Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts

Brief Bioinform. 2021 Nov 5;22(6):bbab186. doi: 10.1093/bib/bbab186.

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.

Keywords: filtering FFPE artifacts; formalin fixation caused mutations; somatic variant calling on FFPE samples.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Artifacts*
  • Cytological Techniques / standards*
  • DNA, Neoplasm
  • Databases, Genetic
  • High-Throughput Nucleotide Sequencing / methods
  • High-Throughput Nucleotide Sequencing / standards*
  • Humans
  • Models, Statistical*
  • Mutation
  • Neoplasms / diagnosis
  • Neoplasms / genetics
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, DNA / standards*
  • Templates, Genetic*

Substances

  • DNA, Neoplasm