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Precision profiling and components of variability analysis for Affymetrix microarray assays run in a clinical context
Thomas M Daly1, Carmen M Dumaual, Crystal A Dotson
1Division of Experimental Medicine, Genomic Medicine Group, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46240, USA. dalytm@lilly.com
The Journal of Molecular Diagnostics : JMD
|July 29, 2005
Summary
This study assessed Affymetrix microarray analytical variability for clinical use. Results show acceptable precision for gene expression profiling assays, supporting clinical validation.
Area of Science:
- Molecular Biology
- Genomics
- Clinical Diagnostics
Background:
- Microarray technology is prevalent in research but underutilized in clinical settings.
- Evaluating analytical variability is crucial for adopting microarray assays in clinical laboratories.
Purpose of the Study:
- To assess the analytical variability of Affymetrix microarray probesets.
- To determine the suitability of microarray technology for clinical laboratory applications.
Main Methods:
- Evaluated two generations of human Affymetrix chips (U95Av2 and U133A).
- Mimicked clinical settings using multiple operators, instruments, and reagent lots over several months.
- Employed mixed model analysis to identify sources of variability.
Main Results:
- Average probeset coefficient of variation (CV) was 21.9% (U95Av2) and 27.2% (U133A).
- Chip-to-chip variability was the largest contributor (40-60%) to overall variation.
- Operator, instrument, and reagent lot variations had minimal impact.
Conclusions:
- The demonstrated approach is suitable for clinical validation of Affymetrix-based assays.
- The analytical precision of microarray technology is adequate for many biological questions in a clinical context.