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COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data

Author

Listed:
  • Etienne Sollier

    (ETH Zürich
    German Cancer Research Center (DKFZ))

  • Jack Kuipers

    (ETH Zürich
    SIB Swiss Institute of Bioinformatics)

  • Koichi Takahashi

    (The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center)

  • Niko Beerenwinkel

    (ETH Zürich
    SIB Swiss Institute of Bioinformatics)

  • Katharina Jahn

    (ETH Zürich
    SIB Swiss Institute of Bioinformatics
    Freie Universität Berlin)

Abstract

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.

Suggested Citation

  • Etienne Sollier & Jack Kuipers & Koichi Takahashi & Niko Beerenwinkel & Katharina Jahn, 2023. "COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40378-8
    DOI: 10.1038/s41467-023-40378-8
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    References listed on IDEAS

    as
    1. Kiyomi Morita & Feng Wang & Katharina Jahn & Tianyuan Hu & Tomoyuki Tanaka & Yuya Sasaki & Jack Kuipers & Sanam Loghavi & Sa A. Wang & Yuanqing Yan & Ken Furudate & Jairo Matthews & Latasha Little & C, 2020. "Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics," Nature Communications, Nature, vol. 11(1), pages 1-17, December.
    2. Jochen Singer & Jack Kuipers & Katharina Jahn & Niko Beerenwinkel, 2018. "Single-cell mutation identification via phylogenetic inference," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    3. Kiyomi Morita & Feng Wang & Katharina Jahn & Tianyuan Hu & Tomoyuki Tanaka & Yuya Sasaki & Jack Kuipers & Sanam Loghavi & Sa A. Wang & Yuanqing Yan & Ken Furudate & Jairo Matthews & Latasha Little & C, 2020. "Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics," Nature Communications, Nature, vol. 11(1), pages 1-1, December.
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