Knome, a personal genomics startups located in Cambridge, MA, announced today the launch of its newest product, a partial genome sequencing package called KnomeSELECT. The service will cost $24,500 for individuals, but is discounted to $19,500 per person for couples and family groups. The firm’s more comprehensive whole-genome sequencing service, KnomeCOMPLETE, costs $99,000. Rather than decoding a person’s entire genetic blueprint, KnomeSELECT looks only at the exome, the protein-coding regions of the DNA.

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It’s getting cheaper by the day to sequence the entire string of 6 billion chemical units of DNA that make up an individual human being. Yesterday, Complete Genomics of Mountain View, CA unveiled plans for what amounts to a democratization of genomics. It will offer a service to sequence full human genomes for just $5,000, beginning in the second quarter of 2009.

At Xconomy, we normally focus on companies based in Boston, Seattle, and San Diego, but we couldn’t resist digging into this one, because it has multiple connections to our network cities. Complete Genomics raised its seed capital in 2006 from OVP Venture Partners in Kirkland, WA, and Enterprise Partners in San Diego. It also counts a pair of Xconomists, Leroy Hood of the Institute for Systems Biology in Seattle, and George Church of Harvard Medical School, as scientific advisers.

So we tracked down OVP managing director (and Xconomist) Chad Waite to find out why he decided to invest in this technology versus all the other sophisticated instruments made by companies like Applied Biosystems, Illumina, 454 Life Sciences, and Helicos Biosciences. (He proudly pointed out that his Harvard Business School connection to CEO Clifford Reid gave him the inside track on this investment, and he invited Drew Senyei of Enterprise in on the action, but more on that later.)

It turns out Waite was sold on Complete Genomics because it has a fundamentally different vision of the market from its rivals. Instead of trying to sell a machine to pharmaceutical companies and top academic labs for hundreds of thousands of dollars, Complete Genomics plans to keep the work in-house on its own proprietary machines and offer sequencing as a service. The company plans to open 10 sequencing centers around the world over the next five years, with the capacity to sequence 1 million complete human genomes. It will have enough bandwidth to sequence an entire genome for $5,000 in about four days, compared with $100,000 and six weeks to six months on currently marketed instruments, Waite says.

“We’re disruptive on technology, and on the business model,” Waite continues. “We’re not going out and trying to sell million-dollar machines. Is there really a competitive advantage for a pharmaceutical company to have the machine? The advantage for them is in the data. They want the data.”

So how might that be really useful for companies or academics? At that high speed and low price, it’s conceivable that drug companies will want to sequence every patient who enters a clinical trial to provide clues as to why some patients respond differently than others to experimental drugs, Waite says. Or, they might want to run big experiments that compare the genomes of 1,000 patients with diabetes to 1,000 other people as healthy controls, to look for tiny genetic variations that might offer clues. They could look at a bunch of prostate cancer tumor samples to try to find genomic markers that explain why the disease spreads more quickly in some people than in others, Waite says.

These concepts are truly mind-boggling when you look at the recent history of …Next Page »

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A local group has finally thrown its hat into the ring for the $10 million Archon X Prize for Genomics, and it’s a biggie: the newly minted Personal Genome X-Team (PGx), led by genomics pioneer George Church.

Church, a Harvard Medical School professor of genetics and co-founder of companies including Cambridge, MA’s Codon Devices and Silicon Valley’s LS9, was one of the main instigators of the Human Genome Project. That project produced one sequence of the DNA of an anonymous person. But Church has been an important advocate for the idea that we all should have access to our individual genomes, and that personal, non-anonymous genome sequencing should be a quick, affordable part of research, healthcare, and our lives. For the last few years, he and his team have been pursuing that vision through what he calls the Personal Genome Project (PGP) , an effort to develop new sequencing technologies, new IT tools for interpreting genomic data, and a solid framework for considering the ethical, legal, and social issues surrounding genomics.

In a sense, the creation of the Personal Genome X-Team marks an intersection of what have been up until now parallel efforts to spur the development of personal genomics—the PGP and the Archon X Prize. The X Prize Foundation launched the its genomics competition in October, 2006, offering $10 million to the first team to sequence 100 human genomes within 10 days for less than $10,000 per genome. By way of context, the last sequencing milestone was Branford, CT-based 454’s decoding of double-helix co-discoverer James Watson’s DNA this summer. It took a few months and a million dollars.

454 is one of the half-dozen entrants in the X Prize competition, and until now it was the closest thing the Boston area had to having a local pony in the race. I asked Xconomist Marc Hodosh, who took the reins of the competition in March, whether it was surprising that more of the area’s many genomics players hadn’t signed up. “All I can say is we’re talking to a number of people and it’s very likely you’ll see more teams in the future,” he said. “George is obviously a significant figure in our industry, and it’s an extreme pleasure to have him competing for the prize.”

For his part, Church (also an Xconomist) says via e-mail that “We are motivated to help the X Prize get some people engaged and educated earlier than otherwise would have happened. Also some corporate sponsors are more interested in the PGx than PGP and vice-versa.” Church explains that while the Personal Genome X-Team and the Personal Genome Project have an overlapping teams and a shared technical infrastructure, the two efforts have slightly different goals. PGP will aim to sequence about one percent of the DNA of each of 100,000 people (starting with 10 prominent volunteers who include Church himself and legendary venture capitalist Esther Dyson). To win the X Prize, PGx will have to sequence 98 percent of each of 100 genomes provided by the X Prize Foundation. Church says that the team will probably start with a practice run on 100 of its own volunteers. The team that takes the prize (hopefully PGx, Church says) will also have the opportunity to sequence the genomes of 100 celebrities–the likes of Richard Branson, Larry Page, and Paul Allen–who Hodosh hopes will become Lance Armstrong-like advocates for personalized medicine.

Entrants in the X Prize competition will have two window for competing each year, Hodosh says—once in January and once in July. “No attempt is likely for at least a year and a half,” he says.

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A little over a week ago, legendary venture capitalist Esther Dyson explained her reasons for being one of the first 10 people to have their genomes sequenced—and made publicly available—for Harvard Medical School professor George Church’s Personal Genome Project. Yesterday, Church revealed all but one of the rest of the folks on that list. (One volunteer evidently wished to remain anonymous.)

Blaine Bettinger at The Genetic Genealogist has nice bios of all the named volunteers. Not surprisingly, several members of the local innovation community are included:

—Keith Batchelder, founder and CEO of Genomic Healthcare Strategies, a personalized-medicine consulting firm in Charlestown

—John D. Halamka, whose many appointments include CIO at Harvard Medical School, Beth Israel Deaconess Medical Center, and Harvard Clinical Research Institute

—Stanley N. Lapidus, president and CEO of gene-sequencing-technology firm Helicos in Kendall Square

—James L. Sherley, the controversial ex-MIT stem-cell scientist

—and, of course, Church himself.

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If you volunteer for Harvard Medical School professor George Church’s Personal Genome Project, you’d better be ready to have your full medical records along with your full gene sequence (once completed) made public. But why would anyone want that kind of exposure? Famous venture capitalist Esther Dyson explained her reasons for being one of Church’s first ten volunteers last week at Fortune’s first iMeme conference in San Francisco.

Church (who is also an Xconomist) hopes to gather enough data from the project to speed research into the links between gene variations and both common and rare human diseases, and to accelerate progress toward more individualized health care based on patients’ genetic profiles. Dyson’s reasons for participating dovetail with Church’s vision:

• She hopes that even with just 10 participants, the project will begin to generate some interesting data.

• She hopes to prove that “doing this isn’t nutty… Putting your genome up [online] isn’t the equivalent of putting up a virtual voodoo doll that people can stick pins in.”

• She wants “to ask why”—to find the genetic explanations for our appearances, behaviors, and illnesses.

Dyson, who sits on the board of West Coast personal genetics startup 23andMe, admits that it’s luck, in part, that’s allowing her to take part in the study. Her boss can’t fire her because she has a “weird gene,” and even if she loses her health insurance, she has the financial wherewithal to cope, she explained.

Ultimately, Dyson says, she hopes the choice the high-profile “first 10” have made will help push society to figure out the implications of so much genetic information becoming available—publicly or privately.

Conference video of Dyson’s (very short) talk: http://money.cnn.com/magazines/fortune/techconference/2007/.

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