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- Title
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.
- Authors
Ostrovnaya, Irina; Seshan, Venkatraman E.; Olshen, Adam B.; Begg, Colin B.
- Abstract
Summary: If 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.Contact: ostrovni@mskcc.org
- Subjects
TUMOR classification; MULTIPLE tumors; COMPUTER software; CANCER patients; LOSS of heterozygosity; BIOINFORMATICS; CLONE cells
- Publication
Bioinformatics, 2011, Vol 27, Issue 12, p1698
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btr267