PipeIT2: A tumor-only somatic variant calling workflow for molecular diagnostic Ion Torrent sequencing data
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Date
2023-03
Publication Type
Journal Article
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Abstract
Precision oncology relies on the accurate identification of somatic mutations in cancer patients. While the sequencing of the tumoral tissue is frequently part of routine clinical care, the healthy counterparts are rarely sequenced. We previously published PipeIT, a somatic variant calling workflow specific for Ion Torrent sequencing data enclosed in a Singularity container. PipeIT combines user-friendly execution, reproducibility and reliable mutation identification, but relies on matched germline sequencing data to exclude germline variants. Expanding on the original PipeIT, here we describe PipeIT2 to address the clinical need to define somatic mutations in the absence of germline control. We show that PipeIT2 achieves a > 95% recall for variants with variant allele fraction >10%, reliably detects driver and actionable mutations and filters out most of the germline mutations and sequencing artifacts. With its performance, reproducibility, and ease of execution, PipeIT2 is a valuable addition to molecular diagnostics laboratories.
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published
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Journal / series
Volume
115 (2)
Pages / Article No.
110587
Publisher
Elsevier
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Software
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Subject
Ion torrent; Somatic mutations; Variant calling; Next-generation sequencing; Cancer genomics; Molecular diagnostics; Singularity
Organisational unit
09568 - Rätsch, Gunnar / Rätsch, Gunnar