ArticleCell systems2020
SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses.
Article in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 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
55 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Statistical Inconsistency of Error-correction Objectives for Perfect Phylogenies.bioRxiv : the preprint server for biology · 2026Article
- LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.Bioinformatics (Oxford, England) · 2026Article
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees.bioRxiv : the preprint server for biology · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data.Genome biology · 2025Article
- Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants.Journal of computational biology : a journal of computational molecular cell biology · 2025Article
- Review
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution.Cell genomics · 2025Article
- Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq.Bioinformatics advances · 2025Article
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution.Nature communications · 2024Article
- Evolving copy number gains promote tumor expansion and bolster mutational diversification.Nature communications · 2024Article
- Computational immunogenomic approaches to predict response to cancer immunotherapies.Nature reviews. Clinical oncology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A small number of somatic mutations drive the development of cancer, but all somatic mutations are markers of the evolutionary history of a tumor. Prominent methods to construct phylogenies from single-cell sequencing data use single-nucleotide variants (SNVs) as markers but fail to adequately account for copy-number aberrations (CNAs), which can overlap SNVs and result in SNV losses. Here, we introduce SCARLET, an algorithm that infers tumor phylogenies from single-cell DNA sequencing data while accounting for both CNA-driven loss of SNVs and sequencing errors. SCARLET outperforms existing methods on simulated data, with more accurate inference of the order in which mutations were acquired and the mutations present in individual cells. Using a single-cell dataset from a patient with colorectal cancer, SCARLET constructs a tumor phylogeny that is consistent with the observed CNAs and suggests an alternate origin for the patient's metastases. SCARLET is available at: github.com/raphael-group/scarlet.
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.