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ShatterProof: operational detection and quantification of chromothripsis.

Shaylan K Govind, Amin Zia, Pablo H Hennings-Yeomans

¹Ontario Institute for Cancer Research, M5G 0A3, Toronto, Canada. Paul.Boutros@oicr.on.ca.

BMC Bioinformatics

|March 21, 2014

Summary

We developed ShatterProof, a new software tool to detect and quantify chromothripsis, a complex genomic rearrangement found in cancers. This automated method improves accuracy and efficiency in analyzing high-throughput sequencing data for cancer research.

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Area of Science:

Genomics
Cancer Biology
Bioinformatics

Background:

Chromothripsis is a complex genomic rearrangement implicated in cancer evolution.
Existing methods for detecting chromothripsis in sequencing data are limited, hindering accurate analysis and comparison.
Automated detection of chromothripsis is crucial for advancing cancer research.

Purpose of the Study:

To introduce ShatterProof, a novel software tool for the detection and quantification of chromothriptic events.
To provide a robust and automated method for identifying chromothripsis in high-throughput sequencing data.
To facilitate accurate comparison of chromothripsis findings across different studies and datasets.

Main Methods:

ShatterProof utilizes structural variation calls (translocations, copy-number variations, etc.) from any algorithm.
It employs an operational definition of chromothripsis and performs statistical tests for prediction.
Validation was performed on clinical datasets, including prostate, colorectal, and SCLC cancer samples.

Main Results:

ShatterProof accurately predicts the presence and location of chromothriptic events.
The tool demonstrates computational efficiency with low memory requirements and near-linear computation time.
Validation confirmed the tool's effectiveness on diverse clinical cancer datasets.

Conclusions:

ShatterProof offers an efficient and accurate solution for detecting and quantifying chromothripsis.
Its computational performance allows integration into standard sequencing analysis pipelines.
This tool will enable routine and precise assessment of chromothripsis in research samples.