IDENTIFICATION OF BRCA1 VARIANTS RS2053936273 AND RS80357670 IN TRIPLE NEGATIVE BREAST CANCER (TNBC) IN THE PAKISTANI POPULATION AT A TERTIARY CARE HOSPITAL IN KARACHI: A SANGER SEQUENCING STUDY

Abstract

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast carcinoma characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and HER2 expression, commonly associated with germline Breast cancer Gene 1 (BRCA1) mutations. These mutations compromise homologous recombination DNA repair and increase cancer susceptibility. Despite the high burden of Triple Negative Breast Cancer in Pakistan, limited genetic data exists on the distribution of BRCA1 variants. Two BRCA1 variants, rs2053936273 and rs80357670, have been reported in major Pakistani studies as pathogenic frameshift mutations leading to truncated protein products; however, their prevalence and clinical relevance in remains unclear. The present study aimed to detect these BRCA1 variants in Triple Negative Breast cancer patients and assess their correlation with clinico-pathological parameters. A cross-sectional study was conducted at Pakistan Navy Station Shifa Hospital in Karachi from November 2024 to October 2025. Fifty female Triple Negative Breast Cancer patients aged 28–60 years were enrolled after biopsy and immunohistochemical confirmation. Genomic DNA was extracted using Qiagen® kits, and Polymerase chain reaction (PCR) amplification was performed at Ziauddin Medical University, Karachi. Sanger sequencing was outsourced to Eurofins, United States of America. Sequence alignment and variant annotation were performed using Molecular Evolutionary Genetic Analysis (MEGA X), BioEdit, and Database Single Nucleotide Polymorphism (dbSNP). Descriptive and associative statistics were analyzed using SPSS v23. Of 50 samples, 39 yielded high-quality sequences suitable for variant analysis. Neither rs2053936273 nor rs80357670 was detected in the study participants. However, two variants of uncertain significance (VUS) were observed in 5.1% of samples. The majority of cases occurred in patients under 50 years, with a subset showing a positive family history. The absence of the targeted BRCA1 variants suggests potential ethnic specificity and highlights the need for expanded genomic studies in the Pakistani TNBC population. VIII In conclusion, the findings emphasize the importance of population-based BRCA1 variant profiling to develop localized genetic testing panels and inform early detection, prevention, and counseling strategies for hereditary breast cancer in Pakistan.