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Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Sanguinetti, Guido

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Volume 4, Issue 1


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Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies

Jochen Jaeger / Dieter Weichenhan / Boris Ivandic / Rainer Spang
Published Online: 2005-04-26 | DOI: https://doi.org/10.2202/1544-6115.1109

We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a small number of individual patient samples. From this Phase-1 data a panel of marker genes is derived. In Phase-2, the expression values of these marker panel genes are measured for a large group of patients and a predictive classification model is learned from this data. Phase-2 does not require the use of expensive whole genome microarrays, thus making EMPD a cost efficient alternative for current trials. The expected performance loss of EMPD is compared to designs which use genome-wide microarrays for all patients. We also examine the trade-off between the number of patients included in Phase-1 and the number of marker genes required in Phase-2. By analysis of five published datasets we find that in Phase-1 already 16 patients per group are sufficient to determine a suitable marker panel of 10 genes, and that this early decision compromises the final performance only marginally.

Keywords: medical diagnostics; diagnostic chip design; microarray; gene expression; marker genes

About the article

Published Online: 2005-04-26

Citation Information: Statistical Applications in Genetics and Molecular Biology, Volume 4, Issue 1, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.2202/1544-6115.1109.

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