ReviewNature protocols2024
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Trial
- Intrapatient tumour heterogeneity and clonal evolution in an autopsy study of metastatic salivary gland cancer.Molecular oncology · 2026Article
- Understanding and overcoming innate and acquired MAPK inhibition resistance in anaplastic thyroid cancer.Cell reports. Medicine · 2026Article
- Article
- Identifying Robust Subclonal Structures through Tumor Progression Tree Alignment.bioRxiv : the preprint server for biology · 2026Article
- Full spatio-temporal analyses of migration and colonization in evolution-dense 3D mapping of cancer metastases provides new insights.Molecular biology and evolution · 2026Article
- Protocol for Chinese lung cancer evolution and microenvironment tracking under therapy study.Journal of translational internal medicine · 2025Article
- Loss of IDH1 and IDH2 mutations during the evolution of metastatic chondrosarcoma.Genome biology · 2025Article
- Divergent Clonal Evolution and Early Dissemination Promote Genetic Heterogeneity of Metastases in Castration-Resistant Prostate Cancer.Cancer research · 2025Article
- MyClone: rapid and precise reconstruction of clonal population structures for tumors.BMC bioinformatics · 2025Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Whole‑exome evolutionary profiling of osteosarcoma uncovers metastasis‑related driver mutations and generates an independently validated predictive classifier.Journal of translational medicine · 2025Article
- PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.Bioinformatics (Oxford, England) · 2025Article
- Integrating model systems and genomic insights to decipher mechanisms of cancer metastasis.Nature reviews. Genetics · 2025Review
- Aberrant basal cell clonal dynamics shape early lung carcinogenesis.Science (New York, N.Y.) · 2025Article
- Convergent Genetic Adaptation in Human Tumors Developed Under Systemic Hypoxia and in Populations Living at High Altitudes.Cancer discovery · 2025Article
- Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- 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
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Authors and funding
11 authors.
Funding
Abstract
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor cell populations. However, accurate inference of tumor subclonal architecture and reconstruction of tumor evolutionary histories from bulk DNA sequencing data remains challenging. Frequently, sequencing and alignment artifacts are not fully filtered out from cancer somatic mutations, and errors in the identification of copy number alterations or complex evolutionary events (e.g., mutation losses) affect the estimated cellular prevalence of mutations. Together, such errors propagate into the analysis of mutation clustering and phylogenetic reconstruction. In this Protocol, we present a new computational framework, CONIPHER (COrrecting Noise In PHylogenetic Evaluation and Reconstruction), that accurately infers subclonal structure and phylogenetic relationships from multisample tumor sequencing, accounting for both copy number alterations and mutation errors. CONIPHER has been used to reconstruct subclonal architecture and tumor phylogeny from multisample tumors with high-depth whole-exome sequencing from the TRACERx421 dataset, as well as matched primary-metastatic cases. CONIPHER outperforms similar methods on simulated datasets, and in particular scales to a large number of tumor samples and clones, while completing in under 1.5 h on average. CONIPHER enables automated phylogenetic analysis that can be effectively applied to large sequencing datasets generated with different technologies. CONIPHER can be run with a basic knowledge of bioinformatics and R and bash scripting languages.
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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.