Journal
BMC BIOINFORMATICS
Volume 11, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1471-2105-11-594
Keywords
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Funding
- European Union [LSHM-C7-2006-037093, HEALTH-F2-2008-202230]
- EuroKUP COST Action [BM0702]
- DECanBio [201333]
- European Community [HEALTH-F2-2009-241544]
- Agence Nationale pour la Recherche [ANR-07-PHYSIO-004-01]
- Inserm
- Direction Regional Clinique (CHU de Toulouse, France)
- Science Foundation Ireland [06/CE/B1129]
- EPSRC [EP/E052029/2, EP/F009429/1] Funding Source: UKRI
- MRC [G0401466] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [EP/E052029/2, EP/F009429/1] Funding Source: researchfish
- Medical Research Council [G0401466] Funding Source: researchfish
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Background: The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As tractable example we define the measurable proteomic differences between apparently healthy adult males and females. We choose urine as body-fluid of interest and CE-MS, a thoroughly validated platform technology, allowing for routine analysis of a large number of samples. The second urine of the morning was collected from apparently healthy male and female volunteers (aged 21-40) in the course of the routine medical check-up before recruitment at the Hannover Medical School. Results: We found that the Wilcoxon-test is best suited for the definition of potential biomarkers. Adjustment for multiple testing is necessary. Sample size estimation can be performed based on a small number of observations via resampling from pilot data. Machine learning algorithms appear ideally suited to generate classifiers. Assessment of any results in an independent test set is essential. Conclusions: Valid proteomic biomarkers for diagnosis and prognosis only can be defined by applying proper statistical data mining procedures. In particular, a justification of the sample size should be part of the study design.
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