A comparative analysis of exome capture

Jennifer S Parla,Mona S Spector,W Richard Mccombie,Ivan Iossifov,Melissa Kramer,Ian Grabill

doi:10.1186/gb-2011-12-9-r97

Abstract

BackgroundHuman exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. We rigorously evaluated the capabilities of two solution exome capture kits. These analyses help clarify the strengths and limitations of those data as well as systematically identify variables that should be considered in the use of those data.ResultsEach exome kit performed well at capturing the targets they were designed to capture, which mainly corresponds to the consensus coding sequences (CCDS) annotations of the human genome. In addition, based on their respective targets, each capture kit coupled with high coverage Illumina sequencing produced highly accurate nucleotide calls. However, other databases, such as the Reference Sequence collection (RefSeq), define the exome more broadly, and so not surprisingly, the exome kits did not capture these additional regions.ConclusionsCommercial exome capture kits provide a very efficient way to sequence select areas of the genome at very high accuracy. Here we provide the data to help guide critical analyses of sequencing data derived from these products.

Highlights

Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases
The results show that the commercial capture methods are roughly comparable to each other and capture most of the human exons that are targeted by their probe sets (as described by Consensus Coding Sequences (CCDS) annotations)
The limitations of the two commercial exome capture kits we evaluated are even more apparent when analyzed in the context of coverage of the more comprehensive Reference Sequence collection (RefSeq) annotations [8,9], which are efficiently covered by whole genome sequencing

Summary

Introduction

Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. The release of commercial capture reagents from both NimbleGen and Agilent that target human exons for resequencing (exome sequencing) has greatly accelerated the utilization of this strategy. As with many competitive commercial products, there have been updates and improvements to the original versions of the NimbleGen and Agilent solution exome capture kits that include a shift to the latest human genome assembly (hg; GRCh37) and coverage of more coding regions of the human genome. We analyzed two version 1 exome capture products and evaluated their performance and compared them against the scope of whole genome sequencing to provide the community with the information necessary to evaluate their own and others’ published data. Our investigation of factors that influence capture performance should be applicable to the solution capture process irrespective of the actual genomic regions targeted

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Discussion

Conclusion