Performance comparison of four types of target enrichment baits for exome DNA sequencing

Hereditas

Research

Yongyong Shi¹  Zhuo Wang¹  Xiaoqi Li¹  Mancang Zhang¹  Juan Zhou¹  Dun Pan¹ 

[1] Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, 200030, Shanghai, People’s Republic of China;

关键词: Next-generation sequencing;    Exome capture efficiency;    Bait type;    Coverage;    GC bias;    SNPs and Indels detection;   

DOI  :  10.1186/s41065-021-00171-3

 received in 2020-11-23, accepted in 2021-01-19,  发布年份 2021

来源: Springer

【 摘 要 】

BackgroundNext-generation sequencing technology is developing rapidly and target capture sequencing has become an important technique. Several different platforms for library preparation and target capture with different bait types respectively are commercially available. Here we compare the performance of the four platforms with different bait types to find out their advantages and limitations. The purpose of this study is to help investigators and clinicians select the appropriate platform for their particular application and lay the foundation for the development of a better target capture platform for next-generation sequencing.ResultsWe formulate capture efficiency as a novel parameter that can be used to better evaluations of specificity and coverage depth among the different capture platforms. Target coverage, capture efficiency, GC bias, AT Dropout, sensitivity in single nucleotide polymorphisms, small insertions and deletions detection, and the feature of each platform were compared for low input samples. In general, all platforms perform well and small differences among them are revealed. In our results, RNA baits have stronger binding power than DNA baits, and with ultra deep sequencing, double stranded RNA baits perform better than single stranded RNA baits in all aspects. DNA baits got better performance in the region with high GC content and RNA baits got lower AT dropout suggesting that the binding power is different between DNA and RNA baits to genome regions with different characteristics.ConclusionsThe platforms with double stranded RNA baits have the most balanced capture performance. Our results show the key differences in performance among the four updated platforms with four different bait types. The better performance of double stranded RNA bait with ultra deep sequencing suggests that it may improve the sensitivity of ultra low frequent mutation detection. In addition, we further propose that the mixed baits of double stranded RNA and single stranded DNA may improve target capture performance.

【 授权许可】

CC BY   
© The Author(s) 2021. corrected publication 2023

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