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Will Inexpensive Haplotype Technology Grant Newcomer PolyGenyx Second Chance at Life?


Though it’s just a two-person outfit, the once-promising Worcester, Mass., SNP genotyping startup PolyGenyx is looking for a second shot at success in the form of an inexpensive haplotyping technology.

The technology, based on the Luminex 100 microbead system, requires less than one hour for users to haplotype samples that involve two-SNP or multi-SNP haplotpyes, according to co-founder John Landers.

In the haplotyping process, allele-specific oligos for one SNP are attached to differently colored Luminex polystyrene beads. The sample, which is then amplified but not purified using PCR, is added to the beads in a test tube. Next, complementary allele-specific oligos labeled with biotin are added in two reaction tubes, along with a hybridization buffer.

The labeled mixture is spun down after 30 minutes of hybridization, then streptavidin-RPE is added and a second 15-minute round of hybridization is performed before analysis on the Luminex 100.

For example, a DNA fragment with a C-T polymorphism and an A-G polymorphism would be tested using allele-specific oligos for each of the C and T alleles, which would each be attached to a different colored bead. Then, detector allele-specific oligos that represent the alleles of the second SNP would be synthesized, biotynylated, and added to the mixture.

If the sample hybridizes to the capture oligos and the detector oligos, the signal would be generated, indicating that a particular haplotype is present.

A haplotype comprising up to 50 SNPs can be determined in just two test tubes, Landers said. The system can do up to 96 samples in a one-hour run.

While the cost per haplotype depends on the number of SNPs being analyzed, Landers said the total cost would be limited to the cost of the beads — “you need about 2,000 beads per SNP per assay, and you get about 107 beads for 100 bucks” — the PCR reaction costs, buffers, labels, oligos, and test tubes.

“There’s no elaborate or expensive reagent,” he said. He presented the technology two weeks ago to attendees of the LabAutomation conference in Palm Springs, Calif.

Landers is targeting HaploScan at the diagnostics market as well as at researchers who want to do inexpensive haplotyping assays on a small number of SNPs in a large number of samples. While he acknowledged there is abundant competition in the market, Landers insisted that “the other ones out there are really not set up for high-throughput analysis and are quite expensive. We feel we are a lot more set up for a diagnostic laboratory setting,” he said.

Landers and his partner in the venture, CEO Christopher Simmons, developed the haplotyping technology with a $99,968 Phase I SBIR grant they received from the NIH in fiscal year 2002.

Work on the technology began after Lander’s first company failed to find continued financing. That company, founded in 1998, hoped to commercialize genotyping technology that Landers developed while a researcher at the MIT Cancer Research Center.

The original investor, West Pharmaceutical Services, funded the company with an initial $3.3 million and promised another $1.8 million but backed out in November 2001, according to a mid-November article in a local newspaper.

The decision not to finance the company further was not due to any failure on the part of Polygenyx, the article quoted West Pharmaceutical’s vice president and treasurer as saying, but rather to West Pharmacueticals’ own investment priorities. In fact, previous PolyGenyx collaborators have said positive things about the company, but instead had assumed it folded.

Now, Landers and Simmons are out on the PowerPoint circuit, looking for funding and commercialization partners. Will they strike success the second time around?



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