Document Details
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Document Type |
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Article In Journal |
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Document Title |
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In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data |
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Document Language |
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English |
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Abstract |
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Four popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka
and MuTect2) were carefully evaluated on the real whole exome sequencing (WES, depth of ~50X)
and ultra-deep targeted sequencing (UDT-Seq, depth of ~370X) data. The four tools returned poor
consensus on candidates (only 20% of calls were with multiple hits by the callers). For both WES and
UDT-Seq, MuTect2 and Strelka obtained the largest proportion of COSMIC entries as well as the lowest
rate of dbSNP presence and high-alternative-alleles-in-control calls, demonstrating their superior
sensitivity and accuracy. Combining different callers does increase reliability of candidates, but narrows
the list down to very limited range of tumor read depth and variant allele frequency. Calling SNV on
UDT-Seq data, which were of much higher read-depth, discovered additional true-positive variations,
despite an even more tremendous growth in false positive predictions. Our findings not only provide
valuable benchmark for state-of-the-art SNV calling methods, but also shed light on the access to more
accurate SNV identification in the future. |
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ISSN |
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2045-2322 |
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Journal Name |
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Scientific reports |
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Volume |
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6 |
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Issue Number |
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1 |
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Publishing Year |
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1437 AH
2016 AD |
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Article Type |
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Article |
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Added Date |
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Tuesday, July 18, 2017 |
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Researchers
| Lei Cai | Cai, Lei | Researcher | Doctorate | |
| Wei Yuan | Yuan, Wei | Researcher | Doctorate | |
| Zhou Zhang | Zhang, Zhou | Researcher | Doctorate | |
| Lin He | He, Lin | Researcher | Doctorate | |
| Kuo-Chen Chou | Chou, Kuo-Chen | Researcher | Doctorate | lcai@sjtu.edu.cn |
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