Germline BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance associated with breast/ovarian cancer: a report from North India

Abstract

Anurag Mehta,1 Smreti Vasudevan,2 Sanjeev Kumar Sharma,1 Dushyant Kumar,1 Manoj Panigrahi,1 Moushumi Suryavanshi,1 Garima Gupta2 1Department of Laboratory and Transfusion Services, Rajiv Gandhi Cancer Institute and Research Centre, Rohini, Delhi 110085, India; 2Department of Research, Rajiv Gandhi Cancer Institute and Research Centre, Rohini, Delhi 110085, India Background: The spectrum of BRCA mutations that predispose to development of breast/ovarian cancer in Indian population remains unexplored. We report incidence and various types of pathogenic, likely pathogenic and variants of unknown significance (VUS) mutations in BRCA1 and BRCA2 genes observed at a tertiary cancer center in North India.Materials and methods: A total of 206 unrelated breast and/or ovarian cancer patients, who met the National Comprehensive Cancer Network (NCCN) guidelines for genetic testing, were screened for germline BRCA1/BRCA 2 mutations on high-throughput sequencing platform; large genomic rearrangements were assessed by multiple ligation probe assay. Mutations were mined in mutational databases, PubMed, and discerned into classes. Furthermore, the clinicopathological correlation of BRCA mutation status with prognostic markers in breast cancer and tumor histology in ovarian cancer was performed.Results: In total, 45/206 and 17/206 cases showed positivity for BRCA1 and BRCA2 mutations, respectively, whereas 1/206 was positive for a mutation in both the genes. Altogether, 33 distinct BRCA1 mutations were observed, among which 27 were deleterious (12 frameshifts, 8 nonsense, 1 missense, 3 splice-site variants, 2 big deletions and 1 large duplication) and 6 were VUS. Five novel BRCA1 mutations (c.541G>T, c.1681delT, c.2295delG, c.4915C>T and exon 23 deletion) were identified. Seven mutations (c.2214_2215insT, c.2295delG, c.3607C>T, c.4158_4162delCTCTC, c.4571C>A, splicesite_3 (C>T) and exon 21–23 duplication) occurred more than once, whereas 16 distinct BRCA2 mutations were noted – 9 were lethal (6 frameshifts, 2 nonsense and 1 big deletion) and 7 VUS. One unique pathogenic BRCA2 mutation (c.932_933insT) was recognized. Two mutations (c.9976A>T and c.10089A>G) recurred twice. No significant difference in hormone receptor status was observed among BRCA1 carriers, BRCA2 carriers and noncarriers.Conclusion: We have documented various pathogenic and VUS mutations in BRCA1 and BRCA2 genes observed in the cohort. Six novel mutations were identified. The knowledge shared would assist genetic testing in enabling more focused site-specific screening for mutations in biological relatives. Keywords: genetic screening, high-throughput sequencing, multiplex ligation-dependent probe amplification assay, novel mutations, recurrent mutations

Keywords

• Genetic screening
• high-throughput sequencing
• Multiplex Ligation-Dependent Probe Amplification assay
• novel mutations
• recurrent mutations