ArticleGenome biology2013
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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Who cites it
133 citing papers in PubMed.
- Trial
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- Homologous recombination deficiency (HRD) testing landscape: clinical applications and technical validation for routine diagnostics.Biomarker research · 2025Review
- Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.Briefings in bioinformatics · 2024Article
- Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression.NPJ precision oncology · 2024Article
- Spatially resolved tissue imaging to analyze the tumor immune microenvironment: beyond cell-type densities.Journal for immunotherapy of cancer · 2024Review
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.Nature communications · 2024Article
- Increased frequency of CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression without inducing homologous recombination deficiency.Research square · 2024Article
- Article
- A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.Genome research · 2024Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI.PLoS computational biology · 2023Article
- Assessing the performance of methods for cell clustering from single-cell DNA sequencing data.PLoS computational biology · 2023Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes.Nature biotechnology · 2023Article
- scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors.Science advances · 2023Article
- Glioma Shapes Blood-Brain Barrier Integrity and Remodels the Tumor Microenvironment: Links with Clinical Features and Prognosis.Journal of clinical medicine · 2022Article
- Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.Bioinformatics (Oxford, England) · 2022Article
- CONET: copy number event tree model of evolutionary tumor history for single-cell data.Genome biology · 2022Article
73 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Tumor samples are typically heterogeneous, containing admixture by normal, non-cancerous cells and one or more subpopulations of cancerous cells. Whole-genome sequencing of a tumor sample yields reads from this mixture, but does not directly reveal the cell of origin for each read. We introduce THetA (Tumor Heterogeneity Analysis), an algorithm that infers the most likely collection of genomes and their proportions in a sample, for the case where copy number aberrations distinguish subpopulations. THetA successfully estimates normal admixture and recovers clonal and subclonal copy number aberrations in real and simulated sequencing data. THetA is available at http://compbio.cs.brown.edu/software/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.