Abstract
BackgroundRecent 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.ResultsEach 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-449) contains supplementary material, which is available to authorized users.
Highlights
Recent developments in deep sequencing technologies are significantly impacting medical research
Asan et al compared NimbleGen Sequence Capture Array, NimbleGen SeqCap EZ, and Agilent SureSelect, and showed that all three technologies achieved a similar accuracy of genotype assignment and single nucleotide polymorphism (SNP) detection, and had similar levels of reproducibility and GC bias [12]
At all the read counts, a disturbing fact was that very few indels were common across the four technologies, especially on coding sequence database (CCDS), Ensembl and RefSeq regions
Summary
Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. Asan et al compared NimbleGen Sequence Capture Array, NimbleGen SeqCap EZ, and Agilent SureSelect, and showed that all three technologies achieved a similar accuracy of genotype assignment and single nucleotide polymorphism (SNP) detection, and had similar levels of reproducibility and GC bias [12]. In another exome capture comparison study, Parla et al showed that both NimbleGen SeqCap EZ Exome Library SR and Agilent SureSelect All Exon were similar to each other in performance, and able to capture most of the human exons targeted by their probe sets. They failed to cover a noteworthy percentage of the exons in the consensus coding sequence database (CCDS) [13]
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