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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.

Francis Blokzijl¹, Roel Janssen¹, Ruben van Boxtel^1,2

¹Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.

Genome Medicine

|April 27, 2018

Summary

MutationalPatterns is a new R/Bioconductor package for analyzing base substitution catalogues. It helps dissect mutational mechanisms and quantify mutational signatures in cancer research.

Keywords:

Base substitutions Mutational processes Mutational signatures R Replicative strand bias Somatic mutations Transcriptional strand bias

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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

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Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

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Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Base substitution catalogues record cellular mutational history.
Mutational processes are characterized by mutation type, sequence context, and genomic features.

Purpose of the Study:

To introduce MutationalPatterns, an R/Bioconductor package.
To enable researchers to characterize mutational patterns and dissect molecular mechanisms.
To provide an efficient method for quantifying mutational signatures in single samples.

Main Methods:

Utilizing R/Bioconductor package for data analysis.
Characterizing base substitution catalogues.
Quantifying mutational signatures and their contributions.

Main Results:

MutationalPatterns facilitates the characterization and visualization of mutational patterns.
The package aids in dissecting underlying molecular mechanisms of mutations.
It enables quantification of known mutational signatures within samples.

Conclusions:

MutationalPatterns supports fundamental research into mutational mechanisms.
The analyses can improve cancer diagnosis and treatment strategies.
The package is freely available for use.