ArticleNature communications2019
Using somatic variant richness to mine signals from rare variants in the cancer genome.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- Divergent Clonal Evolution and Early Dissemination Promote Genetic Heterogeneity of Metastases in Castration-Resistant Prostate Cancer.Cancer research · 2025Article
- Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility.iScience · 2024Article
- Topical hidden genome: discovering latent cancer mutational topics using a Bayesian multilevel context-learning approach.Biometrics · 2024Article
- Scaled Process Priors for Bayesian Nonparametric Estimation of the Unseen Genetic Variation.Journal of the American Statistical Association · 2024Article
- Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants.Genomics, proteomics & bioinformatics · 2023Article
- XCVATR: detection and characterization of variant impact on the Embeddings of single -cell and bulk RNA-sequencing samples.BMC genomics · 2022Article
- Using the "Hidden" genome to improve classification of cancer types.Biometrics · 2021Article
- Mining mutation contexts across the cancer genome to map tumor site of origin.Nature communications · 2021Article
- Testing tumors from different anatomic sites for clonal relatedness using somatic mutation data.Biometrics · 2021Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
To date, the vast preponderance of somatic variants observed in the cancer genome have been rare variants, and it is common in practice to encounter in a new tumor variants that have not been observed previously. Here we focus on probability estimation for encountering such hitherto unseen variants. We draw upon statistical methodology that has been developed in other fields of study, notably in species estimation in ecology, and word frequency estimation in computational linguistics. Analysis of whole-exome and targeted panel sequencing data sets reveal substantial variability in variant "richness" between genes that could be harnessed for clinically relevant problems. We quantify the variant-tissue association and show a strong gene-specific, lineage-dependent pattern of encountering new variants. This variability is largely determined by the proportion of observed variants that are rare. Our findings suggest that variants that occur at very low frequencies can harbor important signals that are clinically consequential.
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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.