Biomedical Engineering Reference
In-Depth Information
Step of the Procedure
Notes
8. Fluorescence scanning
Figure 10.5 shows fluorescence
Fluorescence signals on the slides are detected
images of a microarray scanned
using a four color laser scanner (e.g.
at four different wavelengths
ScanArray
R
5000, Perkin Elmer LifeSciences).
after hybridization of a
The signal intensities are measured with the
cyclic minisequencing product.
analysis software of the scanner (QuantArray
R
).
9. Genotype assignment A software for genotype as-
The mean value of the signals from the duplicate signment for SNPs is the
spots is corrected for the average background
SNPsnapper software, available
in the reaction well. Genotypes are assigned
at:
by calculating the ratio between the signal
http://www.bioinfo.helsinki.fi/
intensity from one of the alleles divided by
SNPSnapper/
the sum of the signals from both alleles
using a Microsoft Excel
TM
macro.
10.4 Conclusion
During the past few years much effort has been targeted at developing
technology for analyzing DNA sequence variation in the microarray format.
Microarray-based methods have also been applied in a number of clinical, ge-
nomic and evolutionary studies. Table 10.2 provides some examples of these
applications. So far the studies have been of modest size, but with the possi-
bility of a high level of multiplexing to bring down the costs of the microarray-
based assays, we can foresee studies on a much larger scale that will increase
our understanding of the role of DNA sequence variation in health and disease.
Table 10.2.
Examples of applications of microarray-based analysis of DNA sequence
variants
Application
Reaction
Comment
Ref.
principle
Comparative sequencing ASO-hybridization Introduction of
[49]
microarray concept
Cystic fibrosis
Affymetrix
First use of GeneChip
R
[50]
mutations
GeneChip
R
for genotyping
Recessive disease muta-
Minisequencing
Proof of principle for
[29]
tions in Finland
primer extension
primer extension on arrays
Mutation detection in
ASO-hybridization Strategy for multiplex
[13]
the ATM gene
GeneChip
R
PCR design
33
P-detection
Risk factors for myocar- Minisequencing
[51]
dial infarction
primer extension
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