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Identification of single nucleotide variants using position-specific error estimation in deep sequencing data.

Journal article
Authors Dimitrios Kleftogiannis
Marco Punta
Anuradha Jayaram
Shahneen Sandhu
Stephen Q Wong
Delila Gasi Tandefelt
Vincenza Conteduca
Daniel Wetterskog
Gerhardt Attard
Stefano Lise
Published in BMC medical genomics
Volume 12
Issue 1
ISSN 1755-8794
Publication year 2019
Published at Sahlgrenska Cancer Center
Institute of Clinical Sciences, Department of Urology
Language en
Links dx.doi.org/10.1186/s12920-019-0557-...
www.ncbi.nlm.nih.gov/entrez/query.f...
Keywords Cancer genomics, Deep sequencing, Error correction, Ion torrent, Liquid biopsies, Next generation sequencing (NGS), Targeted sequencing, Variant calling
Subject categories Cancer and Oncology, Bioinformatics (Computational Biology)

Abstract

Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs).To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection.Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments.AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve .

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