one of these families, two CHEK2 variants, c.470T4C and c.1100delC, have been reported. 10 Seven other families were selected into this study based on the previously described high-risk hereditary BC criteria.…”

“…10,11 In one of these families, two CHEK2 variants, c.470T4C and c.1100delC, have been reported. 10 Seven other families were selected into this study based on the previously described high-risk hereditary BC criteria. 10 The families were recruited from Turku University Hospital, and the index patients had tested negative for BRCA1/2 founder-variants.…”

“…10 Seven other families were selected into this study based on the previously described high-risk hereditary BC criteria. 10 The families were recruited from Turku University Hospital, and the index patients had tested negative for BRCA1/2 founder-variants. From each of the 13 families, one to three breast or breast and ovarian cancer-affected individuals were selected for exome sequencing.…”