DNA Microarray Technology - DNA Microarray Technology and Data Analysis in Cancer Research - page 6

availability and amount of human cells for sorting out a particular cell pop-
ulation can be difficult. In parallel, the different genetic background of
each human patient will cause some differences in gene expression when a
comparison is made among different patients with the same type of cancer.
Regardless of these difficulties, DNA microarray technology has been
found to be useful in the clinic, although there is still a long way to go
before DNA microarray results can be used to support regulatory decision
making or accurate and consistent prediction of patient outcomes.
Here is an excellent example of how to perform a DNA microarray
study using human cancer patient samples. In an elegant study of gene
expression profiles of human breast cancer cells, a comparison of gene
expression was made between breast cancer cells with higher tumorigenic
capacity and normal breast epithelium (Liu et al ., 2007). Specifically, the
tumor cells were low or undetectable levels of CD24 (CD44 + CD24 −/low ),
whereas the phenotype of cells from normal breast epithelium was unknown.
A 186-gene invasion-associated signature obtained from this study sug-
gests that there is a significant association between tumor invasion and
both overall and metastasis-free survival in breast cancer patients. A criti-
cal question to ask is whether the normal breast epithelium is an appro-
priate control in this DNA microarray study. No matter what the answer
is, it is clear that the normal breast epithelium is one of the best controls
available.
1.3. Quality Control
A major issue in DNA microarray technology is its repeatability and repro-
ducibility. Repeatability refers to the ability to provide closely similar
results from replicate samples processed in parallel at the same test location
using the same gene expression assay. Reproducibility refers to the ability
to provide closely similar results from replicate samples processed with
different microarray platforms or at different test locations using the same
gene expression assay. To achieve high repeatability and reproducibility,
quality control has become a key issue in DNA microarray studies.
A major criticism voiced about DNA microarray studies has been the
lack of accuracy and reproducibility of the microarray data. The quality