The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Identification of genetic variants using bar-coded multiplexed sequencing
Open accessAbstract
We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8–90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.
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Cites
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Direct selection of human genomic loci by microarray hybridization
Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., Richmond, T. A., Middle, C. M., Rodesch, M. J., Packard, C. J., et al. (2007) · Nature Methods · doi:10.1038/nmeth1111 · Cited by 681
Cited by
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
Kircher, M., Sawyer, S., & Meyer, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr771 · Cited by 1,106
“(7)], this strategy has several benefits.”
Detection and quantification of rare mutations with massively parallel sequencing
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105422108 · Cited by 1,144
Field guide to next‐generation DNA sequencers
GLENN, T. C. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.03024.x · Cited by 940
Genotyping‐by‐Sequencing for Plant Breeding and Genetics
Poland, J. A., & Rife, T. W. (2012) · The Plant Genome · doi:10.3835/plantgenome2012.05.0005 · Cited by 892
Evaluation of next generation sequencing platforms for population targeted sequencing studies
Harismendy, O., Ng, P. C., Strausberg, R. L., Wang, X., Stockwell, T. B., Beeson, K. Y., Schork, N. J., Murray, S. S., Topol, E. J., Levy, S., et al. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r32 · Cited by 614
Metadata
- Authors
- Craig, D. W., Pearson, J. V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J. J., Pawlowski, T. L., Laub, T., Nunn, G., Stephan, D. A., Homer, N., & Huentelman, M. J.
- Venue
- Nature Methods
- Published
- 2008-09-14
- Volume
- 5
- Issue
- 10
- Pages
- 887-893
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1986474467
- Cited by
- 300
- References
- 4
- FWCI
- 14.52
- Type
- journal article
- Language
- en
- Open access
- green
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- Craig, D. W., Pearson, J. V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J. J., Pawlowski, T. L., Laub, T., Nunn, G., Stephan, D. A., Homer, N., & Huentelman, M. J. (2008). Identification of genetic variants using bar-coded multiplexed sequencing. Nature Methods. https://doi.org/10.1038/nmeth.1251
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