ArticleBioinformatics (Oxford, England)2019
Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed.
- Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression.The Journal of pathology · 2026Article
- Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution.NPJ precision oncology · 2025Article
- Genetic Alterations in Chromatin Regulatory Genes in Upper Tract Urothelial Carcinoma and Urothelial Bladder Cancer.Cancer medicine · 2024Article
- Multi-scale signaling and tumor evolution in high-grade gliomas.Cancer cell · 2024Article
- Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything.Genome biology · 2022Review
- The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder.International journal of cancer · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
summaryThe Clonality R package is a practical tool to assess the clonal relatedness of two tumors from the same patient. We have previously presented its functionality for testing tumors using loss of heterozygosity data or copy number arrays. Since then somatic mutation data have been more widely available through next generation sequencing and we have developed new methodology for comparing the tumors' mutational profiles. We thus extended the package to include these two new methods for comparing tumors as well as the mutational frequency estimation from external data required for their implementation. The first method is a likelihood ratio test that is readily available on a patient by patient basis. The second method employs a random-effects model to estimate both the population and individual probabilities of clonal relatedness from a group of patients with pairs of tumors. The package is available on Bioconductor. AVAILABILITY AND IMPLEMENTATION: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
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.