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.
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.
Authors: Colin B Begg; Irina Ostrovnaya; Jose V Scarpa Carniello; Rita A Sakr; Dilip Giri; Russell Towers; Michail Schizas; Marina De Brot; Victor P Andrade; Audrey Mauguen; Venkatraman E Seshan; Tari A King Journal: Breast Cancer Res Date: 2016-06-23 Impact factor: 6.466
Authors: Thomas van Doeveren; Jose A Nakauma-Gonzalez; Andrew S Mason; Geert J L H van Leenders; Tahlita C M Zuiverloon; Ellen C Zwarthoff; Isabelle C Meijssen; Angelique C van der Made; Antoine G van der Heijden; Kees Hendricksen; Bas W G van Rhijn; Charlotte S Voskuilen; Job van Riet; Winand N M Dinjens; Hendrikus J Dubbink; Harmen J G van de Werken; Joost L Boormans Journal: Int J Cancer Date: 2020-10-13 Impact factor: 7.396