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...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-11-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03106-5 |
| _version_ | 1827603541032697856 |
|---|---|
| author | Palash Sashittal Haochen Zhang Christine A. Iacobuzio-Donahue Benjamin J. Raphael |
| author_facet | Palash Sashittal Haochen Zhang Christine A. Iacobuzio-Donahue Benjamin J. Raphael |
| author_sort | Palash Sashittal |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T05:42:08Z |
| format | Article |
| id | doaj.art-5435dde5ac3e4bb780badd7e110b055f |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-09T05:42:08Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-5435dde5ac3e4bb780badd7e110b055f2023-12-03T12:24:31ZengBMCGenome Biology1474-760X2023-11-0124112310.1186/s13059-023-03106-5ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss modelPalash Sashittal0Haochen Zhang1Christine A. Iacobuzio-Donahue2Benjamin J. Raphael3Department of Computer Science, Princeton UniversityGerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer CenterHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterDepartment of Computer Science, Princeton UniversityAbstract 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.https://doi.org/10.1186/s13059-023-03106-5CancerIntra-tumor heterogeneityTumor phylogenySingle-cell DNA sequencingDollo model |
| spellingShingle | Palash Sashittal Haochen Zhang Christine A. Iacobuzio-Donahue Benjamin J. Raphael ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model Genome Biology Cancer Intra-tumor heterogeneity Tumor phylogeny Single-cell DNA sequencing Dollo model |
| title | ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model |
| title_full | ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model |
| title_fullStr | ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model |
| title_full_unstemmed | ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model |
| title_short | ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model |
| title_sort | condor tumor phylogeny inference with a copy number constrained mutation loss model |
| topic | Cancer Intra-tumor heterogeneity Tumor phylogeny Single-cell DNA sequencing Dollo model |
| url | https://doi.org/10.1186/s13059-023-03106-5 |
| work_keys_str_mv | AT palashsashittal condortumorphylogenyinferencewithacopynumberconstrainedmutationlossmodel AT haochenzhang condortumorphylogenyinferencewithacopynumberconstrainedmutationlossmodel AT christineaiacobuziodonahue condortumorphylogenyinferencewithacopynumberconstrainedmutationlossmodel AT benjaminjraphael condortumorphylogenyinferencewithacopynumberconstrainedmutationlossmodel |