ArticleBioinformatics (Oxford, England)2011
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression.The Journal of pathology · 2026Article
- Molecular analysis of the evolutionary history of endometrial and ovarian carcinoma in Lynch syndrome.International journal of cancer · 2025Article
- The Added Value of Genome-Wide Copy Numbers to Objectively Resolve Clonality of Multiple Tumors With Pulmonary Involvement and Ambiguous or Inconclusive Mutational Diagnosis.JTO clinical and research reports · 2025Article
- Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution.NPJ precision oncology · 2025Article
- Article
- A Case Report of Immunotherapy-Resistant MSI-H Gastric Cancer with Significant Intrapatient Tumoral Heterogeneity Characterized by Histologic Dedifferentiation.Journal of clinical medicine · 2022Article
- Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything.Genome biology · 2022Review
- Chromosome 2q gain and epigenetic silencing of GATA3 in microglandular adenosis of the breast.The journal of pathology. Clinical research · 2021Article
- Commentary: Genomic Analysis Reveals Heterogeneity Between Lesions in Synchronous Primary Right-Sided and Left-Sided Colon Cancer.Frontiers in molecular biosciences · 2021Article
- Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship.Scientific reports · 2020Article
- Highly sensitive MLH1 methylation analysis in blood identifies a cancer patient with low-level mosaic MLH1 epimutation.Clinical epigenetics · 2019Article
- An EM algorithm to improve the estimation of the probability of clonal relatedness of pairs of tumors in cancer patients.BMC bioinformatics · 2019Article
- Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package.Bioinformatics (Oxford, England) · 2019Article
- Colorectal metastasis to the gallbladder mimicking a primary gallbladder malignancy: histopathological and molecular characteristics.Histopathology · 2019Article
- Redefining synchronous colorectal cancers based on tumor clonality.International journal of cancer · 2019Article
- Frequent clonal relations between metastases and non-index prostate cancer lesions.JCI insight · 2019Article
- Article
- Clonal relatedness in tumour pairs of breast cancer patients.Breast cancer research : BCR · 2018Article
- Subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma.The journal of pathology. Clinical research · 2017Article
- Comprehensive Genomic Profiling Aids in Distinguishing Metastatic Recurrence from Second Primary Cancers.The oncologist · 2017Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
summaryIf a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. AVAILABILITY: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.
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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.