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bioRxiv · 10.1101/386417

Strand Orientation Bias Detector (SOBDetector) to remove artifacts from sequencing data of formalin fixed samples

Diossy, M.·Sztupinszki, Z.·Krzystanek, M.·Pedersen, A. G.·Eklund, A. C.·Csabai, I.·Szallasi, Z.
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Abstract

Formalin-fixed paraffin-embedded (FFPE) tissue, the most common tissue specimen stored in clinical practice, presents challenges in the analysis due to formalin-induced artifacts. Here we present SOBDetector, that is designed to remove these artifacts from a list of variants, which were extracted from next-generation sequencing data, using the posterior predictive distribution of a Bayesian logistic regression model trained on TCGA whole exomes. Based on a concordance analysis, SOBDetector outperforms the currently publicly available FFPE-filtration techniques (Accuracy: 0.9 {+/-} 0.015, AUC = 0.96). SOBDetector is implemented in Java 1.8 and is freely available online.

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Diossy, M., Sztupinszki, Z., Krzystanek, M., Pedersen, A. G., Eklund, A. C., Csabai, I., Szallasi, Z.. 2018-08-07. Strand Orientation Bias Detector (SOBDetector) to remove artifacts from sequencing data of formalin fixed samples. https://doi.org/10.1101/386417

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