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

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作者：
Etienne Sollier
Jack Kuipers
Koichi Takahashi
Niko Beerenwinkel
Katharina Jahn
机构：
[1] ETH Zürich,Department of Biosystems Science and Engineering
[2] German Cancer Research Center (DKFZ),Division of Cancer Epigenomics
[3] SIB Swiss Institute of Bioinformatics,Department of Leukemia
[4] The University of Texas MD Anderson Cancer Center,Department of Genomic Medicine
[5] The University of Texas MD Anderson Cancer Center,Department of Mathematics and Computer Science
[6] Freie Universität Berlin,undefined
来源：
Nature Communications | / 14卷
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摘要：
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.
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