23andMe Partners with Illumina – To Offer Genetic Genealogy?

23andMe has been the subject of much discussion in the biotech and personalized medicine circles of the blogosphere (See here, here, here, here, here, here, here, and here for plenty of information/speculation/discussion).

In August, 23andMe announced (“23andMe and Illumina Forge Consumer Genomics Goliath”) that they have partnered together to offer “consumer genotyping” – more about that in a minute. Illumina produces “SNP chips”, chips that can test a genome for thousands of SNPs (single nucleotide polymorphisms) at a time. For example, the company has one chip that tests one million SNPs for as little as $600, and another chip that tests 550,000 SNPs (the HumanHap550) for only $300-$450. Interestingly, Illumina is also able to custom build chips to add specific SNPs if the customer so desires. Additionally, as the announcement touted, Illumina is also exploring the world of inexpensive whole-genome sequencing, suggesting that this partnership with 23andMe could transition from cheap SNP testing to cheap whole-genome sequencing at some point in the future.

Despite all the conversation and information, the company’s products and services have never been explicitly stated. Although the website states the following, the general public has not known how that would translate into a tangible product or service:

“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.”

Yesterday, however, we got a much clearer picture thanks to the Illumina, Inc. Analyst Day in New York City (thanks to Matthew Herper for a great write-up at “Google’s Genetic Start-Up,”). At this meeting, Jay Flatley, chief executive of Illumina, revealed some tantalizing hints about 23andMe’s upcoming launch. Here is a brief outline of the product that has resulted from the partnership between 23andMe and Illumina:

1. Send in a DNA sample (either spit or cheek swab).

2. The DNA is sent to Illumina to for “consumer genotyping”. This means that Illumina uses one of its SNP chips to screen DNA for the presence or absence of certain SNPs, or single nucleotide changes in the DNA sequence.

3. Illumina reports the SNP variations to 23andMe.

4. 23andMe “make[s] that information available through a password-protected Web site” which customers can access to see their personal SNPs.

5. 23andMe will (ultimately) provide information about the meaning or medical/genealogical implication of each individual SNP.

For those of us who are interested in genetic genealogy, It appears that 23andMe’s product might be directed more toward genetic genealogy than medical application:

“Initially, Flatley said, the company will be more focused on ancestry – questions like which parent one got more traits from – than medicine. Many researchers say most genetic discoveries are so far only of limited medical utility.”

Flatley has already scanned his genome and accessed 23andMe’s interface. Additionally, he offered the service free to everyone at the meeting who was willing to sign up (lucky bastards).

You can see the webcast of Jay Flatley’s presentation at Illumina’s website. There hasn’t been much written about this revelation as of today, but I found mention at GigaOM, Genome Technology Online, and Megan’s Roots World.

So what does this partnership between 23andMe and Illumina really mean for someone interested in genetic genealogy? Well, I’m glad you asked. Although some of our personal SNPs are spontaneous, many of them came from either our mother or our father. Genetic genealogists have long taken advantage of SNP inheritance to identify our Y-DNA or mtDNA haplogroup, for example. SNP testing can potentially be one of the most interesting and most lucrative offerings in genetic genealogy, although the field is still in its infancy. Current SNP testing for genetic genealogy, known as “autosomal testing”, involves making conclusions based on a few hundred SNPs and don’t allow something I call “SNP tracking”, the ability to compare SNPs between individuals. 23andMe, potentially, will offer a service that tests million(s) of SNPs, each of which can be individually analyzed and compared.