Gene methylation data--a new challenge for bioinformaticians?
OBJECTIVE
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.
Goebel
G
G
Department of Medical Statistics, Informatics and Health Economics, Innsbruck Medical University, Austria. georg.goebel@uibk.ac.at
Müller
H M
HM
Fiegl
H
H
Widschwendter
M
M
D014408:Biomarkers, Tumor; D003110:Colonic Neoplasms / Q000235:genetics*; D019295:Computational Biology; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005240:Feasibility Studies; D006801:Humans; D012680:Sensitivity and Specificity
D014408:Biomarkers, Tumor