by Dr. Hsien-Hsien Lei
Posted February 25, 2008 in DNA Testing, DNA and Genealogy
Dr. Ann Turner is the most knowledgeable personal genomics customer I know. She has purchased the services of both 23andMe and deCODEme and generously shares her viewpoint. Yesterday on the GENEALOGY-DNA list, she compared 23andMe vs deCODEme with respect to genetic genealogy and gave me permission to reprint her comments here.
Now that 23andMe and deCODEme both have demo records, you can explore the user interface aspects yourself. Both companies are introducing new features lickety split, though, so it’s a moving target.
I don’t think you should make a decision based on mtDNA or Y features, unless you’re only interested in “deep ancestry.” Neither company can provide the resolution of the genealogical HVR/STR tests. However, 23andMe does get down to much more detail in the haplogroup labels. 23andMe is using a smaller number of Y-SNPs (current reports make use of 284, vs 858), but these seem to be more targeted toward the currently defined phylogenetic tree. We don’t know yet how the additional Y-SNPs in the deCODEme set will pan out, and deCODEme is not reporting subclades as deeply as they could right now (i.e. just R1a and R1b). I suspect lots of the extra SNPs will end up being “phylogenetically equivalent” for the deepest splits in the tree, like the long lists of SNPs in that paper by Underhill and Kivisild, but we’ll only know that when we’ve seen actual results for many people in different haplogroups.
Both companies are making use of the HapMap samples for geographic ancestry in the 50-some population cell lines from the Human Genome Diversity Project, and in fact 23andMe partially funded the analysis which is the basis for the current flurry of technical articles. They must be using a slightly different algorithm in their presentations, though — deCODEme says it breaks the chromosomes down into segments for comparison purposes, and that seems to change the rank order slightly. Only deCODEme gives an admixture estimate, and that only for the three broadest categories of European, African, and Asian. You can, however, compare your results to a representative sample from any of the 50 populations at deCODEme on a segment by segment basis.
23andMe has a nice Genome Browser in place, where you can use the web interface to look up individual genes or rs numbers you encounter in the technical literature (or their own Spittoon blog, which has frequent posts about items that crop up in news releases). DeCODEme doesn’t have a genome browser yet, but promises it will be “soon.” In the meantime, you can of course check your own alleles in the big download set and use dbSNP to learn more about the gene.
As for the medical aspects, I think you should thoroughly explore the sample reports and understand what’s really being offered. They are association studies using “common” SNPs, not diagnostic tests for single mutation / single gene disorders, like the ones DNATraits is now offering (with a special emphasis on mutations more commonly found in people with an Ashkenazi Jewish background).
23andMe’s Gene Profiles strike me as chattier, with historical background and interviews with specialists, but both companies cover the fundamentals. Both companies also do an admirable job of providing citations to the literature, with data about the frequency of the genotype in cases and controls, and how that contributes to relative risk. Many pundits are complaining that people might get freaked out by learning that their risk is doubled (the way newspapers often report new findings), but I have to wonder if they’ve examined the actual reports, which provide more details about the absolute frequency etc. Most people will learn that there are multiple genes “associated” with each condition, with some alleles adding to the calculated risk and others subtracting from it, and a doubling of risk might take you from 2% to 4%.
It’s very important to realize that these are population studies, and the statistical associations don’t necessarily apply to an individual case. If you have a “high” relative risk for colon cancer, the odds may still be low in absolute terms that you will contract it. If you have a low relative risk, that does not absolve you from the need for regular examinations, since not all causes of colon cancer are known yet (and may be idiosyncratic for a particular family line, like the George Frye pedigree we discussed recently). That kind of mutation might never be picked up on a chip using common SNPs.
The SNPs aren’t necessarily causal, either, even the small percentage found in actual coding regions. In fact, most of them are probably SNPs in the vicinity of the mutation responsible for the actual effect, and they’re just along for the ride as that segment of the chromosome is passed down through the generations. They are tagging/mapping SNPs that provide guidance for which genes to study in more detail. That’s the main business of deCODE, and they are folding their discoveries into the deCODEme reports as soon as they are published. Of course, 23andMe has access to those articles, too.
The feature I found most intriguing at deCODEme was the graphic display, comparing any two gene profiles on a segment by segment basis (about a million bases). You can do a similar thing at 23andMe, but in practice, it only highlights connections for first degree relatives, who share broader regions of their chromosomes. But now that both companies give access to raw data, anyone can create a novel approach to visualizing data (sort of like open source software) — if people are willing to share their profiles. You don’t need to share data about individual SNPs for the deCODEme display, like the ones I’ve uploaded (zip file).
One remaining difference between the companies is the number of SNPs, and deCODEme has a head start there. That may prove to be the deciding factor for me, as I have a scheme in the back of my mind for locating the mutation responsible for the hereditary hearing loss that runs in my family. We’ve already participated in several genetic studies, but the mutation has not been found. I could test various relatives (for instance the two sons of my first cousin) to see what segments I share with the just one who has the hearing loss. The sticky points are deriving haplotypes from genotypes and downplaying segments that we share because of our generic European ancestry. I’ll need to do some pretty heavy-duty cost-benefit analysis here!
On the other hand, 23andMe has added some custom SNPs to their suite. There are autosomal SNPs, in addition to the ones for mtDNA and Y, but I haven’t seen a comprehensive list of why they were selected. One example is a test for the CCR5-delta32 mutation (HIV resistance), which some of you have ordered as a stand-alone test.
Neither company is really promoting the genealogical possibilities for the autosomal SNPs. They may be (justifiably) pessimistic about that application, since there’s only a 50% chance of passing on a particular DNA segment to the next generation. Nonetheless, all of our DNA came from somewhere, and we now have unprecedented access to huge amounts of data. We ought to be able to mine a few little nuggets out of it, and I’m lobbying the companies to pay attention to this segment of the market.
In the meantime, I think the tests are most suitable for those willing to explore the next frontier, with all its unknowns and with the possibility of less expensive tests coming online within the next few years. The cost-benefit analysis will be tricky for everyone, not just for my own little niche. But if you decide to proceed, I don’t think you can go wrong with either company. There’s a third company, SeqWright, which is flying under the radar right now, due to their “late” entry into the field.
NB: You may also find Jay Cross’s experience with 23andMe interesting.
Update: David Hamilton at VentureBeat has written his own comparison of the online interface for both 23andMe and deCODEme.
Get Your Personal Genome Decoded Here...
What’s In Your DNA? #19...
Personal Genome Results from 23andMe and deCODEme...
Genetic Genealogist Ann Turner’s Opinion on deCODEme, 23andMe, and Whole Genome Testing...
DNA Video: deCODEme...
DNA Video: Peek Inside deCODEme...
SNPs on Chromosome 15 Associated with Smoking and Lung Cancer...
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