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(UPDATED: See below.)

Knome, the Cambridge, Mass., startup that will sequence the entire genomes of 20 customers for $350,000 apiece, launched its business back in November without ever explaining exactly how it planned to carry out the heavy lifting of whole-genome sequencing. At the time, CEO and co-founder Jorge Conde said only that unspecified “partners” would be helping out Knome with the actual work of reading out and analyzing six billion “letters” of DNA for each customer.

Yesterday, however, Knome announced a “strategic alliance” with the Beijing Genome Institute that strongly suggests the startup will be relying on the Chinese research institute for much, if not all, of its early sequencing efforts. (The release is here.) BGI, founded in 2002 — a precursor organization apparently dates back to 1997 — has played a major role in several major sequencing projects over that time. BGI’s Web site states that the institute was responsible for sequencing roughly one percent of the human genome in the Human Genome Project, and later independently mapped the genome of a hybrid strain of Chinese rice. BGI has also participated in international projects to sequence the genomes of pigs, chickens and silkworms.

Although BGI’s Web site isn’t fully translated into English, one page does boast that the institute can sequence 50 billion million “base pairs” (that is, “letters”) a day, with computing power — required to assemble and analyze sequenced DNA fragments — to match. Of course, it seems unlikely that Knome will have access to more than a fraction of that capability, as BGI presumably has multiple other projects underway as well.

Knome, which claims to take an almost paranoid approach to protecting the privacy of its “clients,” has said in the past that it will only send its partners anonymous, coded blood samples for genome sequencing. That, presumably, will be enough to allay any customer concerns about the new arrangement, although it’s impossible not to wonder whether Knome’s well-heeled clients had previously realized that their DNA might travel as far as Beijing for decoding.

Meanwhile, it’s also intriguing that BGI has struck what amounts to a commercial relationship with the U.S. startup. The institute is an arm of the Chinese Academy of Sciences, and according to its published material is devoted purely to scientific and technical advancement (see last paragraph, but be warned — it’s pretty dense).

Given that Knome aims to give its customers “full control” over how their genomic information is used, it’s not immediately clear that BGI stands to gain much in the way of raw knowledge from its work with Knome. As a result, I can’t help wondering how the institute’s stated goals are compatible with taking on work-for-hire for a U.S. startup, although I suppose it’s possible that BGI could look at the project as a sort of test bed for shaking out new sequencing technologies.

UPDATE: As Deepak notes in comments, BGI announced last month that it will begin offering sequencing services to the global market. See, for instance, this GenomeWeb Daily News story from Dec. 24 (registration possibly required), which updates the institute’s capacity to 250 million base pairs a day with standard equipment, and up to four billion a day using next-generation sequencers.

Also, Knome CEO Jorge Conde tells me by email that the company’s arrangement with BGI is exclusive, so it looks like all blood samples taken by Knome will be making the long trip to Beijing.

LATER UPDATE: As noted in comments, I originally wrote “billion” for  “million” in describing BGI’s base-sequencing capacity.

(UPDATED: See below.)

(NOTE: This is the second of two posts on Knome, a newly launched startup that offers to sequence your entire genome for $350,000. For part one, which provides a broad overview of Knome’s whole-genome sequencing and how it differs from services offered by other personal-genomics companies, click here.)

First things first: The company’s name is pronounced “nome,” as in the Alaskan city. A bemused debate over proper pronunciation has circulated among folks in and around the personal-genomics world ever since Knome’s teaser Web site appeared several months ago. (Personally, I’d been hoping we’d all be calling the company “K-nome.”) “The word ‘genome’ sounds a little like ‘Gee, know me’,” says Jorge Conde, Knome’s CEO. “We took off the ‘G’ and just make it ‘know me’.” Only you don’t pronounce a long “e” at the end.

Founded earlier this year, Knome aims to establish whole-genome sequencing as the “gold standard” for personal genomic analysis. (Their press release is here.) The company draws a sharp contrast with other recent personal-genomics companies such as 23andMe, arguing not only that full-genome data is far more solid and reliable than the rough-and-ready scans 23andMe and its ilk rely on, but that Knome is especially devoted to assuring the privacy and confidentiality of its users’ genetic data. (More on that in a moment. For more on the potential benefits of full-genome sequencing, see part one of our Knome coverage.)

Of course, there’s also a larger question hanging over Knome and any other companies that aim to tackle whole-genome sequencing at this early stage: Will they be content to remain boutiques for the wealthy, or will they aggressively drive down prices as sequencing costs fall in order to appeal to a mass market? It’s probably too early to say, although odds are good that competition with other personal-genomics companies will put some serious pressure on prices over time.

So far, however, Knome is most definitely a boutique. One telltale sign: Conde always refers to Knome’s customers, those earliest of early adopters of the new genetic technology, as “clients.” The company isn’t especially forthcoming about most of its operations — where its sequencing technology is involved, for instance, Conde merely emphasizes that Knome is “technology agnostic.” And it has even less to say about its potential clients — some of whom, Conde says, have approached the company via third parties in order to remain completely anonymous.

Knome has received more expressions of interest in being sequenced than it has capacity to process at the moment. As a result, it has limited initial enrollment to 20 people, who will be admitted on a first-come, first-served basis once they’ve completed an initial screening step.

Prospective Knome customers will eventually be able to sign up for the service online, although for now the company’s Web site only lets customers request additional information via email. Even once online registration is available, that step will primarily involve working through an “education and disclosure” process intended to ensure that customers know what they’re getting into, particularly in terms of any potential bad news that might be lurking in their genes.

More following the jump: Read the rest of this entry »

(UPDATED: See below.)

(NOTE: This is the first of two posts taking a close look at Knome. For part two, which examines Knome’s business model and how its service works — based largely on an interview with Knome CEO Jorge Conde — see here.)

First it was genomic pioneers James Watson and Craig Venter. Next up are the first ten volunteers in Harvard geneticist George Church’s Personal Genome Project. And now just about anyone can have their entire genome scanned in loving detail, courtesy of Knome, a Cambridge, Mass., startup that’s launching its service today.

Anyone, that is, who can spare $350,000 to cover the cost of sequencing and subsequent analysis and interpretation of the results. And who’s willing to wait in line, since Knome’s initial service will only be available to 20 people. (See the company’s press release here.) I’ll have more on Knome’s business and how the service will work in a subsequent post, which I’ll link to here when it’s done. (UPDATE: That second post is now up here.)

We’ve extensively covered personal-genomics startups such as 23andMe and Navigenics, which along with DeCode Genetics’ DecodeMe are offering individuals a first broad look at their personal genetic makeup. This is a big deal for a number of reasons, not least of which is the fact that your genome has played a major role in making all of us who we are. Our DNA links us not only to family and ancestors, but to groups of people scattered across the globe who share one or more of our particular genetic quirks. In no small measure, our genomes define what it means to be human.

All this previously invisible information is now increasingly accessible — albeit at first to those with the means to pay for it — and that’s likely to have major repercussions for individuals and society as a whole. For an initial take on that subject, see here.

Companies like 23andMe, however, don’t provide a full readout of a person’s DNA so much as a kind of abbreviated map to the genome. (These companies scan for particular DNA letters — technically known as single-nucleotide polymorphisms, or SNPs — that are known to vary among individuals. Collections of SNPs serve as a kind of catalog to much of the genome.) That shorthand map is still potentially useful in a number of ways, such as tracing ancestry or calculating your genetic predisposition toward heart disease or diabetes. By definition, however, such bare-bones SNP maps will also miss things — perhaps a lot of them. They’re the genomic equivalent of rough first drafts, which will undergo continuous revision as scientific understanding grows, SNP-scanning technology advances and sequencing costs fall.

Knome, by contrast, plans to offer its customers the whole genetic kit and kaboodle — a full readout of all six billion DNA “letters” of your genome. Genomics just doesn’t get any more personal than this. To put this in perspective, 23andMe or DecodeMe between 600,000 and a million SNPs. (The costs to the customer for a SNP scan is roughly $1,000 to $2,500, depending on the company.) In a scientific sense, a whole-genome sequence bears the same relationship to a SNP map that reading a book does to skimming skimming its index. Both expand your knowledge, but one is vastly richer, more detailed and illuminating than the other.

More after the jump: Read the rest of this entry »

Featured companies: American Aerogel, Clinicient, Frazier Healthcare Ventures, Genome Diagnostics, RadPharm, RainDance Technologies, Vivacta

UPDATED: Expanded items on Vitae, RadPharm, Vivacta and Genome Diagnostics. Intelligent Bio-Systems is now covered in a standalone item here.

Vitae Pharma takes in $15M for blood pressure, diabetes drugs — Vitae Pharmaceuticals, a Fort Washington, Pa., biotech focused on new drugs for hypertension and metabolic disorders, raised $15 million in a fourth funding round, VentureWire reports (subscription required). Boehringer Ingelheim, which struck a major partnership with Vitae in mid-October (PDF link), provided the funding.

That partnership calls for the two companies to co-develop Vitae drug candidates that inhibit a protein called 11beta-HSD1, an enzyme that helps regulate the hormone cortisol. The drugs may be useful in treating diabetes, obesity and hypertension. B-I agreed to pay Vitae $36.5 million in cash, research funding and an at-the-time unspecified equity investment, as well as up to $300 million in potential milestone payments.

Vitae’s other major drug program involves compounds that inhibit the protein renin, which regulates blood pressure and vascular function. Renin inhibitors, which could be useful in treating hypertension, have been a white whale of sorts for the drug industry over the past 30 years (see, for instance, this somewhat technical discussion of the history here).

UK’s Vivacta draws in $12M for medical diagnostics — Vivacta, a U.K. medical-diagnostic company formerly known as PanOpSys, raised $12 million in a second funding round. Investors included AGF Private Equity, HBM BioVentures, Spark Ventures and Viking.

Vivacta is developing a fast, “point of care” diagnostic system intended to deliver laboratory-quality test readings from drawn blood in doctors’ offices or at a hospital bedside. The technology is based on a “piezoelectric” film coated with antibodies to particular blood proteins. Piezoelectric devices produce current when compressed, so theoretically this approach should allow a direct measurement of blood proteins by generating current proportional to the density of antibodies that capture any particular blood protein.

RadPharm gets $10M for medical-image reviews — RadPharm, a Princeton, N.J., provider of medical-image review services, raised $10 million in a second funding round. Investors include Siemens Venture Capital, Ampersand Ventures, Adams Street Partners and Tang Capital Management.

RadPharm essentially provides outsourced analysis of medical images ranging from CAT scans to X-rays for clinical trials, whose outcomes can hinge on the way those images are read and analyzed. Trials of cancer drugs, for instance, frequently look at whether tumors shrink, stabilize or grow, and determining that requires someone to look at actual patient X-rays or other images and decide what they actually show. RadPharm’s service provides “centralized, independent, blinded interpretation” of such scans.

Genome Diagnostics, cancer-test maker, aims for $1.6M — Genome Diagnostics, a Pasadena, Calif., developer of cancer diagnostic tests, has raised several hundred thousand dollars toward an anticipated $1.6 million first funding round, VentureWire reports. B.C. Capital of Israel and several individual investors provided the funds.

According to VentureWire, the company aims to produce a diagnostic test for prostate cancer based upon gene variations detected by sequencing a patient’s entire genome. That sounds unlikely on several levels, the first of which is that “whole-genome sequencing” — VentureWire’s description of what the company is doing — is still incredibly expensive, with an estimated cost of $100,000 or more.

It seems far more likely that the company will do a rough-and-ready genome scan that samples only several hundred thousand of the genome’s three billion DNA “letters” that are known to vary between individuals — at least, that is, unless Genome Diagnostics is betting that the cost of whole-genome sequencing will drop to the fabled $1,000 or so by the time it gets its product to market. And maybe that’s exactly what the company is doing, although that would mean that its initial testing costs are going to be extraordinarily high.

It’s also far from clear exactly what sort of prognostic information the company hopes to obtain from a genome scan of either type, since most genetic-association studies can only show increases or decreases in the probability of disease, and with such a margin of error that it’s difficult to see how that information could possibly serve a diagnostic purpose. I’ll try to circle back to the company in order to get a better idea of what they’re up to for a future post.

OTHER HEADLINES OF NOTE:

• Clinicient receives $5M for healthcare revenue-management software (release)
• Genome sequencer Intelligent Bio-Systems raises funding (VW)
• American Aerogel raises $3.2M for biopharma gels (VW)
• Frazier Healthcare Ventures raises $600M life-sciences fund (Seattle P-I)
• RainDance Technologies appoints Christopher McNary as CEO (release)