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OJB®
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. Online J Bioinformatics, 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