Getting More From Whole-transcript Microarrays

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22nd May 2009, 10:24pm - Views: 747

Getting More from Whole-Transcript Microarrays

MELBOURNE, May 22 /Medianet International-AsiaNet/ --

   The widely-used Affymetrix Whole-Transcript Gene 1.0 ST (sense target) microarray platform,

normally used to assay gene expression, can also be utilized to interrogate exon-specific splicing.

Research published today in the open access journal BMC Bioinformatics shows scientists how to

monitor alternative splicing activity on a genome-wide scale, without investing in new exon

microarray technologies.

   Alternative splicing produces a variety of mRNA transcripts from a single gene by splicing

together different combinations of exons, which can give rise to alternative protein forms that are

functionally distinct. Almost 90% of human genes are now considered to exhibit alternative splicing

and to meet the demand to analyse this on a genome-wide scale, Affymetrix have developed their

Exon 1.0 ST platform. However, the study by Mark Robinson and Terence Speed from the

University of Melbourne and the Walter and Eliza Hall Institute of Medical Research in Australia

suggests that the gene platform can also do the job.

   The scientists explored a publicly available dataset of 11 human tissues that were analyzed on

both the Affymetrix Gene 1.0 ST and the Affymetrix Exon 1.0 ST chips. Robinson said, “Our

intention was not to provide a detailed comparison between those platforms and to suggest that

the Gene array should be used as a replacement for the Exon arrays. We simply wanted to

demonstrate that researchers could get information about differential splicing from the Gene

platform in certain circumstances at no additional experimental cost. We, therefore, provide added

value to their collected data.”

   The authors acknowledge that the ability to detect differential splicing depends on various

factors, including the number of probes covering the gene and the nature of the splicing event.

They constructed a new statistical method, called FIRMAGene, that uses information about

adjacent poorly fitting probes to calculate differential expression in the Gene arrays and showed

that it provides comparable results to the Exon array analysis. The approach can only be used in

well-annotated genes and can detect differential splicing involving multiple exons. However, they

suggested that it should work particularly well for genes containing few exons, since for these

genes the coverage of probes in the Gene platform can be greater than the Exon platform.

   Dr Robinson added that, “To the best of our knowledge, this is the first statistical method that

interrogates differential splicing using the Gene 1.0 ST platform. We have used this method for

uncovering differential splicing in human tissues, where typically a small number of tissues exhibit a

distinct pattern. However, we believe it could be useful in a variety of experimental settings.”

FIRMAGene can be applied to human, mouse and rat samples, for which the latest Affymetrix Gene

1.0 ST platforms are available, or any other whole-transcript microarray design.


   The Walter and Eliza Hall Institute is one of the world’s leading biomedical research centres.

Established in 1915 and affiliated with The University of Melbourne and The Royal Melbourne

Hospital, the Institute's mission is ‘Mastery of Disease through Discovery’. Its world-renowned

research teams have been responsible for breakthrough science and pioneering therapies that have

changed the face of disease and human health worldwide. Today they are focused on four big

global medical challenges: cancer, immunity, autoimmunity and infectious diseases. The Walter and

Eliza Hall Institute is located at Parkville, Victoria where it will soon be housed in a state-of-the-art

new building.

Science Information Technology Walter And Eliza Hall Institute Of Medical Research 2 image

   CONTACT: Michelle Trevorrow

            Head, Fundraising, Communications and External Relations

            Ph: +61 3 9345 2639

            Mob: +61 400 603 150


   SOURCE: Walter and Eliza Hall Institute of Medical Research

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