A comparative analysis of exome capture

Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21958622
DOI: 10.1186/gb-2011-12-9-r97

Abstract

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.

Item Type: Paper
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > assays
Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL Cancer Center Shared Resources > DNA Sequencing Service
CSHL Post Doctoral Fellows
CSHL labs > Iossifov lab
CSHL labs > McCombie lab
Stanley Institute for Cognitive Genomics
Depositing User: Matt Covey
Date Deposited: 05 Feb 2013 22:02
Last Modified: 06 Nov 2015 21:21
PMCID: PMC3308060
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27188

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