ArticleBMC medical genomics2019
Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 17 citations in OpenAlex.
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- Pan-cancer discovery of somatic mutations from RNA sequencing data.Communications biology · 2024Article
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- Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application.Frontiers in genetics · 2022Article
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- Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
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7 authors at 2 institutions in 3 countries.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe application of next-generation sequencing in cancer has revealed the genomic landscape of many tumour types and is nowadays routinely used in research and clinical settings. Multiple algorithms have been developed to detect somatic variation from sequencing data using either paired tumour-blood or tumour-only samples. Most of these methods have been developed and evaluated for the identification of somatic variation using Illumina sequencing datasets of moderate coverage. However, a comprehensive evaluation of somatic variant detection algorithms on Ion Torrent targeted deep sequencing data has not been performed.
methodsWe have applied three somatic detection algorithms, Torrent Variant Caller, MuTect2 and VarScan2, on a large cohort of ovarian cancer patients comprising of 208 paired tumour-blood samples and 253 tumour-only samples sequenced deeply on Ion Torrent Proton platform across 330 amplicons. Subsequently, the concordance and performance of the three somatic variant callers were assessed.
resultsWe have observed low concordance across the algorithms with only 0.5% of SNV and 0.02% of INDEL calls in common across all three methods. The intersection of all methods showed better performance when assessed using correlation with known mutational signatures, overlap with COSMIC variation and by examining the variant characteristics. The Torrent Variant Caller also performed well with the advantage of not eliminating a high number of variants that could lead to high type II error.
conclusionsOur results suggest that caution should be taken when applying state-of-the-art somatic variant algorithms to Ion Torrent targeted deep sequencing data. Better quality control procedures and strategies that combine results from multiple methods should ensure that higher accuracy is achieved. This is essential to ensure that results from bioinformatics pipelines using Ion Torrent deep sequencing can be robustly applied in cancer research and in the clinic.
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