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References

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    et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).

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    et al. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat. Genet. 48, 758–767 (2016).

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    et al. Histological transformation and progression in follicular lymphoma: a clonal evolution study. PLoS Med. 13, e1002197 (2016).

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    et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155–160 (2014).

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Acknowledgements

We wish to acknowledge the generous long-term funding provided by the BC Cancer Foundation. The project was supported by a Canadian Cancer Society Research Institute Innovation grant to S.P.S. (702532), a Genome Canada/Genome BC Disruptive Innovation in Genomics grant to S.P.S. and C.N. (232SCG), and a Terry Fox Research Institute Program Project grant to S.P.S. (1021). S.P.S. is supported by the Canada Research Chairs program, a Canadian Institutes for Health Research Foundation Grant (FDN-143246), and is a Michael Smith Foundation for Health Research scholar. M.A.S. and A.M. are supported by NSERC CGS scholarships. A.R. is supported by a CIHR CGS scholarship.

Author information

Author notes

    • Maia A Smith
    •  & Cydney B Nielsen

    These authors contributed equally to this work.

Affiliations

  1. Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada.

    • Maia A Smith
  2. Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

    • Maia A Smith
    • , Cydney B Nielsen
    • , Fong Chun Chan
    • , Andrew McPherson
    • , Andrew Roth
    • , Hossein Farahani
    • , Daniel Machev
    • , Adi Steif
    •  & Sohrab P Shah
  3. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

    • Cydney B Nielsen
    •  & Sohrab P Shah

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Competing interests

S.S. is a founder and shareholder of Contextual Genomics Inc., a genomics-based molecular diagnostics company.

Corresponding author

Correspondence to Sohrab P Shah.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Methods and Supplementary Note 1

Excel files

  1. 1.

    Supplementary Table 1

    Clonal prevalences, clonal phylogeny, and mutations used to generate the TimeScape views of acute myeloid leukemia Patient UPN 933124 in Figure 1 and Supplementary Figure 2.

  2. 2.

    Supplementary Table 2

    Single cell phylogeny, single cell annotations, clonal phylogeny, and mutations used to generate the CellScape and TimeScape views of xenograft SA501 in Supplementary Figure 4.

  3. 3.

    Supplementary Table 3

    Clonal prevalences, clonal phylogeny, mutations, and pixel coordinates used to generate the MapScape view of prostate cancer Patient A21 in Figure 1, Supplementary Figures 5 and 6a-c.

  4. 4.

    Supplementary Table 4

    Clonal prevalences, clonal phylogeny, mutations, and pixel coordinates used to generate the MapScape view of ovarian cancer patient 1 in Supplementary Figure 6d-g.

  5. 5.

    Supplementary Table 5

    Clonal prevalences, clonal phylogeny, mutations, and pixel coordinates used to generate MapScape and TimeScape views of ovarian cancer patient 7 in Supplementary Figure 7.

  6. 6.

    Supplementary Table 6

    Clonal prevalences and clonal phylogeny used to generate the TimeScape views of the transformed follicular lymphoma patients in Supplementary Figure 3.

  7. 7.

    Supplementary Table 7

    Single cell phylogeny, single cell annotations, and copy number alternations used to generate the CellScape view of a triple-negative breast cancer patient in Figure 1.

  8. 8.

    Supplementary Table 8

    Descriptions of CellScape parameters and input formats.

  9. 9.

    Supplementary Table 9

    Descriptions of TimeScape parameters and input formats.

  10. 10.

    Supplementary Table 10

    Descriptions of MapScape parameters and input formats.

Zip files

  1. 1.

    Supplementary Software

    Code for the E-scape suite (CellScape, TimeScape, and MapScape).

About this article

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DOI

https://doi.org/10.1038/nmeth.4303

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