Gene Methylation Data – a New Challenge for Bioinformaticians?

G. Goebel; H. M. Müller; H. Fiegl; M. Widschwendter

doi:10.1055/s-0038-1634002

Methods of Information in Medicine, Table of Contents

Methods Inf Med 2005; 44(04): 516-519
DOI: 10.1055/s-0038-1634002

Original Article

Schattauer GmbH

Gene Methylation Data – a New Challenge for Bioinformaticians?

G. Goebel

¹Department of Medical Statistics, Informatics and Health Economics, Innsbruck Medical University, Innsbruck, Austria

,

H. M. Müller

²Department of General and Transplant Surgery, Innsbruck Medical University, Innsbruck, Austria

,

H. Fiegl

³Department of Gynaecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria

,

M. Widschwendter

³Department of Gynaecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria

› Author Affiliations

Abstract

Summary

Objectives: Changes in the status of DNA methylation, known as epigenetic alterations, are among the most common molecular alterations in human neoplasia. For the first time, we reported on the analysis of fecal DNA from patients with CRC to determine the feasibility, sensitivity and specificity of this approach. We want to present basic information about DNA methylation analysis in the context of bioinformatics, the study design and several statistical experiences with gene methylation data. Additionally we outline chances and new research questions in the field of DNA methylation.

Methods: We present current approaches to DNA methylation analysis based on one reference study. Its study design and the statistical analysis is reflected in the context of biomarker development. Finally we outline perspectives and research questions for statisticians and bioinformaticians.

Results: Identification of at least three genes as potential DNA methylation-based tumor marker genes (SFRP2, SFRP5, PGR).

Conclusions: DNA methylation analysis is a rising topic in molecular genetics. Gene methylation will push the extension of biobanks to include new types of genetic data. Study design and statistical methods for the detection of methylation biomarkers must be improved. For the purpose of establishing methylation analysis as a new diagnostic/prognostic tool the adaptation of several approaches has become a challenging field of research activity.

Keywords

DNA methylation - biological tumor marker - genetic marker - colonic neoplasms - computational biology

Full Text

References

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