Abstract
AbstractWe present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from single-cell DNA sequencing. SIEVE leverages raw read counts for all nucleotides and corrects the acquisition bias of branch lengths. In our simulations, SIEVE outperforms other methods in phylogenetic reconstruction and variant calling accuracy, especially in the inference of homozygous variants. Applying SIEVE to three datasets, one for triple-negative breast (TNBC), and two for colorectal cancer (CRC), we find that double mutant genotypes are rare in CRC but unexpectedly frequent in the TNBC samples.
Funder
H2020 Marie Skłodowska-Curie Actions
Narodowe Centrum Nauki
H2020 European Research Council
Ministerio de Ciencia e Innovación
Xunta de Galicia
Publisher
Springer Science and Business Media LLC
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