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Application of a Cross-Platform
RNA Standard
for Assessing Microarray Data Comparability
To ensure the reliability of microarray data used in regulatory
decision making, there is a need for “best practices” in sample
generation, sample processing, and data analysis. A critical part of
this process is the use of universal RNA standards for gene
expression technologies. Such reference standards should perform
similarly on multiple microarray formats to allow the assessment of
accuracy, reproducibility, and dynamic range of the data.
In conjunction with external collaborators, research scientists at
CDER have designed and tested a reagent that can provide a basis for
performance assessments on Affymetrix RAE230A, GE Healthcare
CodeLink UniSet Rat I, and Agilent G4130A rat oligonucleotide
arrays. The laboratory component of this study conducted at the FDA
was funded by the FDA Office of Science & Health Coordination for
FY-03.
The reagent is a set of two mixes of tissue RNA samples formulated
to contain different ratios of RNA for each of four rat tissues
(brain, liver, kidney, and testes). The subset of gene probes that
are tissue-selective and present on all 3 platforms are used as
reference probes. Tissue-selectivity was calculated using the
average baseline expression levels in single tissue samples from
control animals. These probes were selected to span the dynamic
range and to map to the same exemplar transcript sequence on all 3
platforms.
This reagent forms the basis of a ratiometric assay in a complex
biological background that can be used to objectively assess the
effect of different array processing methods and conditions on
microarray data comparability within and across platforms. This
approach could be a paradigm for similar performance standards for
mouse and human arrays.
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Date created: June 8, 2005 |
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