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Microarray Inspector: tissue cross contamination detection tool for microarray data.

Piotr Stępniak1, Matthew Maycock1, Konrad Wojdan2

  • 1Transition Technologies S.A., Warszawa, Poland.

Acta Biochimica Polonica
|January 17, 2014
PubMed
Summary
This summary is machine-generated.

Microarray Inspector software detects mixed tissue types in samples using raw expression data. This tool ensures high-quality biological samples for research by identifying contamination post-experiment.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microarray technology generates vast expression data, crucial for life sciences research.
  • High sample quality is essential, but pre-experimental quality assessment is often missing.
  • Tissue heterogeneity and cross-contamination, especially in oncological studies, can invalidate transcription profiling data.

Purpose of the Study:

  • To develop a post-experimental method for detecting tissue contamination in microarray datasets.
  • To introduce Microarray Inspector, a user-friendly software for identifying mixed tissue samples.

Main Methods:

  • Microarray Inspector analyzes raw expression data files independently for each array.
  • The software allows users to customize analysis criteria based on research needs.
  • It identifies contaminant biomarkers, specifically for adipose tissue contamination.

Main Results:

  • The software demonstrated high specificity in detecting contamination using real-world public datasets.
  • Adipose tissue admixture was detected in 4% to 13% of tested surgical samples.
  • The tool provides detailed reports on contamination assessment, including test parameters and results.

Conclusions:

  • Microarray Inspector is an effective tool for detecting tissue contamination in post-experimental phases.
  • The software enhances the reliability of microarray-based research by ensuring sample quality.
  • Customizable analysis and user-friendly reports make it a valuable resource for the scientific community.