ArticleGenome biology2014
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Competing subclones and fitness diversity shape tumor evolution across cancer types.Bioinformatics (Oxford, England) · 2026Article
- Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia.Genome research · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Clonal dynamics of aggressive systemic mastocytosis on avapritinib therapy.Blood cancer journal · 2024Article
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
- Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia.bioRxiv : the preprint server for biology · 2024Article
- A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.Genome research · 2024Article
- Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies.Genome medicine · 2021Article
- DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution.Cell systems · 2021Article
- A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data.Bioinformatics (Oxford, England) · 2021Article
- Clonal reconstruction from time course genomic sequencing data.BMC genomics · 2019Article
- Parameter, noise, and tree topology effects in tumor phylogeny inference.BMC medical genomics · 2019Article
- Algorithmic approaches to clonal reconstruction in heterogeneous cell populations.Quantitative biology (Beijing, China) · 2019Article
- Finding cancer driver mutations in the era of big data research.Biophysical reviews · 2019Review
- Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective.Leukemia · 2018Article
- QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.Bioinformatics (Oxford, England) · 2018Article
- Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees.Current protocols in bioinformatics · 2018Article
- Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies.Scientific reports · 2017Article
- Combating subclonal evolution of resistant cancer phenotypes.Nature communications · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.
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