What a week...

What a wild couple of days...

First, deCODE Genetics unstealths its deCODEme foray into the personalized genomics market.

Then, just when you think they've been completely beaten to the punch, 23andMe throws a counterpunch.

I'd been wondering for a while what deCODE was up to in this arena, as they clearly have the infrastructure and the track record to make a serious play in personalized genomics.

Interestingly, even though many would argue that the Navigenics approach is the most responsible one, getting results on 20 or so SNPs is looking so "last week" right now. 

Just in case you've been in a sound-proof bubble the last few days, here are some links to a few articles and posts about the events of the last few days:

• NY Times article about deCODEme launch
• CNN Money on deCODEme launch
• NY Times article about 23andMe launch
• Wired article mostly focusing on 23andMe
• Garett Rogers post

While much has been said about the product launches, I find it interesting that there has been relatively little talk about something that is being left out of the products offered to the public (at least at the moment as far as I can tell).  Specifically, that something is copy number variation. 

For those not familiar with the concept, in addition to variation at single DNA base pairs, it is also crystal clear that individuals differ enormously from each other in terms of the presence or absence or elevated copy number of entire large "chunks" of DNA.  These studies, pioneered by Evan Eichler and others, have shown that our genomes are more dynamic than was previously recognized.  Thus, when copy number variation involves important genes or other important stretches of DNA not in genes, it can have an important impact on disease susceptibility.  For example, copy number for a stretch of DNA containing the CCL3L1 gene has been beautifully shown to very significantly influence HIV/AIDS susceptibility.  Likewise, low copy number of a gene called FCGR3B is associated with the development of the kidney disease, glomerulonephritis, in individuals with systemic lupus erythematosus.

Although first generation SNP genotyping approaches didn't always do so well with detecting copy number variation, more recent iterations have the ability to detect copy number variation (although a different technique called array comparative genomic hybridization is more commonly utilized to detect this clinically).  For example, Affymetrix states on their website that their 500K arrays provide copy number variation information (Navigenics is partnering with Affymetrix for genotyping).  Likewise, Illumina (23andMe's genotyping partner) points out that their product can also identify copy number variants.

Although the launch of genotyping services by 23andMe and deCODE Genetics appears likely to provide dramatically more information to the consumer than the small number of SNP results that will be reported by Navigenics, it would appear that both 23andMe and deCODE may have access to information related to copy number variation that can have important implications with respect to disease risk and which may not be reported back to the consumer.  It will be interesting to see how this is dealt with in the future.

Comments

[Steven Murphy MD]

Even crazier is the fact that they may be testing SNPs, but only those on the platform with which the companies have aligned. Last time I checked, there were other SNPs and CNVs of statistical and medically meaningful significance.
-Steve
www.thegenesherpa.blogspot.com