DNA Microarray Technology - DNA Microarray Technology and Data Analysis in Cancer Research - page 7

of DNA microarray results is associated with technical, instrumental,
computational, and interpretative factors (Casciano and Woodcock,
2006). For the same samples tested, results obtained at different loca-
tions and between different microarray platforms could be different,
making it difficult to use and interpret microarray data. Optimization
and standardization of microarray procedures are critical steps. In this
regard, the US Food and Drug Administration (FDA) has initiated
a MicroArray Quality Control (MAQC) project among researchers in
academic, government, and industrial institutions to seek to experimen-
tally address the key issues surrounding the reliability of DNA microar-
ray data. As part of this effort, since 2004 the FDA has started accepting
voluntary genomic data submission with accompanying information
related to the number and scope of DNA microarray-based expression
data (Anonymous, 2006). The MAQC project aims to establish quality
control metrics and thresholds for an objective assessment of the per-
formance achievable by different microarray platforms, and for evalua-
tion of the merits and limitations of various data analysis methods
(Casciano and Woodcock, 2006). The specific concerns of the MAQC
project relate to the impact of microarray data quality on genomic data
submission (Frueh, 2006; Ji and Davis, 2006), the framework for the use
of genomics data (Dix et al ., 2006), comparisons of different commer-
cial microarray platforms (Canales et al ., 2006; Patterson et al ., 2006;
Shippy et al ., 2006), the use of external RNA controls (Tong et al .,
2006), interplatform and intraplatform reproducibility of gene expres-
sion measurements (Shi et al ., 2006), and analytical consistency across
microarray platforms (Guo et al ., 2006).
The main conclusion of the MAQC project is that, with careful experi-
mental design and appropriate data transformation and analysis, microar-
ray data can indeed be reproducible and comparable between different
formats and laboratories, and that fold change results from microarray
experiments correlate closely with results from well-accepted assays such
as quantitative reverse transcription-polymerase chain reaction (qRT-PCR)
(Anonymous, 2006). However, there is still a long way to go before we can
answer the key remaining question: when can microarray data be used in a
regulatory decision-making process?