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SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.

Senbai KangNico BorgsmüllerMonica ValechaJack KuipersJoao M AlvesSonia Prado-LópezDébora ChantadaNiko BeerenwinkelDavid PosadaEwa Szczurek
Published in: Genome biology (2022)
We 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.
Keyphrases
  • single cell
  • rna seq
  • copy number
  • high throughput
  • single molecule
  • circulating tumor
  • cell free
  • stem cells
  • big data
  • genome wide
  • mesenchymal stem cells
  • circulating tumor cells
  • data analysis
  • bone marrow