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Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes

  • 0School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Plos Genetics +

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May 4, 2021

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May 4, 2021

View abstract on PubMed

Summary

This summary is machine-generated.

A new bioinformatics tool, sigminer, aids in analyzing copy number alterations in cancer. This tool identified five copy number signatures in prostate cancer, revealing tumor heterogeneity and potential biomarkers for improved prognosis.

Area Of Science

  • Genomics
  • Bioinformatics
  • Cancer Research

Background

  • Genome alteration signatures offer insights into cancer evolution.
  • Single base substitution (SBS) signatures are well-studied, but tools for copy number alteration (CNA) signatures are lacking.
  • CNAs are key drivers in cancer progression.

Purpose Of The Study

  • To develop a user-friendly bioinformatics tool for CNA signature extraction, analysis, and visualization.
  • To apply the tool to prostate cancer (PC) to identify and characterize CNA signatures.
  • To explore the utility of CNA signatures for understanding PC heterogeneity and clinical outcomes.

Main Methods

  • Development of the open-source bioinformatics tool "sigminer" for CNA signature analysis.
  • Application of sigminer to human PC genomes.
  • Identification and illustration of underlying mutational processes for each CNA signature.
  • Clustering of PC samples based on CNA signature exposure.

Main Results

  • Identification of five distinct CNA signatures in human PC.
  • Illustration of the mutational processes driving each identified CNA signature.
  • Demonstration of significant PC heterogeneity through sample clustering based on CNA signatures.
  • CNA signatures showed a stronger association with PC clinical outcomes compared to SBS signatures.

Conclusions

  • The sigminer tool facilitates the study of CNA signatures.
  • CNA signature analysis provides novel insights into PC etiology and heterogeneity.
  • CNA signatures may serve as potential biomarkers for PC stratification and prognosis.