kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.

BMC Genomics
Xue LinJian Li

Abstract

Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations "violent storm", which is just what the Greek word "kataegis" means. There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package "kataegis" to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions. The kataegis package is available on Bionconductor/Github ( https://github.com/flosalbizziae/kataegis ), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.

References

Mar 8, 2005·Mutation Research·Gerd P PfeiferAhmad Besaratinia
Mar 9, 2007·Nature·Christopher GreenmanMichael R Stratton
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
Dec 20, 2012·Biology Direct·Artem G LadaYouri I Pavlov
Feb 28, 2013·BMC Genomics·Gro NilsenOle Christian Lingjaerde
May 21, 2013·Nature Genetics·Allen S HoTimothy A Chan
Aug 16, 2013·Nature·Ludmil B AlexandrovMichael R Stratton
Dec 22, 2015·Cell·John MaciejowskiTitia de Lange

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