Refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples.

ABSTRACT:

Objective

RNA-seq delivers valuable insights both to transcriptional patterns and mutational landscapes for transcribed genes. However, as tumour cell lines frequently lack their matched-normal counterpart, variant calling without the paired normal sample is still challenging. In order to exclude variants of common genetic variation without a matched-normal control, filtering strategies need to be developed to identify tumour relevant variants in cell lines.

Results

Here, variants of 29 breast cancer cell lines were called on RNA-seq data via HaplotypeCaller. Low read depth sites, RNA-edit sites, and low complexity regions in coding regions were excluded. Common variants were filtered using 1000 genomes, gnomAD, and dbSNP data. Starting from hundred thousands of single nucle

SUBMITTER: Eberth S 

PROVIDER: S-EPMC11829467 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature