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Online
Journal of Bioinformatics ©
Volume
7 (2): 101-117, 2006.
A flexible spot
recognition method for SNP microarray systems.
Huang
CY1, Liu L2.
1Center for Pharmacogenomics and
Complex Disease Research, University of Medicine & Dentistry of New Jersey,
Newark, NJ 07101, USA 2Department
of Applied Mathematics, Chung Yuan Christian University, Chung-Li, Taiwan
32023, ROC
ABSTRACT
Huang
CY, Liu L., A flexible spot recognition method for SNP microarray systems.
Onl J Bioinform, Volume 7 (2) :
101-117, 2006. Image based Microarray processing
has recently found widespread application in biotechnology. With the dramatic
increase in the number of genotyping assays, microarray systems can be utilized
in a high throughput setting to analyze large numbers
of samples and SNPs quickly and efficiently. The flexibility on different
number of SNPs and sample size becomes more and more important to accommodate
different types of research. However, the key in employing this technology
successfully is the ability to accurately detect the spotted samples during
image processing on different image layout. In this paper, we propose a highly
flexible and automated method to acquire spot intensity and status to achieve
this goal. Since there could be many different combinations on the microarray
layout, the image processing method was designed with two distinct processes; a
rough and precise detection using a Circular Template image bipartition, and
mesh algorithms that can automatically and accurately process spot layouts with
minimal information required. For a high throughput system, automatically
detecting the spots with their intensity and classifying the status of spots are
important tasks for automated genotype calling. The methodology presented in
this paper can automatically locate spots on an assay plate and reports their
Foreground Intensity, Background Intensity and status. The approach described
in this paper can be applied on plate, slide, or other type of container for
both gene-expression and SNP genotyping image based system. The overall
accuracy of spot detection was 99.98%. The total processing time is fast enough
to generate more than 1 million genotyping assays per day to be a
high-throughput system.
Keywords: microarray, image, SNP,
genotype, spot, high throughput