Ann Turner on Personal Genomics Companies 23andMe vs deCODEme

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.

Ann Turner
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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.

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Eye on DNA Headlines for 15 February 2008

by Dr. Hsien-Hsien Lei
Posted February 15, 2008 in DNA Testing, DNA and Genealogy, Eye on DNA Headlines

• The Teaching Company sells a 24-lecture intro to genetics course, Understanding Genetics: DNA, Genes, and Their Real World Applications, taught by Dr. David Sadava of The Claremont McKenna, Pitzer, and Scripps Colleges. After watching a preview, I can say that it’s not much more interesting than the lectures I sat through in college but for people who learn better by listening and watching, rather than reading, it may be valuable. (HT: GENEALOGY-DNA)
• Please welcome the latest members of The DNA Network. We now number 46!

  *Next Generation Sequencing from CLC bio
  *Mailund on the Internet
  *Buzzyeah
  *FinchTalk
  *Genetic Future
  *PredictER

• Gotta have this squishy, squashy, lumpy light-up DNA ball from HearthSong! (HT: Kristina)
• An oldie but funny on genetic genealogy from one of my favorite writers at the New York Times - Michelle Slatalla.

  Marie Antoinette, Is That You?

• Mary Beth Faller of The Arizona Republic asks: Is a gene test right for you? It’s got a negative slant to it (of course) but the right sidebar has some good basic information on DNA testing.

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Author Jon Entine on Genetic Genealogy

by Dr. Hsien-Hsien Lei
Posted December 12, 2007 in DNA and Genealogy

Recently, there have been a slew of articles decrying genealogy DNA tests as scams. Blaine at The Genetic Genealogist has covered the controversy in depth. And today, I’ve invited author Jon Entine back to Eye on DNA to share his thoughts on genetic genealogy. As you can see, it is possible to recognize the power of genetic genealogy as well as its limitations without writing the whole thing off.

What can DNA genealogy tests really tell us?
23notME

by Jon Entine

I was bemused by the headlined stories over the past month touting new genetic genealogy services, including the start-up, 23andME, launched by the wife of the founder of Google, and AfricanDNA, the brainchild of Harvard scholar Henry Louis Gates, Jr. in cooperation with FamilyTreeDNA. According to 23andME, its service will “shed new light on your distant ancestors, your close family and most of all, yourself.”

But what do these services really offer? I have more than a passing interest in this question because my recently published book, Abraham’s Children: Race, Identity and the DNA of the Chosen People, is the first of a new genre: using DNA to help us connect with our common ancestors—our ethnic identities. DNA can do that. The more responsible genetic genealogy testing firms, like FTDNA, are very clear about what current technology can do. What DNA testing services can’t do, however, at least not yet, is provide the average identity seeker with anything but a vague snapshot of our personal genetic profile and ancestry.

Remember a few years ago when Adrian Targett, an English schoolteacher, was linked by DNA to a 9,000-year-old skeleton found in a cave near where he lived in Cheddar, a tourist town famed for the distinctive cheese made there. “Cheddar Man Found Alive in South of England,” touted one headline. Well, not really. The genetic test—identical to some of the tests sold to the public today by commercial firms–indicated only that the two were linked to the same female ancestor. In kinship terms, they were cousins approximately 450 times removed. But they share only a few bases out of more than 3 billion nucleotide pairs in the human genome. Applying exponential math, Targett has inherited the DNA from many trillions of other relatives as well (though because of intermarriage among cousins and community members, the actual number of his ancestors is far less). His relationship to Cheddar Man is certainly fascinating and important for researchers, but it’s genealogically tenuous, to say the least.

Going back ten generations we each have about 1,000 ancestors, which means we share about one millionth of a random neighbor’s DNA by direct descent. Twenty-five generations ago, about the time when Columbus happened on the shores of the Americas, the number of our potential ancestral cousins swells to an astronomical 30 million, almost all of the world’s population at that time. Yet, we have only one continuous male and female lineage. The male and female lines have become popular markers of identity because of the historical importance of surnames and the fact that these two DNA lineages are so easy to track. Yet, they are only two of millions of ancestral lines that we each carry. Many millions and perhaps billions of people living today are genetically linked to Cheddar Man, although that extremely distant connection might not show up in the few sections of the DNA that current technology can track.

This vast majority of the human genome, which amounts to more than 99 percent of our DNA, remains beyond the reach of current commercial DNA tests. Services such 23andME do provide glimpses of this genetic bounty but the information is virtually meaningless. Yes, its reports may indicate that we have a gene that is linked to weight gain, ear wax build up, or IQ, but even these seemingly simple traits are rarely the result of individual genes. There are more than 10 million tiny differences, known as single nucleotide polymorphisms, or SNPs scattered across the 23 pairs of human chromosomes and potentially interrelated in a myriad of ways. They are activated—“expressed” is the term used by geneticists—by gene-gene and gene-environmental interactions.

Make no mistake about it. Genetic genealogy is fascinating and it provides scientists with greater insight into our distant ancestors. We are also learning more and more about diseases, which is particularly of interest to Jews, who are subject to more than 40 disorders as a consequence of their separatist history. In fact, Bennett Greenspan’s FTDNA is launching an Ashkenazi Genetic disease panel this week that will test for 25 common Ashkenazi diseases for only $500, an example of the responsible use of genetic genealogy.

But for the vast majority of us, DNA genealogy is little more than expensive entertainment, and potentially misleading. Those in search of certifying their identity or evaulating behavioral quirks using DNA tests may find disappointment as much as illumination. For example, in my book, I mention the case of Lisa Black, a systems administrator in Oakland who is African American. She was shocked to find that the DNA lineage that current technology can track, her female ancestors, was a blend of Native Americans, Chinese, and Sardinians. It came as a major blow to a veteran of the Black Power movement of the 1960s. “For me to have a whole half of my identity to come back and say, ‘Sorry, no African here.’ It just negates it all. … What does this mean? Who am I then?”

Tags: genetics, genes, dna, genetic genealogy, genealogy, dna testing, genetic testing, 23andme, family tree dna, ftdna, african dna

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DNA Video: Jon Entine of Abraham’s Children

by Dr. Hsien-Hsien Lei
Posted December 8, 2007 in DNA Podcasts and Videos, DNA and Genealogy

One of the most popular posts here at Eye on DNA has been the one written by Jon Entine, author of Abraham’s Children. Here he is in part 1 (out of 7) of his talk at the 2007 International Association of Jewish Genealogical Societies (IAJGS) Conference in Salt Lake City.

via Tracing the Tribe

Tags: genetics, genes, dna, jon entine, abraham’s children, jewish genealogy

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Eye on DNA Headlines for 3 December 2007

by Dr. Hsien-Hsien Lei
Posted December 3, 2007 in DNA and Disease, DNA and Genealogy, Eye on DNA Headlines

• Writer Ian Brown has begun a three part series in The Globe and Mail–The Boy in the Moon–about his son, Walker, who was born with cardio-facio-cutaneous syndrome (CFC). Now 11 years old, Walker is one of only 300 people worldwide with CFC, a rare single gene disorder. Four genes have been associated with CFC, BRAF, MEK1, MEK2 and KRAS, with most affected individuals having a sporadic mutation in BRAF. (HT: Eric)
• Speaking of doggie DNA, K9 Genetics Corp is offering DNA analysis for dogs to help determine the best formulation of Personalized Chow and Personalized Treats for them. Nutrigenomics for dogs!! A new DNA development every day, I tell ya. (HT: Trish)
• Amanda Bower of Fast Company trial runs Navigenics and finds out she has “some of the lowest risk” of disease that they’ve seen. Now how many people would they have seen so far since Navigenics isn’t officially accepting customers yet?
• Tim Agazio of Genealogy Reviews Online has put together a round-up of his DNA testing articles covering his experiences with Family Tree DNA and DNA Ancestry (a partner with my company, DNA Direct). Worthwhile reading if you’re considering venturing into the land of DNA and genealogy.
• Whole genome scans and genetic testing are being likened to “health horoscopes“! Wonder if that’s trademarked?
• Throw some confetti for the folks at Personal Genome Project! They’ve got a newly designed website with some graphics created by DNA Network member Ricardo Vidal. Jason Bobe, who’s in charge of PGP community and planning, has more on the redesign. If you’re at all interested in signing up to learn more about your genome as well as getting the chance to donate your DNA to science, you have to check out the Personal Genome Project.

Tags: genetics, genes, dna, navigenics, family tree dna, dna ancestry, genetic genealogy, nutrigenomics

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DNA Video: Putting the Genes in Genealogy with Dick Eastman

by Dr. Hsien-Hsien Lei
Posted December 1, 2007 in DNA Podcasts and Videos, DNA and Genealogy

Dick Eastman of Eastman’s Online Genealogy Newsletter gives the keynote address at the 2007 BYU Computerized Family History and Genealogy Conference.

Tags: genetics, genes, dna, genealogy, dick eastman

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DNA Video: DNA and Your Roots by Gina Paige

by Dr. Hsien-Hsien Lei
Posted November 24, 2007 in DNA Podcasts and Videos, DNA and Genealogy

Learn more about genetic genealogy from Gina Paige, president and co-founder of African Ancestry.

Tags: genetics, genes, dna, genealogy, african ancestry, gina paige

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DNA Video: DNA Testing with Chris Haley

by Dr. Hsien-Hsien Lei
Posted November 17, 2007 in DNA Podcasts and Videos, DNA and Genealogy, Personalities with DNA

Chris Haley, nephew of Alex Haley, shows us what it’s like to use a buccal cotton swab to take a sample of DNA from the inside of your cheek. Not only is it not painful, it’s hilarious!

The Genetic Genealogist has the results of Chris Haley’s Y-DNA test.

via Megan’s Roots World

Tags: chris haley, alex haley, genetics, genes, genealogy, dna, dna collection, buccal swab, cotton swab

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Genetic Genealogy and the Chinese

by Dr. Hsien-Hsien Lei
Posted November 7, 2007 in DNA and Genealogy

Last week’s Nature news article about personalized genomics was interesting in more ways than one. I was particularly intrigued by the picture they used showing three generations of East Asian (probably Chinese) women looking at a laptop. It got me wondering if they were at all representative of the type of consumer who’s interested in personalized genomics. What does the Chinese community think of genetic genealogy anyway?

Generally speaking, I don’t believe genetic genealogy companies based outside of Asia can provide much information for Asians primarily because their databases are made-up of people who are not Asian. If you look at any article about genealogy using DNA testing, the same ethnic groups or populations pop up again and again - whites, Europeans, Africans, Native Americans, and Jews. What are the chances that a genealogy DNA testing company in the US or UK has enough data on other Chinese people like me so that I can learn more about my family tree or find matches with distant relatives?

In Singapore, there are Chinese clan associations that keep detailed records of descendants - but only male descendants really count because they carry on the family name. Some of my Chinese-American friends have gone to China to visit their family’s village and can trace their family trees back many generations. Me? I can barely trace further than my grandparents.

One company that has done some testing of Chinese DNA is Family Tree DNA. Group administrator Ivan Shim runs the China/Chinese DNA Project which aims to map “the distribution of the various Chinese haplogroups & subclades around the world.” As of today, 42 Y-DNA tests have been run and of these, most appear to come from the O haplogroup. Eighteen mtDNA tests have been performed with seven people in the M* haplogroup.

The Genographic Project uses Y-DNA and mtDNA to trace ancestry which can be interesting for anyone, including the Chinese. Two years ago, a Chinese reporter from Singapore’s Todayonline (article offline) participated in The Genographic Project and was surprised to find that her DNA mapped to haplogroup H, which is associated with more than half of all Europeans, many North Africans and Middle Easterners, and some Northern Indians and central Asians. She apparently belonged to an understudied branch of haplogroup H.

Jeff Yen in Singapore got his Genographic results late last month. His genetic markers showed that he belonged to haplogroup O2. Jeff’s ancestors most likely started in Africa, traveled through the Middle East, Iran or southern Central Asia, then Central or East Asia, and finally East Asia approximately 30,000 years ago. Interestingly, one commenter pointed out that Jeff’s haplogroup is unusual for a Chinese person and indeed there is only one person in the Family Tree DNA China Project that belongs to haplogroup O2. For Genographic Project results that typify Chinese males, see this pdf file for haplogroup O.

Have you taken a genealogy DNA test before? Why or why not? Were your results what you expected? I’m especially interested in hearing from people of Chinese heritage.

For more about genetic genealogy, Blaine Bettinger of The Genetic Genealogist is the one to visit. You may want to start with his free eBook - 10 DNA Testing Myths Busted and Other Favorite Posts.

Tags: chinese, genetics, genes, dna, genealogy, genographic project, family tree dna

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Eye on DNA Headlines for 18 October 2007

by Dr. Hsien-Hsien Lei
Posted October 18, 2007 in DNA and Genealogy, DNA and the Law, Eye on DNA Headlines

• This photo of a protest in France on October 13, 2007 against DNA testing of immigrants is from François Bouchet’s flickr album. The sign this man is wearing translates to (according to Babel Fish): The family is no business of DNA Family isn’t a matter of DNA*.
• Genetic genealogy has been in the news this week. DNA Network member David Hamilton at Venture Beat has more - Genetic genealogy hits the big time.
• DNAPrint, the maker of ancestry DNA test AncestrybyDNA, has formed a partnership with BioServe to perform ancestry analyses on nearly 600,000 human biological samples. (via The Genetic Genealogist)

  Richard Gabriel, CEO and President of DNAPrint® Genomics: By removing the question of ancestry from a clinical sample researchers can more readily evaluate which medicines will produce side effects within certain ethnic groups, and which medicines will work for the widest spectrum of a population.

• I don’t know what else to say except that Dr. James Watson is in a heapa trouble. I suspect that he might not really care, though. At his age and with his reputation, what’s he got to lose?
• Alan Boyle of Cosmic Log looks at The Secrets in Your Genome.
• Clinical geneticist Dr. Hugh Rienhoff of the wiki MyDaughtersDNA.org is featured in Nature News - Personal Genomics: His Daughter’s DNA.
• Is there a gene for homosexuality? Some hope not because of worries over discrimination, prenatal DNA testing, and abortion. Others hope there is a gay gene so that the courts will rule against discrimination.
• Welcome Chris Della Vedova who’s joined The DNA Network as our 32nd member with his science category feed!

*Thanks, Amélie!

Tags: genetics, genes, dna hugh rienhoff, james watson, dnaprint, ancestrybydna, ancestry by dna, genetic genealogy

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