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Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

Abstract

Intratumor heterogeneity (ITH) drives neoplastic progression and therapeutic resistance. We used the bioinformatics tools 'expanding ploidy and allele frequency on nested subpopulations' (EXPANDS) and PyClone to detect clones that are present at a ≥10% frequency in 1,165 exome sequences from tumors in The Cancer Genome Atlas. 86% of tumors across 12 cancer types had at least two clones. ITH in the morphology of nuclei was associated with genetic ITH (Spearman's correlation coefficient, ρ = 0.24–0.41; P < 0.001). Mutation of a driver gene that typically appears in smaller clones was a survival risk factor (hazard ratio (HR) = 2.15, 95% confidence interval (CI): 1.71–2.69). The risk of mortality also increased when >2 clones coexisted in the same tumor sample (HR = 1.49, 95% CI: 1.20–1.87). In two independent data sets, copy-number alterations affecting either <25% or >75% of a tumor's genome predicted reduced risk (HR = 0.15, 95% CI: 0.08–0.29). Mortality risk also declined when >4 clones coexisted in the sample, suggesting a trade-off between the costs and benefits of genomic instability. ITH and genomic instability thus have the potential to be useful measures that can universally be applied to all cancers.

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Figure 1: Tumor metagenomes and subclonal genomes in 12 tumor types from TCGA.
Figure 2: Intratumor genetic heterogeneity in 12 tumor types.
Figure 3: Association of driver-gene mutations with clone size and clone number.
Figure 4: Intratumor nuclear diversity accompanies intratumor genetic diversity.
Figure 5: Clone number and CNV burden appear to be universal prognostic biomarkers.

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Acknowledgements

This work was supported in part by the US National Institutes of Health (NIH) (grant no. P01 CA91955 (C.C.M.), R01 CA149566 (C.C.M.), R01 CA170595 (C.C.M.), R01 CA185138 (C.C.M.), R01 CA140657 (C.C.M.), P01 HG000205 (H.P.J.), U01CA151920 (H.P.J.), U01CA17629901 (H.P.J.), R01 HG006137 (H.P.J.), R01 CA164746 (C.P.), R01 NS08061904 (C.P.) and R01 HG006137 (L.C.X.)). Additional support to C.C.M. came from the Breast Cancer Research Program Breakthrough Award (award no. BC132057), a Congressionally Directed Medical Research Program (CDMRP). Additional support to H.P.J. came from the Doris Duke Clinical Foundation Clinical Scientist Development Award, a Research Scholar Grant from the American Cancer Society (award no. RSG-13-297-01-TBG) and a Howard Hughes Medical Institute Early Career Grant. N.A. was supported by awards from the Don and Ruth Seiler Fund and the National Cancer Institute (NCI) Cancer Target Discovery and Development (CTDD) Consortium (grant no. U01CA17629901). T.A.G. was supported by the Higher Education Founding Council for England (HEFCE). We are grateful to W. Mewes for advice on the presentation of our results and for insightful discussions about their implications; S.T. Jensen for advice on statistical data analysis; and C.W. Turck and M. Oft for reviewing the manuscript. The results presented here are in part based upon data generated by TCGA Research Network. We thank Hoffmann H. (University of Bonn, Germany) for the availability of the MATLAB function 'violin' that we used to generate the violin plots for the distribution of clone numbers and clone sizes.

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N.A. developed analytic methods, analyzed data and wrote the manuscript. T.A.G. developed analytic methods, gave technical support and conceptual advice, and wrote the manuscript. M.J. analyzed the histopathology images and provided advice on data visualization and interpretation. L.C.X. provided advice on the choice of statistical methods and the design of the statistical analysis. C.A.A. gave technical support and conceptual advice. C.C.M. developed analytic methods, wrote the manuscript and supervised the project. H.P.J. wrote the manuscript and supervised the project. C.P. supervised the project. All authors edited the manuscript.

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Correspondence to Hanlee P Ji or Carlo C Maley.

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Andor, N., Graham, T., Jansen, M. et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med 22, 105–113 (2016). https://doi.org/10.1038/nm.3984

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