ArticleCell systems2019
CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 69 citations in OpenAlex.
- Trial
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- MyClone: rapid and precise reconstruction of clonal population structures for tumors.BMC bioinformatics · 2025Article
- New insights into the genetic progression of cancer through longitudinal analysis of oral lesions.The Journal of pathology · 2025Article
- Genomic landscape of hormone therapy-resistant HR-positive, HER2-negative breast cancer.Breast cancer research and treatment · 2025Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Fast tumor phylogeny regression via tree-structured dual dynamic programming.Bioinformatics (Oxford, England) · 2025Article
- Persistent postremission clonal hematopoiesis shapes the relapse trajectories of acute myeloid leukemia.Blood advances · 2025Article
- A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer.NPJ precision oncology · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Orchard: Building large cancer phylogenies using stochastic combinatorial search.PLoS computational biology · 2024Article
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Early drivers of clonal hematopoiesis shape the evolutionary trajectories ofmedRxiv : the preprint server for health sciences · 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
- Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma.Cancer research · 2023Article
- A weighted distance-based approach for deriving consensus tumor evolutionary trees.Bioinformatics (Oxford, England) · 2023Article
- Longitudinal Analyses of Mutational Subclonal Architecture and Tumor Subtypes in Recurrent Bladder Cancer.International journal of molecular sciences · 2023Article
- Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Longitudinal DNA sequencing of cancer patients yields insight into how tumors evolve over time or in response to treatment. However, sequencing data from bulk tumor samples often have considerable ambiguity in clonal composition, complicating the inference of ancestral relationships between clones. We introduce Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction (CALDER), an algorithm to infer phylogenetic trees from longitudinal bulk DNA sequencing data. CALDER explicitly models a longitudinally observed phylogeny incorporating constraints that longitudinal sampling imposes on phylogeny reconstruction. We show on simulated bulk tumor data that longitudinal constraints substantially reduce ambiguity in phylogeny reconstruction and that CALDER outperforms existing methods that do not leverage this longitudinal information. On real data from two chronic lymphocytic leukemia patients, we find that CALDER reconstructs more plausible and parsimonious phylogenies than existing methods, with CALDER phylogenies containing fewer tumor clones per sample. CALDER's use of longitudinal information will be advantageous in further studies of tumor heterogeneity and evolution.
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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.