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Systematic comparison of variant calling pipelines of target genome sequencing cross multiple next-generation sequencers

Targeted genomic sequencing (TS) greatly benefits precision oncology by rapidly detecting genetic variations with better accuracy and sensitivity owing to its high sequencing depth. Multiple sequencing platforms and variant calling tools are available for TS, making it excruciating for researchers to choose. In this study, we use two different capture reagenst (TSO500和TargetSeq One), choose 3 typical sample types (FFPE,cf DNA and cell line) and validated by 6 different platforms (GenoLab M,FASTASeq 300,SURFSeq 5000,NovaSeq 6000,NextSeq 550,MGISEQ 2000).

Four sequencing platforms returned highly concordant results, and considering the dissimilarity of variant calls across different pipelines for datasets from the same platform, we recommended an integration of multiple tools to improve variant calling sensitivity and accuracy for the cancer genome. In a word, both Illumina and GeneMind technologies can be used independently or together by public health laboratories performing tumor TS with highest sensitivity and precision in high-confidence variants calling.

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