The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
Open accessAbstract
The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.
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Cites
Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (2003) · doi:10.1201/9780429258480 · Cited by 27,276
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774
Nowell, P. C. (1976) · Science · doi:10.1126/science.959840 · Cited by 6,471
Greaves, M., & Maley, C. C. (2012) · Nature · doi:10.1038/nature10762 · Cited by 3,162
Distant metastasis occurs late during the genetic evolution of pancreatic cancer
Yachida, S., Jones, S., Bozic, I., Antal, T., Leary, R., Fu, B., Kamiyama, M., Hruban, R. H., Eshleman, J. R., Nowak, M. A., et al. (2010) · Nature · doi:10.1038/nature09515 · Cited by 2,502
Recurring mutations found by sequencing an acute myeloid leukemia genome
Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0903840 · Cited by 2,219
Self-citationWard, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.01.020 · Cited by 2,020
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., et al. (2012) · Nature · doi:10.1038/nature10738 · Cited by 1,993
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., et al. (2012) · Nature · doi:10.1038/nature10933 · Cited by 1,967
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Cited by
Clonal heterogeneity and tumor evolution: past, present, and the future
McGranahan, N., & Swanton, C. (2017) · Cell · doi:10.1016/j.cell.2017.01.018 · Cited by 2,840
Roh, W., Chen, P.-L., Reuben, A., Spencer, C. N., Prieto, P. A., Miller, J. P., Gopalakrishnan, V., Wang, F., Cooper, Z. A., Reddy, S. M., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah3560 · Cited by 859
Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing
Rasche, L., Chavan, S. S., Stephens, O. W., Patel, P. H., Tytarenko, R., Ashby, C., Bauer, M., Stein, C., Deshpande, S., Wardell, C., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00296-y · Cited by 417
Kim, H., Zheng, S., Amini, S. S., Virk, S. M., Mikkelsen, T., Brat, D. J., Grimsby, J., Sougnez, C., Muller, F., Hu, J., et al. (2015) · Genome Research · doi:10.1101/gr.180612.114 · Cited by 411
Gillis, N. K., Ball, M., Zhang, Q., Ma, Z., Zhao, Y., Yoder, S. J., Balasis, M. E., Mesa, T. E., Sallman, D. A., Lancet, J. E., et al. (2017) · The Lancet Oncology · doi:10.1016/s1470-2045(16)30627-1 · Cited by 317
Metadata
- Authors
- Miller, C. A., White, B. S., Dees, N. D., Griffith, M., Welch, J. S., Griffith, O. L., Vij, R., Tomasson, M. H., Graubert, T. A., Walter, M. J., Ellis, M. J., Schierding, W., DiPersio, J. F., Ley, T. J., Mardis, E. R., Wilson, R. K., & Ding, L.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-08-07
- Volume
- 10
- Issue
- 8
- Pages
- e1003665
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W1979115864
- Cited by
- 454
- References
- 16
- FWCI
- 11.37
- Type
- journal article
- Language
- en
- Open access
- gold
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- Miller, C. A., White, B. S., Dees, N. D., Griffith, M., Welch, J. S., Griffith, O. L., Vij, R., Tomasson, M. H., Graubert, T. A., Walter, M. J., Ellis, M. J., Schierding, W., DiPersio, J. F., Ley, T. J., Mardis, E. R., Wilson, R. K., & Ding, L. (2014). SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1003665
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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.
