Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts. Issue 6 (20th May 2021)

• Record Type: Journal Article
• Authors: Diossy, Miklos; Sztupinszki, Zsofia; Krzystanek, Marcin; Borcsok, Judit; Eklund, Aron C; Csabai, István; Pedersen, Anders Gorm; Szallasi, Zoltan
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 6(2021)
• Publication Date: 2021-05-20
• Subjects: filtering FFPE artifacts -- formalin fixation caused mutations -- somatic variant calling on FFPE samples; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbab186
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Formalin-fixed paraffin-embedded tissue, the most common tissue specimen stored in clinical practice, presents challenges in the analysis due to formalin-induced artifacts. Here, we present Strand Orientation Bias Detector (SOBDetector), a flexible computational platform compatible with all the common somatic SNV-calling pipelines, designed to assess the probability whether a given detected mutation is an artifact. The underlying predictor mechanism is based on the posterior distribution of a Bayesian logistic regression model trained on The Cancer Genome Atlas whole exomes. SOBDetector is a freely available cross-platform program, implemented in Java 1.8.