Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: Update of the Clonality R package Review

   

Authors:	Mauguen, A.; Seshan, V. E.; Begg, C. B.; Ostrovnaya, I.
Review Title:	Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: Update of the Clonality R package
Abstract:	SUMMARY: The 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. © The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Journal Title:	Bioinformatics
Volume:	35
Issue:	22
ISSN:	1367-4803
Publisher:	Oxford University Press
Date Published:	2019-11-15
Start Page:	4776
End Page:	4778
Language:	English
DOI:	10.1093/bioinformatics/btz486
PUBMED:	31198957
PROVIDER:	scopus
PMCID:	PMC6853680
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074961692&doi=10.1093%2fbioinformatics%2fbtz486&partnerID=40&md5=b990c96b2d13c321a1c6d423d957edff
Notes:	Source: Scopus

https://synapse.mskcc.org/synapse/works/has_related_data_chk/156790