©1996-2007 All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
OJB®
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
journal of 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