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Plan B Pathway Prediction Nets GenMetrics $3.8M in Series A

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On route to becoming “another SNP discovery company,” San Jose, Calif.-based startup GenMetrics decided to take a turn and become a protein pathways discovery company instead. Investors did not seem to think this was a bad move — last month, Spaulding Ventures and Rainforest Ventures invested $3.8 million in a series A round in the company, which has three employees at the moment but expects to grow to 10 this month.

The eight founders — coming from Incyte, HySeq, Stanford University, and elsewhere — had worked together in the past and formed GenMetrics in November 2000. Originally planning to study SNPs in certain Chinese populations, they developed various technologies that would help them find drug target candidates based on SNP data. As they put the finishing touches on their toolkit in December, they made a serendipitous discovery: “[We] found out that it could work to predict novel protein pathways,” said CEO Chris Piercy.

At first, the company intended to stick to its original SNP-based business plan, but “after we kept working on it and working on it, we realized that this technology was a lot more powerful,” said Piercy — powerful enough to become the foundation of the entire company, at least for now.

The company’s patent-pending technology combines sequence comparisons, classical dynamic programming, and statistical clustering to predict protein pathways. It draws from a custom database that GenMetrics has been building by integrating hand-curated protein pathway data extracted from the scientific literature with public and proprietary genomic and gene expression data. In a test run, the engine predicted known pathways as well as novel ones, which GenMetrics is now trying to validate experimentally. But before offering its software products — PMsearch, PMpredict, MamPath and MicroPath — to others in the summer, GenMetrics is planning to patent a number of pathway-based drug target candidates. “We believe that because by definition we show function …, that they will have value similar to the SNP drug target candidates,” Piercy said. “Initially we were going to start by selling the tool products,” he explained, “but that’s kind of like selling the picks and shovels to the gold mine.” He is also hoping for partnerships with pharma companies, some of which are currently beta-testing GenMetrics’ pathway engines.

For now, the company — which counts former employers Incyte and Hyseq, as well as Millennium and Genentech among its main competitors — will make use of the new funding by expanding its staff, moving into 9,000 square feet of lab space in April, and increasing its protein pathway database, said Piercy. — JK

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