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Backed by New Investors, LightSpeed Genomics Plans to Test its Detection Tech for Sequencing

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After going through a restructuring phase at the end of last year in which it temporarily laid off its entire staff, LightSpeed Genomics has secured new investors and continues to develop its optical-detection technology, which it plans to integrate with a new sequencing chemistry this year, In Sequence has learned.

The startup, based in Sunnyvale, Calif., said it believes that the resulting sequencing system will provide "dramatically improved cost and speed of sequencing."

The three new investors — which LightSpeed co-founder and CEO Josh Ryu said are "very committed to the growth of the company" — are the Korea Technology Investment Company, Hanmi Venture Capital, and sequencing service provider Macrogen.

Besides Ryu, LightSpeed was co-founded by former MIT colleague Stanley Hong, and others. Its platform is based on optical detection technology developed by Ryu and others at MIT (see In Sequence 2/5/2008). George Church, a professor at Harvard Medical School, is a member of the firm's scientific advisory board.

In January 2007, LightSpeed, which has not yet publicly revealed its technology or business plans, received an undisclosed amount of funding in its first financing round from venture capital firm Rockhill Partners and other investors.

Ryu, a former Affymetrix staff scientist, told In Sequence last week that at the end of January, the company closed its new financing round of undisclosed size with the Korean DNA sequencing-service provider and the two Korean VC firms.

Originally, LightSpeed had reached an agreement with the investors in November, but due to "financial turmoil" in Korea at that time, that agreement fell through and the investor trio came up with a new proposal, he said.

Because the company ran out of cash before that round closed, in December it was forced to temporarily lay off all of its employees — fewer than 10 at the time — according to Ryu.

The Rockhill Partners website states that Rockhill is no longer an investor in the company. After its initial 2007 investment, it says, Rockhill helped LightSpeed obtain a venture debt financing by Western Technology Ventures, and a strategic equity investment by Macrogen in 2008.

The website also states that "LightSpeed was successfully acquired by Macrogen Corporation and the Korea Technology Investment Corporation in February 2009." However, Ryu said this is not true — they have merely invested in LightSpeed — and that the company remains an independent firm.

The January round enabled LightSpeed to become operational again in February and to hire new staff, and some but not all of the original employees, including Ryu. He declined to comment on whether Stan Hong, LightSpeed's co-founder and chief technology officer, is still with the company.

"We are continuing to develop the same core technology at the same location in California," Ryu said.

The size of the company is about the same as it was before the restructuring, according to Ryu. "We have a suitable combination of expertise that will get the technology into commercialization," he said. "Overall, we are moving much faster."

Later this year, he said, the company plans to test its optical-detection technology with "new and advanced" sequencing chemistry. "Such synergistic integration will lead to a new sequencing system with dramatically improved cost and speed of sequencing," he said. He did not elaborate on the nature of the sequencing chemistry.

LightSpeed's detection technology "dramatically improves the data conversion between the chemical domain and the electronic domain," according to Ryu.

The technology involves selectively exciting DNA particles on a substrate and is described in two patent applications by Ryu, Hong, and another inventor that the US Patent and Trademark Office published last month.

The patent applications, No. 20090061526 and 20090061505, cover "Nucleic Acid Sequencing by Selective Excitation of Microparticles" and an apparatus for exciting DNA microparticles, respectively.

According to the applications, existing optical DNA sequencing technologies suffer from low throughput because the rate at which they can detect optical signatures of DNA features, for example from fluorescent labels, is limited.

"This is largely due to the use of conventional non-selective excitation patterns, followed by optical imaging using optical microscopy," according to the application.

LightSpeed's new method, on the other hand, selectively excites DNA microparticles that are being sequenced, images them at a resolution that is not sufficient to resolve them individually, and uses image processing algorithms to extract their optical signatures.

A relatively low-resolution optical microscope can be used for imaging, and the detection can be performed "with an extremely large field of view and depth of field." Also, the low-resolution images of the particles "are a more efficient data representation of the sequence information than high-resolution images of microparticles with non-selective excitation," according to the application.

As a result, imaging is faster and the amount of data collected is "greatly reduced," the application says.

Ryu said LightSpeed is "making a lot of progress" on developing its detection technology, and has a technology collaboration with undisclosed academic and commercial partners ongoing.

The company is also collaborating strategically with its investor Macrogen on developing an "ultra-low-cost, ultra-high-throughput sequencing technology and process", Ryu said, and applying it "to personalized medicine." He did not elaborate.

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