Whole Exome Analysis to Analyse the Mutational Profiles of Taiwanese Patients with Breast Cancer

The evolution that next sequencing technologies (NGS) and computational tools have witnessed led to the discovery of analyses such as whole-exome sequencing (WES). Exome sequencing is sophisticated, efficient and affordable for dismembering the genetic basis and traits of diseases. This technique accomplished many results that traditional gene discovery strategies failed to achieve. This study aims at combining algorithms for NGS analysis with a bioinformatic pipeline in order to detect single nucleotide polymorphisms (SNPs) and be able to delete/insert polymorphisms (InDel) within DNA sequences retrieved by using whole-exome sequencing. The pipeline was applied on public data of WES of breast cancer (BC) tissues from Taiwanese patients. A total of 892,314 variants were considered after filtering. The majority were SNPs (740,430) affecting protein sequence (56%), including 0.9% missense mutations. Seventeen genes with frequent variants were found including Nogo receptor 1(NGR1) (5.4%), Erb-B2 Receptor Tyrosine Kinase 4 (ERBB4) (4.1%), Tachykinin receptor 1 (TACR1) (2.5%), and Thyroid Peroxidase (TPO) (2%). These genes are known for their involvement in cancer. This study provides valuable insights into genomic variations and gene-specific variant frequencies and their relationship with BC.