ArticlePLoS computational biology2021
Statistical tests for intra-tumour clonal co-occurrence and exclusivity.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 14 citations in OpenAlex.
- Review
- Bayesian inference of fitness landscapes via tree-structured branching processes.Bioinformatics (Oxford, England) · 2025Article
- Oncotree2vec - a method for embedding and clustering of tumor mutation trees.Bioinformatics (Oxford, England) · 2024Article
- A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer.bioRxiv : the preprint server for biology · 2024Article
- Modeling and predicting cancer clonal evolution with reinforcement learning.Genome research · 2023Article
- Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees.Nature communications · 2023Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Intra-tumoural pairs of mutations that are overrepresented in a co-occurring or clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical testing framework, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our framework for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 1 clonally co-occurring and 8 clonally exclusive gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways.
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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.