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Reproducibility of variant calls in replicate next generation sequencing experiments

ABSTRACT: In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. Seventeen breast cancer samples were sequenced in duplicate (n=14) or triplicate (n=3) to assess concordance of all calls and single nucleotide variant (SNV) calls.

PROVIDER: EGAS00001000826 | EGA |

REPOSITORIES: EGA

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Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments.

Qi Yuan Y Liu Xiuping X Liu Chang-Gong CG Wang Bailing B Hess Kenneth R KR Symmans W Fraser WF Shi Weiwei W Pusztai Lajos L

PloS one 20150702 7

Nucleotide alterations detected by next generation sequencing are not always true biological changes but could represent sequencing errors. Even highly accurate methods can yield substantial error rates when applied to millions of nucleotides. In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.2 Mb) using the SOLiD v4 platform. ...[more]

PMID: 26136146

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