Bayesian biomarker identification based on marker-expression proteomics data

We are studying variable selection in multiple regression models in which molecular markers and/or gene-expression measurements as well as intensity measurements from protein spectra serve as predictors for the outcome variable (i.e., trait or disease state). Finding genetic biomarkers and searching...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2008-12, Vol.92 (6), p.384-392
Main Authors: Bhattacharjee, M., Botting, C.H., Sillanpää, M.J.
Format: Article
Language:English
Subjects:
Association analysis
Bayes Theorem
Bayesian hierarchical models
Biomarkers - analysis
CFS
Fatigue Syndrome, Chronic - genetics
Fatigue Syndrome, Chronic - metabolism
Gene Frequency
Genetic Carrier Screening
Genetic Markers
High-throughput analysis
Humans
Markov Chains
Mathematical Computing
Models, Biological
Monte Carlo Method
Polymorphism, Single Nucleotide
Proteomics - statistics & numerical data
Regression Analysis
Variable selection
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Summary:We are studying variable selection in multiple regression models in which molecular markers and/or gene-expression measurements as well as intensity measurements from protein spectra serve as predictors for the outcome variable (i.e., trait or disease state). Finding genetic biomarkers and searching genetic–epidemiological factors can be formulated as a statistical problem of variable selection, in which, from a large set of candidates, a small number of trait-associated predictors are identified. We illustrate our approach by analyzing the data available for chronic fatigue syndrome (CFS). CFS is a complex disease from several aspects, e.g., it is difficult to diagnose and difficult to quantify. To identify biomarkers we used microarray data and SELDI-TOF-based proteomics data. We also analyzed genetic marker information for a large number of SNPs for an overlapping set of individuals. The objectives of the analyses were to identify markers specific to fatigue that are also possibly exclusive to CFS. The use of such models can be motivated, for example, by the search for new biomarkers for the diagnosis and prognosis of cancer and measures of response to therapy. Generally, for this we use Bayesian hierarchical modeling and Markov Chain Monte Carlo computation.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2008.06.006