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Search: L773:0219 7200 OR L773:1757 6334 > A variational bayes...

A variational bayes beta mixture model for feature selection in DNA methylation studies

Ma, Zhanyu, 1982- (author)
KTH,Kommunikationsteori
Teschendorff, Andrew E. (author)
Statistical Genomics Group, Paul O'Gorman Building, UCL Cancer Institute, University College London
 (creator_code:org_t)
2013
2013
English.
In: Journal of Bioinformatics and Computational Biology. - 0219-7200 .- 1757-6334. ; 11:4, s. 1350005-
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • An increasing number of studies are using beadarrays to measure DNA methylation on a genome-wide basis. The purpose is to identify novel biomarkers in a wide range of complex genetic diseases including cancer. A common difficulty encountered in these studies is distinguishing true biomarkers from false positives. While statistical methods aimed at improving the feature selection step have been developed for gene expression, relatively few methods have been adapted to DNA methylation data, which is naturally beta-distributed. Here we explore and propose an innovative application of a recently developed variational Bayesian beta-mixture model (VBBMM) to the feature selection problem in the context of DNA methylation data generated from a highly popular beadarray technology. We demonstrate that VBBMM offers significant improvements in inference and feature selection in this type of data compared to an Expectation-Maximization (EM) algorithm, at a significantly reduced computational cost. We further demonstrate the added value of VBBMM as a feature selection and prioritization step in the context of identifying prognostic markers in breast cancer. A variational Bayesian approach to feature selection of DNA methylation profiles should thus be of value to any study undergoing large-scale DNA methylation profiling in search of novel biomarkers.

Subject headings

NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Signalbehandling (hsv//swe)
ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Signal Processing (hsv//eng)

Keyword

Feature selection
beta mixture
DNA methylation
variational Bayes
SRA - Molecular Bioscience
SRA - Molekylär biovetenskap
SRA - ICT
SRA - Informations- och kommunikationsteknik

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