Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- May 20, 2021
- Source ID
- 10.1093/bib/bbab186
Entities
People
- Anders Gorm Pedersen
- Aron C Eklund
- István Csabai
- Judit Börcsök
- Marcin Krzystanek
- Miklos Diossy
- Zoltán Szállási
- Zsófia Sztupinszki
Organizations
- Danish Cancer Society
- Danish Council for Independent Research | Medical Sciences
- Eötvös Loránd University
- Harvard Medical School
- Novo Nordisk Fonden
- The Breast Cancer Research Foundation
- University of Copenhagen
- Velux Stiftung