Performance comparison of four exome capture systems for deep sequencing

BMC Genomics

Leonardo A Meza-Zepeda²  Ola Myklebost¹  Eivind Hovig³  Jinchang Sun²  Daniel Vodák³  Mohammed-Amin Madoui²  Susanne Lorenz²  Chandra Sekhar Reddy Chilamakuri¹ 

[1]Norwegian Cancer Genomics Consortium, Oslo, Norway

[2]Genomics Core Facility, Oslo University Hospital, Oslo, Norway

[3]Department of Informatics, University of Oslo, Oslo, Norway

关键词: Indel;    Single nucleotide variant;    GC bias;    Enrichment efficiency;    Coverage efficiency;    Next-generation sequencing;    Exome capture technology;   

Others  :  1216642
DOI  :  10.1186/1471-2164-15-449

 received in 2013-11-15, accepted in 2014-05-27,  发布年份 2014

【 摘 要 】

Background

Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen’s SeqCap EZ v3.0, Agilent’s SureSelect v4.0, Illumina’s TruSeq Exome, and Illumina’s Nextera Exome, all applied to the same human tumor DNA sample.

Results

Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content.

Conclusions

We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.

【 授权许可】

   
2014 Chilamakuri et al.; licensee BioMed Central Ltd.

【 图 表 】

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