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Genotyping steps up a gear

16-Jan-2004

Applied Biosystems has launched a new product, based on the combination of a new set of reagents with a software package, that promises to speed up genotyping studies carried out on the firm's 3730 and 3730xl analysers, first introduced in 2002.

Genotyping - the scoring of a single point mutation or single nucleotide polymorphism (SNP) in a patient - has become increasingly important to the pharmaceutical industry as it tackles the issue of pharmacogenomics.

In pharmacogenomics, companies use genotyping experiments to uncover links between SNPs and disease or drug response genes, in the hope that this will help guide their drug development efforts and allow them to target their existing products to the most appropriate patients based on their genetic profiles.

 

The SNPlex Genotyping System uses multiplexing - carrying out a number of reactions in a single tube or well - to identify multiple target sequences in a single biological sample.

 

This means it can be used to carry out both large-scale, genomic discovery studies involving thousands of SNPs, as well as smaller studies involving select SNPs for targeted research.

 

Michael Hunkapiller, Applied Biosystems ' president, said that the new system would allow gene hunters to perform a range of integrated genotyping applications, including microsatellite or SNP-based linkage mapping, fine mapping of SNPs, and resequencing, on the same instrument.

 

Researchers can now genotype 48 SNPs simultaneously in a single biological sample and detect 4,500 SNPs in parallel in as little as 15 minutes. This analysis process equates to a capacity in excess of 400,000 genotypes per 24-hour period. This should lead to economies of scale, driving down the cost of genotyping which to date has held back progress in pharmacogenomics.

 

Future enhancements to the SNPlex System are expected to enable production scale laboratories to analyse more than one million genotypes per instrument per day by genotyping 192 SNPs simultaneously per sample.

 

In the initial release of the product, SNPlex System assays are available in two formats: either as custom-designed assays based on customer-provided SNPs, or as off-the-shelf SNP assays from Applied Biosystems.

 

The first off-the-shelf assay set is the Human Linkage Mapping set, consisting of approximately 3,500 markers based on SNPs taken from The SNP Consortium and the Applera Genomics Initiative, which have been validated across four different populations. The company expects to release additionalfixed assay panels in the coming months.

 

Analysts said that the availability of the new product could help drive sales of Applied Biosystems' analyser range in what is becoming a crowded sector, with competition from the likes of Illumina, Orchid Biosciences, Sequenom and Third Wave Technologies in the US, as well as Qiagen and Biotage in Europe.

 

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