BRCA Gene Mutations in dbSNP: A Visual Exploration of Genetic Variants

TL;DR

This study provides a comprehensive visual analysis of BRCA gene mutations in dbSNP, revealing mutation distribution, clinical significance, and mutation hotspots, enhancing understanding of genetic variations related to cancer risk.

Contribution

It offers a detailed computational exploration of BRCA mutations in dbSNP, highlighting mutation patterns, significance, and distribution that were previously under-characterized.

Findings

Most BRCA mutations in dbSNP have unknown clinical significance.

Exon 11 contains most mutations but mutation rates per base are similar across exons.

Pathogenic intronic mutations are near splicing regions.

Abstract

BRCA genes, comprising BRCA1 and BRCA2 play indispensable roles in preserving genomic stability and facilitating DNA repair mechanisms. The presence of germline mutations in these genes has been associated with increased susceptibility to various cancers, notably breast and ovarian cancers. Recent advancements in cost-effective sequencing technologies have revolutionized the landscape of cancer genomics, leading to a notable rise in the number of sequenced cancer patient genomes, enabling large-scale computational studies. In this study, we delve into the BRCA mutations in the dbSNP, housing an extensive repository of 41,177 and 44,205 genetic mutations for BRCA1 and BRCA2, respectively. Employing meticulous computational analysis from an umbrella perspective, our research unveils intriguing findings pertaining to a number of critical aspects. Namely, we discover that the majority of BRCA mutations in dbSNP have unknown clinical significance. We find that, although exon 11 for both genes contains the majority of the mutations and may seem as if it is a mutation hot spot, upon analyzing mutations per base pair, we find that all exons exhibit similar levels of mutations. Investigating mutations within introns, while we observe that the recorded mutations are generally uniformly distributed, almost all of the pathogenic mutations in introns are located close to splicing regions (at the beginning or the end). In addition to the findings mentioned earlier, we have also made other discoveries concerning mutation types and the level of confidence in observations within the dbSNP database.