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A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies
09:32

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

Published on: September 23, 2014

Extending the tissue microarray data exchange specification for inclusion of data analysis results.

Oliver Lyttleton1, Alexander Wright, Darren Treanor

  • 1Institute of Life Science, School of Medicine, University of Wales, Swansea, SA2 8PP, U.K.

Journal of Pathology Informatics
|May 17, 2011
PubMed
Summary

We extended the Tissue Microarray Data Exchange Specification (TMA DES) to include statistical analysis results. This enhances data sharing and ensures compatibility with existing TMA DES data.

Keywords:
CDEsDTDTMA Data Exchange SpecificationXMLstatistical analysistissue microarray

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Standards

Background:

  • The Tissue Microarray Data Exchange Specification (TMA DES) is an XML standard for encoding tissue microarray experiment data.
  • TMA DES defines Common Data Elements (CDEs) for describing TMA data, which is often analyzed using statistical tests.
  • Statistical analysis results from TMA data require standardized recording and storage alongside the experimental data.

Purpose of the Study:

  • To extend the TMA DES by incorporating CDEs for describing statistical analysis results.
  • To develop a machine-readable and human-readable format for annotating TMA DES data with analysis outcomes.
  • To ensure the proposed extension is syntactically and semantically valid, error-checking capable, and backward compatible.

Main Methods:

  • Developed new CDEs for statistical analysis results and integrated them into the TMA DES.
  • Created a Document Type Definition (DTD) file for syntax and ISO 11179 entries for semantics.
  • Implemented an R program to process TMA DES data, perform analyses, and generate extended XML files.
  • Validated the extended DTD using XML parsers for syntax checking, error detection, and backward compatibility.

Main Results:

  • Successfully encoded statistical analysis results using the proposed CDEs within TMA DES XML files.
  • Confirmed syntactic correctness and adherence to the extended DTD rules via XML parsers.
  • Demonstrated the extended DTD's capability for error checking and backward compatibility with existing TMA DES data.

Conclusions:

  • The proposed extension to TMA DES effectively annotates TMA data with statistical analysis results.
  • The enhanced TMA DES facilitates improved data sharing and integration of analytical findings.
  • Experimental validation confirmed the proposed CDEs' utility, syntactic correctness, and backward compatibility.