Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 34015811.
- Also identified by DOI 10.1093/bib/bbab186.
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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.
Medical subject headings
- Artifacts
- Cytological Techniques
- High-Throughput Nucleotide Sequencing
- Models, Statistical
- Sequence Analysis, DNA
- Templates, Genetic