ZygosityPredictor

Bioinform Adv. 2024 Feb 6;4(1):vbae017. doi: 10.1093/bioadv/vbae017. eCollection 2024.ABSTRACTSUMMARY: ZygosityPredictor provides functionality to evaluate how many copies of a gene are affected by mutations in next generation sequencing data. In cancer samples, the tool processes both somatic and germline mutations. In particular, ZygosityPredictor computes the number of affected copies for single nucleotide variants and small insertions and deletions (Indels). In addition, the tool integrates information at gene level via phasing of several variants and subsequent logic to derive how strongly a gene is affected by mutations and provides a measure of confidence. This information is of particular interest in precision oncology, e.g. when assessing whether unmutated copies of tumor-suppressor genes remain.AVAILABILITY AND IMPLEMENTATION: ZygosityPredictor was implemented as an R-package and is available via Bioconductor at https://bioconductor.org/packages/ZygosityPredictor. Detailed documentation is provided in the vignette including application to an example genome.PMID:38560552 | PMC:PMC10980564 | DOI:10.1093/bioadv/vbae017

Source: Adv Data - April 1, 2024 Category: Epidemiology Authors: Marco Rheinnecker Martina Fr öhlich Marc R übsam Nagarajan Paramasivam Christoph E Heilig Stefan Fr öhling Richard F Schlenk Barbara Hutter Daniel H übschmann Source Type: research