Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer.

ABSTRACT: Whole exome sequencing (WES), targeted gene panel sequencing and single nucleotide polymorphism (SNP) arrays are increasingly used for the identification of actionable alterations that are critical to cancer care. Here, we compared The Cancer Genome Atlas (TCGA) and the Genomics Evidence Neoplasia Information Exchange (GENIE) breast cancer genomic datasets (array and next generation sequencing (NGS) data) in detecting genomic alterations in clinically relevant genes. We performed an in silico analysis to determine the concordance in the frequencies of actionable mutations and copy number alterations/aberrations (CNAs) in the two most common breast cancer histologies, invasive lobular and invasive ductal carcinoma. We found that targeted sequencing identified a larger number of mutational h

SUBMITTER: Kaur P 

PROVIDER: S-EPMC6365517 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature