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BioTrove Beta-Launches Custom SNP Chip at Tri-Conference: Parallel PCR Array Alternative

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BioTrove went live last week with a version of its living chip — a nanofluidics system for parallel biological analysis — that can genotype over 3,000 SNPs at a time.

The four-year-old Woburn, Mass., company chose the Molecular Medicine Tri-conference, held last week at San Francisco’s Moscone Convention Center, to launch the chip, in an effort to find beta testers for this application.

The Tri-conference is one “where you do get, traditionally, a lot of thought leaders,” said Bob Ellis, the company’s CEO.

The chip is based on technology licensed from MIT researchers Ian Hunter and Colin Brenan, and includes thousands of nanoliter-volume holes, each with hydrophilic coating on the inside, and sandwiched between two hydrophobic surfaces, Ellis said.

These chips come in two formats: the microplate size and the 1 x 3 inch slide format.

While the company has long term plans to use these parallel nanoliter-volume chambers for numerous applications, including cell-based assays, “we decided to focus where [there was] a market opportunity,” Ellis said. And this immediate opportunity was in genetics and genomics. “What we’re announcing is the first in a series of genomics and genetics products, which would lead into protein products, which would lead into [cell-based assay] products,” Ellis said.

Seasoned in SNPs

Ellis has ample experience launching products in the genomic space. Before joining BioTrove in October 2003, he had served as executive vice president at Affymetrix, where he oversaw R&D related to commercialization of the company’s GeneChip technology (Affymetrix launched a mapping 10,000-spot array for SNP analysis last July.) Prior to working at Affymetrix, between 1998 and 2001, Ellis was president of Genometrix, a now-defunct microarray startup based in the Woodlands, Texas. The company marketed an array-based SNP genotyping technology and under one collaboration, worked with researchers in Nippon Medical School in Tokyo to validate osteoporosis-related SNPs.

Prior to joining Genometrix, Ellis cut his teeth in the field at Applied Biosystems, and its predecessor company, PerkinElmer, where he started as a product manager and eventually became manager of a business unit.

Parallel PCR

The SNP chip has 3,072 holes, and comes with pre-dried down PCR primers. The idea is to be able to query thousands of SNPs per sample, as with a microarray, but with the quantitative accuracy of PCR, Ellis said. The product can be used with a standard scanner, along with a flatbed thermocycler.

In January, the company began alpha testing the SNP chip with a psychiatry group at Massachusetts General Hospital. In a pilot study, the group genotyped 90 Coriell CEPH DNA samples using 130 Taqman SNP detection probes from Applied Biosystems. They then transferred the assays from microplates into BioTrove’s chip using its reformatting technology.

Jesen Fagerness, Project Manager for the Psychiatry Department, assessed the data and found an 88.5 percent assay pass rate with an average genotyping call rate of 96.3 percent, BioTrove reported at the conference. The company also said that the results were 99.4 percent concordant with the genotype calls from the HapMap project. “I am pleased with the pilot’s outcome and impressed with BioTrove’s rapid technical progress,” Fagerness said in a statement.

The company plans to launch the SNP chip as a custom service in July to customers that already have TaqMan probe primer sets. “We will gladly load those into the chips and run the chips,” Ellis said.

By the end of the year, BioTrove also plans to launch a Living Chip product that can do transcript analysis, along with a real-time scanning thermocycler.

The company also has designed a 25,000-hole 25 nanoliter plate in a 3 x 5 inch microplate format, for screening applications.

Future products in genomic and genetic analysis may include a 9,000- SNP chip, and the company is “also toying with the data in the HapMap project,” Ellis said.

— MMJ

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