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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., & Reich, D. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0624 · Cited by 572
Wagle, N., Berger, M. F., Davis, M. J., Blumenstiel, B., DeFelice, M., Pochanard, P., Ducar, M., Van Hummelen, P., MacConaill, L. E., Hahn, W. C., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0184 · Cited by 533
Lu, R., Neff, N. F., Quake, S. R., & Weissman, I. L. (2011) · Nature Biotechnology · doi:10.1038/nbt.1977 · Cited by 451
Statistical Design and Analysis of RNA Sequencing Data
Auer, P. L., & Doerge, R. W. (2010) · Genetics · doi:10.1534/genetics.110.114983 · Cited by 393
Integrative analysis of the melanoma transcriptome
Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., et al. (2010) · Genome Research · doi:10.1101/gr.103697.109 · Cited by 305
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
Lister, R., Gregory, B. D., & Ecker, J. R. (2009) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.11.004 · Cited by 274
Characterization of genetic sequence variation of 58 STR loci in four major population groups
Novroski, N. M. M., King, J. L., Churchill, J. D., Seah, L. H., & Budowle, B. (2016) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2016.09.007 · Cited by 157
Krueger, F., Andrews, S. R., & Osborne, C. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016607 · Cited by 102
Management of High-Throughput DNA Sequencing Projects: Alpheus
Andrew F, N. A. (2008) · Journal of Computer Science & Systems Biology · doi:10.4172/jcsb.1000013 · Cited by 75
Huentelman, M. J., Muppana, L., Corneveaux, J. J., Dinu, V., Pruzin, J. J., Reiman, R., Borish, C. N., De Both, M., Ahmed, A., Todorov, A., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0135076 · Cited by 52
Self-citation
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
