ArticleBlood cancer discovery2022
Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree.
Article in Blood cancer discovery, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
- Trial
- Early EGFR Inhibition Triggers Actionable Tumor and Microenvironmental Remodeling in Lung Cancer.Cancer research communications · 2026Article
- Article
- Inferring cancer type-specific patterns of metastatic spread using Metient.Nature methods · 2026Article
- Identifying Robust Subclonal Structures through Tumor Progression Tree Alignment.bioRxiv : the preprint server for biology · 2026Article
- Inferring and summarizing tumor phylogenies from bulk DNA data.Algorithms for molecular biology : AMB · 2026Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression.Nature genetics · 2025Article
- Fast tumor phylogeny regression via tree-structured dual dynamic programming.Bioinformatics (Oxford, England) · 2025Article
- PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.Bioinformatics (Oxford, England) · 2025Article
- Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles.Nature communications · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Orchard: Building large cancer phylogenies using stochastic combinatorial search.PLoS computational biology · 2024Article
- A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer.bioRxiv : the preprint server for biology · 2024Article
- Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data.Bioinformatics (Oxford, England) · 2024Article
- CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction.Nature protocols · 2024Review
- Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways.Cancer discovery · 2023Article
- The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations.Nature cancer · 2023Article
- Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis.Nature communications · 2023Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions. SIGNIFICANCE: Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible. See related commentary by Miller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
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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.