Variant Analysis OF ATM, PTEN and BRCA2 Genes In Breast Cancer In Karachi, Pakistan

Abstract

Breast carcinoma is the cancer of epithelial cells. The most frequent types of breast cancer are ductal and lobular carcinoma. Pakistan has a significant incidence of breast cancer. Single nucleotide variants (SNVs) in ATM, PTEN, and BRCA2 genes are reported to be involved in breast cancer. Many SNVs have been identified in different populations along with novel intron variants in ATM exon 13, PTEN exon 2, and BRCA2 exon 10. We selected thirteen breast cancer patients from Karachi, Pakistan and their blood and breast tumor samples were collected. Primers were designed to the specific hotspots of breast cancer-related genes i.e. ATM exon 13, PTEN exon 2, and BRCA2 exon 10. Sanger sequencing was done to sequence the DNA samples. Bioinformatics tools were utilized to analyze the data. In the case of ATM and PTEN, non-coding regions exhibit more variants. Three novel SNVs were observed in the case of ATM intron 13; among them, two were found to be associated with branch point defects that can interfere during mRNA splicing, five in the case of PTEN and five in case of BRCA2 which were highly pathogenic in nature.