Bayesian methods for proteomic biomarker development

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Title: Bayesian methods for proteomic biomarker development
Authors: Hernández, Belinda
Pennington, S. R. (Stephen R.)
Parnell, Andrew C.
Permanent link: http://hdl.handle.net/10197/7966
Date: Dec-2015
Abstract: The advent of liquid chromatography mass spectrometry has seen a dramatic increase in the amount of data derived from proteomic biomarker discovery. These experiments have seemingly identified many potential candidate biomarkers. Frustratingly, very few of these candidates have been evaluated and validated sufficiently such that that they have progressed to the stage of routine clinical use. It is becoming apparent that the statistical methods used to evaluate the performance of new candidate biomarkers are a major limitation in their development. Bayesian methods offer some advantages over traditional statistical and machine learning methods. In particular they can incorporate external information into current experiments so as to guide biomarker selection. Further, they can be more robustto over-fitting than other approaches, especially when the number of samples used for discovery is relatively small. In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.
Funding Details: European Commission - Seventh Framework Programme (FP7)
Health Research Board
Irish Research Council
Science Foundation Ireland
Type of material: Journal Article
Publisher: Elsevier
Copyright (published version): 2015 Elsevier
Keywords: Bayesian statistics;R;Proteomics biomarker discovery;LC–MS
DOI: 10.1016/j.euprot.2015.08.001
Language: en
Status of Item: Peer reviewed
Appears in Collections:Conway Institute Research Collection
Mathematics and Statistics Research Collection
Medicine Research Collection
Insight Research Collection

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