Identification of novel large genomic rearrangements at the BRCA1 locus in Malaysian women with breast cancer

Abstract 

Background: The incidence of breast cancer has been on the rise in Malaysia. It is suggested that a subset of breast cancer cases were associated with germline mutation in breast cancer susceptibility (BRCA) genes. Most of the BRCA mutations reported in Malaysia were point mutations, small deletions and insertions. Here we report the first study of BRCA large genomic rearrangements (LGRs) in Malaysia. We aimed to detect the presence of LGRs in the BRCA genes of Malaysian patients with breast cancer. Methods: Multiplex ligation-dependent probe amplification (MLPA) for BRCA LGRs was carried out on 100 patients (60 were high-risk breast cancer patients previously tested negative/positive for BRCA1 and BRCA2 mutations, and 40 were sporadic breast cancer patients), recruited from three major referral centres, Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Hospital Kuala Lumpur (HKL) and Hospital Putrajaya (HPJ). Results: Two novel BRCA1 rearrangements were detected in patients with sporadic breast cancer; both results were confirmed by quantitative PCR. No LGRs were found in patients with high-risk breast cancer. The two large genomic rearrangements detected were genomic amplifications of exon 3 and exon 10. No BRCA2 genomic rearrangement was found in both high-risk and sporadic breast cancer patients. Conclusion: These results will be helpful to understand the mutation spectrum of BRCA1 and BRCA2 genes in Malaysian patients with breast cancer. Further studies involving larger samples are required to establish a genetic screening strategy for both high-risk and sporadic breast cancer patients.

Abbreviations: ALB, albumin, BRCA1, breast cancer genes 1, BRCA2, breast cancer genes 2, Ct, threshold cycle, DNA, deoxyribonucleic acid, dNTP, deoxyribonucleotide triphosphate, EDTA, ethylenediaminetetraacetic acid, ER, estrogen receptor, HKL, Hospital Kuala Lumpur, HPJ, Hospital Putrajaya, LGRs, large genomic rearrangements, MLPA, multiplex ligation-dependent probe amplification, PCR, polymerase chain reaction, qPCR, quantitative PCR, UKMMC, Universiti Kebangsaan Malaysia Medical Centre, USA, United States of America

Keywords: BRCA1, Sporadic breast cancer, Large genomic rearrangements, Malaysia, MLPA, QPCR