The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
The evolution of tumour phylogenetics: principles and practice
Open accessAbstract
Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies. We survey the range of methods and tools available to the researcher, their key applications, and the various unsolved problems, closing with a perspective on the prospects and broader implications of this field.
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
Signatures of mutational processes in human cancer
Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660
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 · cited 2×
“…beyond the theoretical evolutionary model of Nowell 2 to reveal the enormous complexity of the actual processes of tumour evolution 14,20,26,171 , and to uncover the hetero geneity of those processes both patient to patient 101,110,172 and lin eage to lineage in a single patient 3,8,21,40,73,145 .”
BackgroundNowell, P. C. (1976) · Science · doi:10.1126/science.959840 · Cited by 6,471
Genetic instabilities in human cancers
Lengauer, C., Kinzler, K. W., & Vogelstein, B. (1998) · Nature · doi:10.1038/25292 · Cited by 4,168 · cited 1×
“…as CNVs violate the model assumption that changes in distinct vari ant regions accumulate independently; instead, CNVs accumulate at multiple scales, from localized genescale variants to variation at the scale of large chromosome segments, whole chromosomes or even wholegenome ploidy 17,74,159 .”
BackgroundGreaves, M., & Maley, C. C. (2012) · Nature · doi:10.1038/nature10762 · Cited by 3,162
Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade
McGranahan, N., Furness, A. J. S., Rosenthal, R., Ramskov, S., Lyngaa, R., Saini, S. K., Jamal-Hanjani, M., Wilson, G. A., Birkbak, N. J., Hiley, C. T., et al. (2016) · Science · doi:10.1126/science.aaf1490 · Cited by 3,065
Massive genomic rearrangement acquired in a single catastrophic event during cancer development
Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., Pleasance, E. D., Lau, K. W., Beare, D., Stebbings, L. A., et al. (2011) · Cell · doi:10.1016/j.cell.2010.11.055 · Cited by 2,414
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
High burden and pervasive positive selection of somatic mutations in normal human skin
Martincorena, I., Roshan, A., Gerstung, M., Ellis, P., Van Loo, P., McLaren, S., Wedge, D. C., Fullam, A., Alexandrov, L. B., Tubio, J. M., et al. (2015) · Science · doi:10.1126/science.aaa6806 · Cited by 1,770
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma
Johnson, B. E., Mazor, T., Hong, C., Barnes, M., Aihara, K., McLean, C. Y., Fouse, S. D., Yamamoto, S., Ueda, H., Tatsuno, K., et al. (2014) · Science · doi:10.1126/science.1239947 · Cited by 1,362
Cited by
Tumour heterogeneity and metastasis at single-cell resolution
Lawson, D. A., Kessenbrock, K., Davis, R. T., Pervolarakis, N., & Werb, Z. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0236-7 · Cited by 606
Quantitative evidence for early metastatic seeding in colorectal cancer
Hu, Z., Ding, J., Ma, Z., Sun, R., Seoane, J. A., Scott Shaffer, J., Suarez, C. J., Berghoff, A. S., Cremolini, C., Falcone, A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0423-x · Cited by 490
Classifying the evolutionary and ecological features of neoplasms
Maley, C. C., Aktipis, A., Graham, T. A., Sottoriva, A., Boddy, A. M., Janiszewska, M., Silva, A. S., Gerlinger, M., Yuan, Y., Pienta, K. J., et al. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.69 · Cited by 423
Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
Yang, D., Jones, M. G., Naranjo, S., Rideout, W. M., Min, K. H. (., Ho, R., Wu, W., Replogle, J. M., Page, J. L., Quinn, J. J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.015 · Cited by 334
Intratumor and Intertumor Heterogeneity in Melanoma
Grzywa, T. M., Paskal, W., & Włodarski, P. K. (2017) · Translational Oncology · doi:10.1016/j.tranon.2017.09.007 · Cited by 299
Metadata
- Authors
- Schwartz, R., & Schäffer, A. A.
- Venue
- Nature Reviews Genetics
- Published
- 2017-02-13
- Volume
- 18
- Issue
- 4
- Pages
- 213-229
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W2588969809
- Cited by
- 318
- References
- 21
- FWCI
- 3.59
- 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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The evolution of tumour phylogenetics: principles and practice. https://app.cochat.ai/papers/10.1038/nrg.2016.170
- The paper
- Schwartz, R., & Schäffer, A. A. (2017). The evolution of tumour phylogenetics: principles and practice. Nature Reviews Genetics. https://doi.org/10.1038/nrg.2016.170
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.
