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Updated: Jul 13, 2025

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection.

Daan M Hazelaar¹, Job van Riet^1,2, Youri Hoogstrate³

¹Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD, Rotterdam, the Netherlands.

|October 17, 2023

Summary

Katdetectr is a new R package for detecting genomic hypermutation regions (kataegis) in cancer. It offers robust, fast, and accurate identification, characterization, and visualization of these significant cancer mutation patterns.

Keywords:

Bioconductor R-package cancer changepoint analysis kataegis

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Last Updated: Jul 13, 2025

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Area of Science:

Genomics
Cancer Biology
Bioinformatics

Background:

Kataegis describes regional genomic hypermutation in various cancers, characterized by high local mutation rates.
Identifying kataegis loci is crucial due to their biological significance and potential clinical relevance in malignancies.

Purpose of the Study:

To introduce Katdetectr, an open-source R/Bioconductor package for detecting kataegis loci in genomic data.
To provide functionalities for characterizing and visualizing kataegis, facilitating subsequent analyses.

Main Methods:

Katdetectr processes standard genomic formats (MAF, VCF, VRanges).
It employs unsupervised changepoint analysis using the Pruned Exact Linear Time (PELT) algorithm to identify mutation hotspots.
Kataegis calling is performed based on user-defined parameters.

Main Results:

Katdetectr demonstrated robustness against varying tumor mutational burden.
It achieved the fastest mean computation time compared to other evaluated tools.
Katdetectr exhibited superior accuracy (0.99) and Matthews correlation coefficient (0.98) on both synthetic and real cancer datasets.

Conclusions:

Katdetectr provides a robust, flexible, and fast workflow for kataegis detection, characterization, and visualization.
The package is available on Bioconductor, offering a valuable tool for cancer genomics research.