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This article is part of a special issue on exome sequencing.

Open Access Highly Accessed Research

A comparative analysis of exome capture

Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer and W Richard McCombie*

  • * Corresponding author: W Richard McCombie mccombie@cshl.edu

  • † Equal contributors

Author Affiliations

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA

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Genome Biology 2011, 12:R97  doi:10.1186/gb-2011-12-9-r97

Published: 29 September 2011

Abstract

Background

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. 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.

Results

Each 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.

Conclusions

Commercial 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.