The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
Open accessAbstract
Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these methods: Molecular Inversion Probes (MIP), Solution Hybrid Selection (SHS), and Microarray-based Genomic Selection (MGS). Using HapMap DNA samples, we compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes (2.61 Mb). For sequence analysis, we developed and used a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG). All three capture methods were effective, but sensitivities (percentage of targeted bases associated with high-quality genotypes) varied for an equivalent amount of pass-filtered sequence: for example, 70% (MIP), 84% (SHS), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of >99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and >99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data.
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Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Self-citationGnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433
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
Self-citationMicrodroplet-based PCR enrichment for large-scale targeted sequencing
Tewhey, R., Warner, J. B., Nakano, M., Libby, B., Medkova, M., David, P. H., Kotsopoulos, S. K., Samuels, M. L., Hutchison, J. B., Larson, J. W., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1583 · Cited by 454
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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
NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program, Le Gallo, M., O'Hara, A. J., Rudd, M. L., Urick, M. E., Hansen, N. F., O'Neil, N. J., Price, J. C., Zhang, S., England, B. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2455 · Cited by 419
Self-citationZhou, Q., Lee, G.-S., Brady, J., Datta, S., Katan, M., Sheikh, A., Martins, M. S., Bunney, T. D., Santich, B. H., Moir, S., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.006 · Cited by 374
Metadata
- Authors
- Teer, J. K., Bonnycastle, L. L., Chines, P. S., Hansen, N. F., Aoyama, N., Swift, A. J., Abaan, H. O., Albert, T. J., Program, N. C. S., Margulies, E. H., Green, E. D., Collins, F. S., Mullikin, J. C., & Biesecker, L. G.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-09-01
- Volume
- 20
- Issue
- 10
- Pages
- 1420-1431
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2058140004
- Cited by
- 206
- References
- 4
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Teer, J. K., Bonnycastle, L. L., Chines, P. S., Hansen, N. F., Aoyama, N., Swift, A. J., Abaan, H. O., Albert, T. J., Program, N. C. S., Margulies, E. H., Green, E. D., Collins, F. S., Mullikin, J. C., & Biesecker, L. G. (2010). Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Research. https://doi.org/10.1101/gr.106716.110
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