ArticleCell systems2021
DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution.
Article in Cell systems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 38 citations in OpenAlex.
- Trial
- A guide to understanding tumour evolution through the lens of population genetics.Nature reviews. Cancer · 2026Review
- Novel driver gene MDC1 confers homologous recombination repair deficiency and genomic instability in chemoresistant relapsing ovarian cancer.Journal of translational medicine · 2026Article
- Inferring cancer type-specific patterns of metastatic spread using Metient.Nature methods · 2026Article
- Unmasking the "targetless" illusion: branched clonal evolution ofFrontiers in immunology · 2026Article
- Loss of IDH1 and IDH2 mutations during the evolution of metastatic chondrosarcoma.Genome biology · 2025Article
- MyClone: rapid and precise reconstruction of clonal population structures for tumors.BMC bioinformatics · 2025Article
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- Fast tumor phylogeny regression via tree-structured dual dynamic programming.Bioinformatics (Oxford, England) · 2025Article
- The Evolutionary Forest of Pancreatic Cancer.Cancer discovery · 2025Article
- Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer.Nature communications · 2025Article
- Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER.Nature genetics · 2025Article
- Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives.Frontiers in oncology · 2025Review
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.Nature communications · 2024Article
- Article
- CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction.Nature protocols · 2024Review
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- ZygosityPredictor.Bioinformatics advances · 2024Article
- Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma.Cancer research · 2023Article
Corrections and comments
- Commented on by
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The cancer cell fraction (CCF), or proportion of cancerous cells in a tumor containing a single-nucleotide variant (SNV), is a fundamental statistic used to quantify tumor heterogeneity and evolution. Existing CCF estimation methods from bulk DNA sequencing data assume that every cell with an SNV contains the same number of copies of the SNV. This assumption is unrealistic in tumors with copy-number aberrations that alter SNV multiplicities. Furthermore, the CCF does not account for SNV losses due to copy-number aberrations, confounding downstream phylogenetic analyses. We introduce DeCiFer, an algorithm that overcomes these limitations by clustering SNVs using a novel statistic, the descendant cell fraction (DCF). The DCF quantifies both the prevalence of an SNV at the present time and its past evolutionary history using an evolutionary model that allows mutation losses. We show that DeCiFer yields more parsimonious reconstructions of tumor evolution than previously reported for 49 prostate cancer samples.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.