The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
High-resolution mapping of copy-number alterations with massively parallel sequencing
Open accessAbstract
Cancer results from somatic alterations in key genes, including point mutations, copy-number alterations and structural rearrangements. A powerful way to discover cancer-causing genes is to identify genomic regions that show recurrent copy-number alterations (gains and losses) in tumor genomes. Recent advances in sequencing technologies suggest that massively parallel sequencing may provide a feasible alternative to DNA microarrays for detecting copy-number alterations. Here we present: (i) a statistical analysis of the power to detect copy-number alterations of a given size; (ii) SegSeq, an algorithm to segment equal copy numbers from massively parallel sequence data; and (iii) analysis of experimental data from three matched pairs of tumor and normal cell lines. We show that a collection of ∼14 million aligned sequence reads from human cell lines has comparable power to detect events as the current generation of DNA microarrays and has over twofold better precision for localizing breakpoints (typically, to within ∼1 kilobase).
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Cites
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Self-citationMapping and sequencing of structural variation from eight human genomes
Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119
Copy-number variation and association studies of human disease
McCarroll, S. A., & Altshuler, D. M. (2007) · Nature Genetics · doi:10.1038/ng2080 · Cited by 622
Array comparative genomic hybridization and its applications in cancer
Pinkel, D., & Albertson, D. G. (2005) · Nature Genetics · doi:10.1038/ng1569 · Cited by 585
Cited by
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,905
Tumour evolution inferred by single-cell sequencing
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D., et al. (2011) · Nature · doi:10.1038/nature09807 · Cited by 2,598
Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
van de Wetering, M., Francies, H. E., Francis, J. M., Bounova, G., Iorio, F., Pronk, A., van Houdt, W., van Gorp, J., Taylor-Weiner, A., Kester, L., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.053 · Cited by 2,408
Self-citationBullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-94 · Cited by 1,680
“These high-throughput sequencing technologies have already been applied to monitor genome-wide transcription levels (mRNA-Seq), DNA-protein interactions (ChIP-Seq), chromatin structure, and DNA methylation [ 1-9 ].”
MethodInfluentialGenome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630
Metadata
- Authors
- Chiang, D. Y., Getz, G., Jaffe, D. B., O'Kelly, M. J. T., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M., & Lander, E. S.
- Venue
- Nature Methods
- Published
- 2008-11-30
- Volume
- 6
- Issue
- 1
- Pages
- 99-103
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2090144921
- Cited by
- 510
- References
- 5
- FWCI
- 20.92
- Type
- journal article
- Language
- en
- Open access
- green
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- Chiang, D. Y., Getz, G., Jaffe, D. B., O'Kelly, M. J. T., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M., & Lander, E. S. (2009). High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods. https://doi.org/10.1038/nmeth.1276
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