Parla, J. S., Iossifov, I., Grabill, I., Spector, M. S., Kramer, M., McCombie, W. R. (September 2011) A comparative analysis of exome capture. Genome Biology, 12 (9). R97. ISSN 1474-7596
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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: | 29 September 2011 |
| Date Deposited: | 05 Feb 2013 22:02 |
| Last Modified: | 06 Nov 2015 21:21 |
| PMCID: | PMC3308060 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27188 |
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