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First, it was self-described 23andMe investor Martin Varsavsky who spilled some early information about the secretive personal-genomics startup founded by Sergey Brin’s new wife, Anne Wojcicki, and now backed by Google and Genentech. (See our coverage here.) Now more details about 23andMe’s plans to help individuals map their own genomes are emerging, courtesy of Illumina, a gene-scanning company partnered with the startup.

At an investor conference yesterday, Illumina CEO Jay Flatley sketched out 23andMe’s plans and even reviewed its first product, Forbes’ Matthew Herper reports. (The meeting was Webcast here.)

The fundamentals aren’t too different from what Varsavsky has described previously. 23andMe customers will take a DNA sample — Flatley suggests it could involve either saliva or a cheek swab — and send it in to Illumina for genotyping. Instead of scanning the whole genome letter-by-letter, Illumina’s microbead-based scanners detect hundreds of single-letter DNA variations that give a useful but rough approximation of what the full genome would look like. (The upside is that scanning for these variations, technically known as single-nucleotide polymorphisms, or SNPs, is far faster and cheaper than reading through the entire genome.) 23andMe would then throw that information up on a secure Web page, where users could then analyze it to their hearts’ content.

Flatley said 23andMe’s initial emphasis will be on ancestry, although it seems likely that disease-related SNPs are also likely to get a lot of attention, particularly given how scientists have successfully used similar gene scans to identify dozens of disease-related SNPs over the past year. (See our previous coverage here.) Flatley said he’s already tried out the service and now keeps his own genotype on his iPhone, although he didn’t say much about what he learned from it — in sharp contrast to, say, Craig Venter.

Perhaps most interesting, Flatley then passed out sign-up cards for 23andMe and said anyone who registered on the spot could get the service for free, although Herper doesn’t say how many folks took him up on the offer. According to Flatley, 23andMe will start to show off their software over the next few months — which will be none too soon, given that at least one competitor, Navigenics, is also on the march. (Our coverage is here.) Rumors of yet a third, still stealthy, personal-genomics startup are also swirling around the Valley.

(UPDATED: See below.)

Navigenics, a new personal genetics startup with some serious backing, threw back the curtain over the weekend by unveiling its Web site. The Redwood Shores, Calif., startup says it aims to provide individuals with their genetic profiles and then to “arm” them with ways to improve their future heath.

This is very similar to what 23andMe, a similar startup backed by Google and Genentech (see our coverage here and here), intends to do. Adding to the intrigue is the fact that Navigenics has some influential supporters of its own, including Kleiner Perkins Caufield & Byers and Sequoia Capital. KP’s uber-VC John Doerr also has a seat on its board. KP, of course, was an early backer of Google, whose co-founder Sergey Brin just happens to be married to 23andMe co-founder Anne Wojcicki.

Navigenics isn’t anywhere near so shy as 23andMe, which remains largely mum despite some fairly significant disclosures by its investors. From the Navigenics Web site:

Thanks to advances in genomic research, medicine and technology, we can now determine your genetic predisposition for certain diseases, perhaps years or decades before they develop. These insights enable you to take action before a disorder strikes to delay or even prevent the illness altogether.

In other words, Navigenics essentially intends to get people to have their genomes scanned in a rough-and-ready fashion — in other words, they’ll scan your genes with chips that look for single-letter variations in the genetic code, instead of laboriously reading it out letter by letter — and then to match up what they find with the latest information on the diseases to which your genes might predispose you. Navigenics so far seems focused on the question of what your genes might say about disease, whereas 23andMe is apparently also interested in helping people trace their genealogy and creating social networks where they can compare and contrast their genetics.

Needless to say, the privacy implications of all this activity are fairly profound, and neither company has come close to explaining exactly how it plans to protect users’ privacy. That’s a particular concern given that existing online services can be forced to divulge your personal information to the government without even informing you of the fact.

It’s also not clear how long this will take or what it will cost. According to a video on its site, Navigenics says will obtain your genetic information via a “saliva collection kit” — i.e., you’ll spit into a cup and mail it to the company, which will scan it for your genetic details and then presumably post them online where you can look at them. Navigenics also plans to provide users with information that can help them make the best of their genetic predispositions, although exactly how that will work in practice remains to be seen.

At the very least, though, it’s clear Navigenics has come loaded for bear. In addition to the blue-chip VC backing — there’s no information on their Web site as to how much money the company has raised, and so far we haven’t heard back from anyone involved with the company — Navigenics boasts some heavy hitters among its board members, co-founders and partners. For instance, David Brailer, until recently the Bush administration’s point man on electronic health records and more recently chairman of Health Evolution Partners, a private-equity fund that invests in healthcare, sits on the board. So do the company’s co-founders, Dietrich Stephan, a director at the Translational Genomics Research Institute, and David Agus, a protein-biomarker researcher at Cedars-Sinai Medical Hospital in Los Angeles. The company has also lined up some important advisors, including the politically connected Greg Simon, now president of Michael Milken’s FasterCures organization and previously Al Gore’s chief domestic policy adviser.

Navigenics also boasts close ties to Affymetrix, the big gene-chip maker — Affy’s former associate general counsel Stephen Moore will be Navigenics’ general counsel, and Affy founder Stephen Fodor appears in a video on Navigenics’ site, so it’s not too difficult to conclude that the company will be using Affy’s gene chips to sift users’ genetic info. (23andMe, by contrast, was recently reported to have signed a deal with Affy competitor Illumina.) The company has also hired David Ansley, former science editor at Consumer Reports, to run “editorial” (presumably the section providing scientific info about genetic links to disease that customers will be anxious to find), and Amy DuRoss, late of California’s Proposition 71 stem-cell initiative and the California Institute for Regenerative Medicine, as head of policy and “business affairs.” (DuRoss is also apparently Navigenics’ spokeswoman.) The company has also hired Colleen Yoo, formerly e-business director for Blue Shield of California and director of product management for WebMD, as head of product management.

Which is not to say the company doesn’t have a few discordant notes, starting with CEO Mari Baker, recently a KP “executive in residence” and before that president of BabyCenter, a J&J-owned Web site for parents, and a vice president at Intuit. On the other hand, if 23andMe has anywhere near this much depth among its executive team and backers, we have yet to hear about it. Yes, 23andMe has backing from Google and Genentech, not to mention VC firms Mohr Davidow Ventures and New Enterprise Associates, and Esther Dyson — one of the ten volunteers for George Church’s Personal Genome Project, by the way — is on the board. But we haven’t heard much else about what 23andMe has lined up yet.

UPDATE: We’re still waiting for comment from Navigenics, although we’re promised something later this week. That’s something of an eternity in Internet time, but check back by Thursday or so, as I’ll post whatever we learn from them. Meanwhile, Navigenics board member Dana Mead, a partner at KP, tells us by email that Navigenics is doing something “different” from 23andMe and that he sees the company as “more complimentary than competitive” to 23andMe. It will be interesting to see how they pull that off, even assuming Mead wasn’t just suggesting that Navigenics plans on being exceedingly polite where 23andMe is concerned.

(UPDATED: see below.) 23andMe, a stealthy Mountain View, Calif., “personal genetics” startup, has raised a first round of funding from some heavy hitters — Google, Genentech and two blue-chip VC firms, Mohr Davidow Ventures and New Enterprise Associates.

That’s some significant megatonnage for a low-profile and potentially controversial startup, although it all starts to make sense once you realize that Google co-founder Sergey Brin is newly married to 23andMe co-founder Anne Wojcicki. In addition, Genentech CEO Art Levinson sits on Google’s board. Those insider ties triggered disclosure requirements for Google, which revealed its new $3.9 million stake in 23andMe earlier this afternoon in an SEC filing. Among other things, the financing allowed 23andMe to pay back $2.6 million it had previously borrowed from Brin.

23andMe didn’t disclose the overall size of the round, although I’m told it’s in the vicinity of $10 million. None of the four named investors officially took a lead role in the financing, according to Michael Goldberg, a Mohr Davidow partner.

According to the company’s bare-bones release, 23andMe aims to help people “access, explore and better understand” their own genetic profiles via the latest DNA-analysis techniques and Web-based software tools. (The company’s name is a play on the 23 pairs of chromosomes that carry each individual’s DNA.) That service isn’t likely to launch until the end of this year, and in the meantime, 23andMe officials aren’t talking.

Which is not to say that 23andMe’s business is a total mystery. The company’s Web site suggests that it will allow people to analyze their own genomes and then share or compare that information via social networks of some sort (emphasis added):

Even though your body contains trillions of copies of your genome, you’ve likely never read any of it. Our goal is to connect you to the 23 paired volumes of your own genetic blueprint (plus your mitochondrial DNA), bringing you personal insight into ancestry, genealogy, and inherited traits. By connecting you to others, we can also help put your genome into the larger context of human commonality and diversity.

Toward this goal, we are building on recent advances in DNA analysis technologies to enable broad, secure, and private access to trustworthy and accurate individual genetic information. Combined with educational and scientific resources with which to interpret and understand it, your genome will soon become personal in a whole new way.

How this will work in practice isn’t entirely clear, although there are hints scattered here and there. Maverick tech entrepreneur Martin Varsavsky, for instance, wrote on his blog in January that 23andMe will take in saliva samples through the mail, then subject them to a fast and relatively inexpensive genetic analysis. That data, he suggested, would go into a database that people could search for both personal and scientific reasons — a vision that, if true, would also help explain Google’s involvement, given the company’s oft-stated desire to index all of human knowledge. (An individual familiar with 23andMe told me that Varsavsky’s description sounds “well informed.”)

Mohr Davidow’s Goldberg explains that 23andMe hopes to stand at the intersection of “personalized medicine” and consumer-driven healthcare by offering individuals the tools they need to make medical decisions based on their genetic makeup. “Consumers have to become educated,” he says. “They have to understand that genetics isn’t scary science, that it’s all about what makes me who I am.”

Of course, no one knows at this point how people might react to the notion of storing — much less sharing — their genetic information online. Goldberg emphasized that 23andMe is “extraordinarily committed” to maintaining user privacy. It also can’t hurt that Congress appears poised to ban genetic discrimination with respect to employment and health insurance, which could do a lot to alleviate peoples’ anxiety about hanging out their genetic laundry online.

UPDATE: Turns out Martin Varsavsky is also a 23andMe investor. At least, that’s what he says on his blog. No wonder he’s “well informed.”