ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model Journal Article
| Authors: | Sashittal, P.; Zhang, H.; Iacobuzio-Donahue, C. A.; Raphael, B. J. |
| Article Title: | ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model |
| Abstract: | A tumor contains a diverse collection of somatic mutations that reflect its past evolutionary history and that range in scale from single nucleotide variants (SNVs) to large-scale copy-number aberrations (CNAs). However, no current single-cell DNA sequencing (scDNA-seq) technology produces accurate measurements of both SNVs and CNAs, complicating the inference of tumor phylogenies. We introduce a new evolutionary model, the constrained k -Dollo model, that uses SNVs as phylogenetic markers but constrains losses of SNVs according to clusters of cells. We derive an algorithm, ConDoR, that infers phylogenies from targeted scDNA-seq data using this model. We demonstrate the advantages of ConDoR on simulated and real scDNA-seq data. © 2023, The Author(s). |
| Keywords: | single nucleotide polymorphism; genetics; mutation; neoplasm; neoplasms; animal; animals; mutational analysis; algorithms; algorithm; genomic dna; sequence analysis, dna; birds; phylogeny; dna copy number variations; copy number variation; single cell analysis; phylogenetic tree; dna sequencing; cancer; humans; human; article; intra-tumor heterogeneity; bird; malignant neoplasm; clustering algorithm; k means clustering; tumor phylogeny; dollo model; single-cell dna sequencing; constrained dollo reconstruction |
| Journal Title: | Genome Biology |
| Volume: | 24 |
| ISSN: | 1465-6906 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2023-11-01 |
| Start Page: | 272 |
| Language: | English |
| DOI: | 10.1186/s13059-023-03106-5 |
| PUBMED: | 38037115 |
| PROVIDER: | scopus |
| PMCID: | PMC10688497 |
| DOI/URL: | |
| Notes: | Article -- Source: Scopus |
