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Interactive analysis and assessment of single-cell copy-number variations

Nature Methods volume 12, pages 10581060 (2015) | Download Citation

Abstract

We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

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Acknowledgements

We thank N. Navin and P. Andrews for their helpful discussions and for assisting with data access. The project was supported in part by the US National Institutes of Health (award R01-HG006677 to M.C.S.), the US National Science Foundation (DBI-1350041 to M.C.S.), the Starr Cancer Consortium (I7-A723 to G.S.A.), the Breast Cancer Research Foundation (BCRF) (to M.W. and J.H.), the Simons Foundation, Simons Center for Quantitative Biology (SFARI award number 235988 to M.W.), the Susan G. Komen Foundation (llR13265578 to J.H.), the Prostate Cancer Foundation (Challenge Award to J.H.), the Cold Spring Harbor Laboratory (CSHL) Cancer Center (Support Grant 5P30CA045508) and the Watson School of Biological Sciences at CSHL through a training grant (5T32GM065094) from the US National Institutes of Health.

Author information

Author notes

    • Timour Baslan

    Present address: Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Tyler Garvin
    •  & Robert Aboukhalil

    These authors contributed equally to this work.

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Tyler Garvin
    • , Robert Aboukhalil
    • , Jude Kendall
    • , Timour Baslan
    • , Gurinder S Atwal
    • , James Hicks
    • , Michael Wigler
    •  & Michael C Schatz
  2. Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York, USA.

    • Timour Baslan

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Contributions

T.G. and R.A. developed the software and conducted the computational experiments. M.C.S., M.W., J.H. and G.S.A. designed the experiments. T.B. and J.K. assisted with the analysis and helped design the experiments. All of the authors wrote and edited the manuscript. All of the authors read and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael C Schatz.

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    Supplementary Text and Figures

    Supplementary Figures 1–13, Supplementary Tables 1–3 and Supplementary Note

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    Supplementary Software

    Gingko software

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DOI

https://doi.org/10.1038/nmeth.3578

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