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SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data

Derek J Nancarrow1, Herlina Y Handoko, Mitchell S Stark

  • 1Oncogenomics, Queensland Institute of Medical Research, Herston, Queensland, Australia. derekN@qimr.edu.au

Plos One
|November 1, 2007
PubMed

Insights

Interpreting cancer DNA copy number changes is challenging due to normal tissue contamination. We developed Simulated DNA Copy Number (SiDCoN), a visual tool to accurately analyze these complex genomic alterations.

Area of Science:

  • Genomics
  • Cancer Research
  • Bioinformatics

Background:

  • Genome-wide SNP microarrays offer sensitive detection of cancer DNA copy number aberrations.
  • Interpreting these genomic changes is complex, especially with stromal contamination in tumor samples.
  • Existing automated scoring algorithms require significant manual correction for uncultured specimens.

Purpose of the Study:

  • To develop a visual tool, Simulated DNA Copy Number (SiDCoN), to aid in the analysis of DNA copy number data.
  • To address limitations in interpreting complex genomic changes and stromal contamination in tumor samples.
  • To provide a flexible application for simulating and analyzing DNA copy number alterations.

Main Methods:

  • Developed SiDCoN, a spreadsheet-based application for simulating B-allele and logR plots.
  • The tool simulates all known tumor DNA copy number changes with or without stromal contamination.
  • Users can specify stromal contamination levels, up to 3 DNA copy number aberrations, and analyze up to 5000 data points (SNPs).

Main Results:

  • SiDCoN accurately simulates various DNA copy number changes and stromal contamination effects.
  • The tool enables estimation of stromal contamination levels in tumor samples.
  • Demonstrated application in deciphering complex, heterogeneous copy number changes observed in tumor series.

Conclusions:

  • SiDCoN is a valuable visual tool for analyzing DNA copy number data in cancer research.
  • The application aids in estimating stromal contamination and interpreting complex genomic alterations.
  • SiDCoN serves as both a training resource and an analytical aid for researchers studying DNA copy number changes.

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