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By Malorye A. Branca

February 18, 2004 | Today's genotyping tool companies don't just want to be faster, better, and cheaper — they also want to sell into every segment of this diverse market. For example, Sequenom and Illumina recently released "benchtop" systems for customers working on smaller projects.

In the throughput race, several companies have broken away from the pack, offering platforms that allow hundreds of thousands to millions of genotypes to be performed in a day. But those leaders are not complacent. "There are some big players like Affymetrix and Applied Biosystems moving into this market," says Illumina's president and CEO Jay Flatley.

Developed for use on ABI's 3730 DNA analyzer, the new ABI SNPlex technology nicely complements the company's current products for the lower-throughput market. "There is no consensus yet about how many markers will be needed," says Michael Rhodes, senior application specialist at ABI. SNPlex accommodates low to high levels of multiplexing, which makes it flexible. The company aims to raise the throughput to a million genotypes a day. It has also launched a free site, www.allsnps.com/snpbrowser, to help researchers in their design studies.

Affymetrix, meanwhile, is counting on its ability to provide bigger and bigger sets of SNPs, economically, according to Greg Yap, senior director of DNA analysis marketing at Affymetrix. "The target is the association study market," he says.

Newcomer ParAllele BioScience's unique technology allows the study of as many as 12,000 SNPs in a single reaction, according to company president Nick Naclerio. "Our strength is where you are doing thousands of SNPs," he says. The technology is also aimed at finding rare SNPs.

Accuracy is a priority, given that error rates can be as high as 6 percent. This is largely due to operator experience. All the platforms used in the HapMap project, for example, are reaching about 99.5 percent accuracy, according to Lisa Brooks of the National Human Genome Research Institute. Experts advise groups tackling very large projects to use at least two platforms, to cross-validate results and to provide insurance against technical error.

Some companies foresee diagnostic applications. Dynametrix's DASH (dynamic allele-specific hybridization) system is "ideal for low- to medium-throughput research projects, or diagnostic and mutation scanning," says Anthony Brookes, the company's founder. Dynametrix touts the high accuracy and low cost of its method, which are critical for diagnostic applications.


Some High-End Genotyping Platforms

Company  Selected Products Highest Genotyping Throughput
Affymetrix GeneChip Mapping Array; soon launching a 100,000 SNP GeneChip Currently 10,000 genotypes per chip; developing 100,000 SNP chip
Applied Biosystems SNPlex More than 1 million genotypes per instrument per day
Beckman Coulter GenomeLab SNPstream 4,600 to more than 800,000 genotypes per day
Illumina BeadArray platform and GoldenGate assay More than 2 million per day, 1,520 SNPs per well
Luminex xMAP microsphere technology Up to 50,000 genotypes per day
ParAllele Molecular Inversion Probe (MIP) assays More than 12,000 genotyping reactions in a single tube, more than 1 million genotypes per day
PerkinElmer FP-DTI (fluorescent polarization detection with template directed dye terminator Incorporation assay) More than 50,000 genotypes per day
Sequenom MassArray platform, and MassEXTEND reagents 20K model can do up to 200,000 genotypes per day multiplexing



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