Interested in learning about the unique inheritance of the X chromosome through the use of some cool visual charts? Look no further:
And be sure to check out Debbie Parker Wayne’s great charts at “X-DNA Inheritance Charts“!
Interested in learning about the unique inheritance of the X chromosome through the use of some cool visual charts? Look no further:
And be sure to check out Debbie Parker Wayne’s great charts at “X-DNA Inheritance Charts“!
Following a trend inspired by discussions at the recent Conference for Family Tree DNA Group Administrators, Family Tree DNA has released a new set of updates. This week’s update includes the ability to change the location for your most distant known maternal or paternal ancestors, and the ability to determine which of your Family Finder matches actually match each other. Although this functionality was previously available, it was cumbersome and was not accompanied by any visualization.
From Family Tree DNA:
Matches Maps Locations Clear Button
Some users have requested the ability to clear their stored map coordinates for their most distant known maternal or paternal ancestors. We have added a Remove Location button to Step 3 of the Update Most Distant Ancestor’s Location wizard.
Family Tree DNA myFTDNA BETA Family Finder – Matrix
Today, we are happy to release our new BETA Family Finder – Matrix page. The Matrix tool can tell you if two or more of your matches match each other. This is most useful when you discover matches with wholly or partly overlapping DNA segments on the Family Finder – Chromosome Browser page.
Due to privacy concerns, the suggested relationship of your two matches (if related) is not revealed. However, we can tell you whether they are related according to our Family Finder program. To use it, you select up to 10 names from the Match list on the left side of the page and add them to the Selected Matches list on the right side of the page. A grid will populate below the lists. It will indicate whether there is a match (a blue check mark) or there is not a match (an empty white tile).
You access the BETA Family Finder – Matrix page through the Family Finder menu in your myFTDNA account.
The page starts out with two list areas: Matches and Selected Matches. You add Matches to the Selected Matches list by clicking on a name and then on the Add button.
Here is a screenshot of the BETA Family Finder – Matches page with a few matches added to the Selected Matches list.
You can change the order of names in the matrix by clicking on a name and then either the Move Up or the Move Down button.
To remove someone from the Selected Matches list, click on their name and then the Remove button.
Yesterday, 23andMe provided an update on its blog (see “23andMe Provides An Update Regarding FDA’s Review”) about how it will respond to the FDA’s recent warning letter. In a nutshell, the company will continue to sell the same Personal Genome Service (“PGS”) kits, but new customers will only have access to ancestry-related genetic information and tools, and to their raw data. No health-related information will be provided, for now. Existing customers will continue to have access to all tools, including health-related information.
I’ll note that this is exactly what I predicted would happen in my blog post about the FDA warning letter (see “The FDA Orders 23andMe to Stop Marketing Medical Tests”). You heard it here first! It’s really the most logical approach while 23andMe communicates with the FDA.
The blog post spells out the breakdown:
Because the actual testing procedure remains unchanged, new customers will not have to undergo additional testing if the issue with the FDA is resolved and 23andMe can again offer health-related information. At that point, 23andMe will be able to simply activate these tools using the customer’s existing data.
Will 23andMe Survive?
Some are already predicting the demise of 23andMe. I disagree, and caution you to beware the naysayers. With the exception of the new lawsuit, costs for which are currently minimal, 23andMe’s expenses aren’t increasing drastically as a result of the FDA warning letter.
However, sales will certainly go down as a result of not being able to offer health-related information for now (I believe they’ve experienced a significant sales jump in the last few weeks, but that will probably be temporary). That being said, 23andMe has never made much money from the sale of each PGS kit, and based on the cost of SNP chips, kit processing, and general overhead, they probably lose money per kit.
Further, based on 23andMe’s known funding milestones (available at Cruchbase), they likely have a deep reservoir of capital reserves, as well as the inherent value of their database, which is currently 500,000 kits strong.
Accordingly, it is my opinion that reports of 23andMe’s death are greatly exaggerated (ht: Mark Twain). As long as 23andMe and the FDA are able to eventually work out these issues and allow health-related information in some form, I’m predicting that 23andMe will weather this storm just fine.
A Boon for Genetic Genealogists?
It’s possible that this latest course of events may even prove to be a boon for genetic genealogists. With no access to health-related information for new customers in the foreseeable future, 23andMe may feel market pressure to boost the quality and quantity of ancestry-related information provided to customers. Instead of focusing on health, 23andMe can focus on new developments in ancestry to entice new customers.
Here are a few other articles about 23andMe’s latest response:
The following appear to be written by people who obviously are blissfully unaware of the entire field of genetic genealogy:
Ironically, these journalists have no idea that the ancestry-related information provided by 23andMe is far more informative and actionable than the health-related information!
But the award for the worst article goes to the following, which is just plain incorrect:
So by now you’ve no doubt heard that on November 22, 2013, the Direct-to-Consumer genetics testing company 23andMe received a uncharacteristically biting letter from the Food and Drug Administration (“FDA”), a federal agency that protects public health by monitoring and regulating various products such as food, medicine, and supplements.
In the letter, the FDA expresses its belief that the 23andMe Personal Genome Service (“PGS”) is a medical product because “it is intended for use in the diagnosis of disease or other conditions or in the cure, mitigation, treatment, or prevention of disease, or is intended to affect the structure or function of the body.” Accordingly, the FDA concludes, the PGS requires “premarket approval or de novo classification” by the FDA.
Most surprisingly, however, the FDA indicates that although there has been “more than 14 face-to-face and teleconference meetings, hundreds of email exchanges, and dozens of written communications,” the FDA has not heard from 23andMe since May, 2013, six months ago.
The FDA ended the letter ordering 23andMe to stop marketing the PGS until it receives FDA authorization, and 23andMe has 15 days to notify the FDA in writing of the steps it has taken to remedy the issues in the letter.
23andMe’s Response – So Far
23andMe responded first with a statement, and then with a blog post at the Spittoon (“An Update Regarding The FDA’s Letter to 23andMe”). In these responses, 23andMe indicated that it believes working with the FDA is important, and that they will continue to do so.
Medical – NOT Genealogical
This applies ONLY to the medical aspects of the 23andMe PGS, and NOT to the genealogical aspect. Any regulation of DTC genetic genealogy tests (which the ASHG and other entities have stated they are no longer interested in doing) would have to come from new legislation or some other federal entity, as the FDA would have no jurisdiction over purely genealogical testing.
It’s possible that 23andMe may split the PGS into medical and genealogical aspects, or temporarily block access to the medical information, at least until the FDA is appeased. In any event, there’s every reason in the world for 23andMe to keep at least its genealogical tools available and for sale, and that’s what I’m predicting they will do.
I don’t know. This is the question everyone is asking. Regardless of whether you believe 23andMe’s PGS should be regulated, the lack of communication with the FDA is frustrating. I note that we’ve only heard one side of the story here, and it’s possible there’s some explanation for a 6-month delay. For example, 23andMe’s General Counsel Ashley Gould left the company in July 2013 (see her LinkedIn profile, for example), which could have delayed a response. It’s also possible, although unlikely, that this is an intentional tactic to force a confrontational resolution to the issue.
It won’t (at least not the genealogical data). This letter from the FDA does not signal the end for 23andMe, as some have predicted. As I said above, I doubt that 23andMe will block access to their genealogical tools for current customers, and I predict that they will continue to market the PGS in some form while they work with the FDA, even if it’s purely a genealogical test (maybe including the “traits” which are arguably not medical). It wouldn’t change the test in any way, all the same SNPs will still be tested and available for download, and they could “reactivate” the medical side interpretations depending on how the FDA issues are resolved.
My Prediction: If you’re only interested in the genealogical tools, you likely won’t be affected by the FDA’s letter, other than a slowing in new matches if it negatively impacts sales. On the flip side, sometimes even negative publicity turns out to be good publicity.
Maybe, a little. To the extent that the FDA wants to ensure that the SNPs and interpretations are accurate and provided to customers in an understandable way, I’m fine with limited regulation. While consumers have proven to be valuable self-regulators of 23andMe, pointing out errors and bugs, there could be future snake oil companies that are less than reputable and not as open as 23andMe has been. Regulations would help ensure that testing is done only in reputable labs, and interpretations are accurate and robust.
However, to the extent the FDA wants to set up any barrier between me and my genetic information, I am vehemently opposed. I have a fundamental human right to my genetic information and the interpretation of that information, and setting up any paywall – including a physician or geneticist – is an unethical violation of that right. Although genetic information has proven to be far less predictive and actionable than almost everyone expected, it has the potential to benefit thousands or millions of people. Overreaching regulation by the FDA would only delay that benefit.
For More Information
If nothing good comes out of this situation, at least it has sparked a great deal of debate and discussion. Here are links to other geneablogger articles on the issue:
And here is an extensive round-up of some of the best links discussing the FDA’s letter, both pro and con, in no particular order (these articles provide some insight rather than just re-hashing the letter and 23andMe’s response):
What About You?
I want to know what you think. Leave a comment below!
The 9th International Genetic Genealogy Conference for Administrators is currently being held by Family Tree DNA in Houston, Texas. As they try to do every year, there have been several buzz-worthy announcements already.
Family Tree DNA has announced the new Big Y test:
Here are some of the basics about the new Big Y test:
The “Y-DNA SNP testing chart” page at the ISOGG wiki has already been updated to reflect the Big Y test.
For more about the test, see these great posts:
There’s also a great deal of discussion already going on at all the major DNA-related mailing lists and groups.
Will you be ordering the new Big Y test?
Understanding the complexities of autosomal DNA can be very challenging for newbies.
However, there are a few basic tenets that I believe can help these newbies. These tenets are essentially tools that newbies can use to analyze an autosomal DNA problem for themselves.
For example, here are the two very basic tenets that I typically introduce in my autosomal DNA lectures especially for the newbies:
So many of the issues that newbies run into can be resolved or prevented through understanding of these concepts.
The Coop Lab
The lab of Graham Coop, an associate professor in the Department of Evolution and Ecology at UC Davis, maintains a blog where they often discuss genetics. Today they published an interesting blog post entitled ”How much of your genome do you inherit from a particular ancestor? In the post, they perform a handful of different analyses using data they had for one generation of transmissions which was compounded over multiple generations.
For example, they also calculate the probability that you inherit zero (large) blocks of your genome from a specific ancestor, which is presented in a great chart. Interestingly, at about 7 generations ancestors may start dropping off of your Genealogical Family Tree. They also calculate the probability of inheriting zero blocks of your genome from a specific ancestor by chromosome. Definitely click over to the blog post to learn more.
Luke Jostins – Genetic Inference
The Coop Lab post is very similar to a 2009 post by Luke Jostins at Genetic Inference entitled “How Many Ancestors Share Our DNA?“, in which Jostins calculates the probability that someone inherits DNA from an ancestor. This is one of my favorite blog posts of all time, and Jostins’ calculations suggest that ancestors can start to fall off the Genealogical Family Tree at about 5 generations.
More Data! More Data!
There are some differences between the Coop and Jostins calculations, and it will be interesting to see these refined with better data. For example, these are the types of questions that large datasets combining detailed family trees and DNA (i.e., Genealogical Family Trees and Genetic Family Trees) can help answer.
For now, I may update my second basic tenet to say 5-7 generations.
23andMe today launched the African Ancestry Project, which has been in the works for some time now. Participants in this project will receive 1 free 23andMe kit.
The project aims to shed light on the health and ancestry of people with African ancestry, an underrepresented group in almost every database (both genealogical and health-related.
Participants in the African Ancestry Project will receive 1 free kit per family, if they are eligible. Eligible individuals must:
And only one free kit per family!
In 1991, German tourists in the Alps discovered the mummified remains of a man who died approximately 5,000 years ago. Named Ötzi, the remains have been studied extensively and have revealed a wealth of information about life in this region.
Of note to genetic genealogists, Ötzi’s DNA has also been the subject of extensive analysis. In February 2012, sequencing of Ötzi’s full genome was announced (see here and here) which revealed, among other things, that the Iceman probably had brown eyes, belonged to blood group O, and was lactose intolerant. He may also have had Lyme disease, as the genome of the infectious agent Borrelia burgdorferi was also identified in the sequencing effort.
Ötzi’s Y-DNA belongs to a subclade of Haplogroup G defined by the SNPs M201, P287, P15, L223 and L91 (G-L91). As far as I know, he has not yet been typed for any of the subclades downstreaming from G-L91. More information can be found at the G-L91 page of the Haplogroup G Project, and elsewhere online.
Ötzi’s Relatives – NOT his descendants!
Researchers from the Institute of Legal Medicine at the Innsbruck Medical University in Austria have published research in which they analyze the Y-DNA of 3,700 male blood donors from the Tyrol region of Austria where Ötzi was found (“High resolution mapping of Y haplogroup G in Tyrol (Austria)“). They found that about 4% of haplogroup G members, or about 19 people, belonged to G-L91. These individuals are, therefore, relatives of Ötzi through their paternal line.
This month, the media has taken this story and run with it, making a few mistakes along the way. For example, Discovery News writes in “Living Relatives of Iceman Mummy Found“:
“These men and the Iceman had the same ancestors,” Walther Parson, the forensic scientist who carried out the study, told the Austrian Press Agency.
Having carried Y chromosome haplogroup analysis, Parson was able to trace only the male descendants of the Neolithic man.
Despite the journalist’s inaccurate statement, we can never know for sure whether these individuals are just relatives or actual descendants of the Iceman.
It will be interesting to see whether additional analysis of Ötzi’s Y-DNA will reveal more specific SNPs and lead to better identification of his male relatives.
23andMe and co-founder Anne Wojcicki are featured in the cover story of the November issue of Fast Company entitled “Anne Wojcicki Is The Most Daring CEO In America.”
Accompanying the cover story are a number of different online articles, including the following:
Article #1 – “Inside 23andMe Founder Anne Wojcicki’s $99 DNA Revolution” by Elizabeth Murphy (not her real name – it was changed to protect the identity of her adopted daughter, who 23andMe testing revealed has an extremely high propensity for Alzheimer’s disease)
Article #2 - “Behind the Scenes of the Ad Campaign for 23andMe’s $99 DNA Test” – a brief look at how 23andMe is trying to recruit 1 million new customers. The article features a handful of tv spots, and reveals that many of the actors took a 23andMe test.
Article #3 - “To Know You is to Really Know You” – some interesting statistics about 23andMe customers, including that they are 50/50 male/female, and that fully 60% of the database is over the age of 40.
Article #4 – “The Marketing Challenge of $99 DNA Testing Company 23andMe” – discusses the issues raised by 23andMe’s recent patent, including the challenge it may present to recruiting new customers.
There are a lot of interesting tidbits here, be sure to check out all the articles.
There has been a great deal of coverage this week of the new patent issued to genetic testing company 23andMe. U.S. Pat No. 8,543,339 is entitled “Gamete donor selection based on genetic calculations” and is directed to methods for predicting traits for a child based on the DNA of candidate parents, and selecting a preferred donor based at least in part on the prediction.
Some of the coverage (including an editorial in Genetics in Medicine) has suggested that the methods are “hugely ethically controversial” and “‘GATTICA’-like,” and could lead to a “design-your-own-baby DNA test” and “designer babies.” Another popular genetic genealogy blogger, Roberta Estes, also addressed the patent on her blog earlier this week (“23andMe Patents Technology for Designer Babies”).
23andMe preemptively addressed the patent in their blog the Spittoon (“A 23andMe Patent”), and stated that “[t]he company never pursued the concepts discussed in the patent beyond our Family Traits Inheritance Calculator, nor do [they] have any plans to do so.”
Too Much Hype?
The negative hype surrounding the patent, however, is based entirely on the misguided theory of genetic exceptionalism (the belief that genetic information is special and must therefore be treated differently from other types of medical information), and is unwarranted.
Here is a brief summary of my hypothesis, which I’ll get into in more detail below:
#1 – Selecting A Donor Without DNA
Although some may disagree with points #2 and 3 above, point #1 is indisputable. People have been screening potential donors for at least 50-60 years based on one or more of the factors listed above. Things such as personal and family health history have a very strong genetic component, and in almost every way are better predictors of health in offspring. For better and for worse, DNA has not turned out to be the strong predictor scientists thought it would be.
And even before gamete donation, there was the simple selection of mate based on appearances and behavior, which can be very closely tied to genotype.
Regardless, there is no doubt that donors have been screened for decades. However, I’ve never heard anyone suggest that donors should not be screened, or that there should be regulation of donor selection to prevent screening based on certain traits. Indeed, none of the coverage has suggested that any screening be stopped, other than DNA-based screening. At best, a few of the better articles have mentioned in passing that non-DNA factors are routinely used for donor selection.
#2 – The Myth of Genetic Exceptionalism
The 23andMe patent describes methods of using genotype (DNA) to predict the possible traits of a child and thus allows the selection of a particular donor based on the “best odds.” How is that process different from selecting a donor with the highest level of education and hoping that it corresponds to intelligence in the child? Or selecting a tall donor with dark hair in the hopes that the child will be tall with dark hair? Or selecting a thin donor in hopes that the child will be thin?
The difference is likely only that many people believe that DNA is different or special, that selecting for an “A” at position rs123456 is somehow different than selecting “dark hair” or “175 lbs.”
There is also a knee-jerk reaction that any screening or selection based on DNA is “eugenics,” although people have been selecting mates (and later, donors) based on the outward expression of DNA for millennia (facial features, hair color, eye color, height, weight, etc…). The fear of eugenics is a good and necessary fear, but calling any selection or screening based on DNA eugenics is crying wolf.
#3 – The Danger of Genetic Exceptionalism
Unfortunately, genetic exceptionalism and genetic paternalism go hand-in-hand. Many, including many bioethicists, believe that since DNA is “special” it should be regulated in order to protect the consumer. There should be, some argue, a physician or geneticist that can guide the consumer through the process. Others argue that there should be no ability whatsoever to take certain DNA tests. The theory that consumers need a “protector” from their DNA is what I call “genetic paternalism.” In my home state of New York, for example, I am unable to spit my DNA into a tube for testing without a physician to order the test.
Much of the discussion of potential regulation of direct-to-consumer tests such as those offered by 23andMe, Family Tree DNA, and Ancestry.com is framed in terms of “protecting” the consumer:
Not surprisingly, here has been no call for regulation of traditional donor screening, but there has been plenty of call during the last week for regulation of genetic screening.
And The Scientific Limitations
There are also some serious scientific limitations to the concerns. At Wired, personal genomics aficionado Daniel MacArthur provided the following:
Geneticist Daniel MacArthur of Massachusetts General Hospital said he’s not especially concerned about moral objections to selecting offspring traits with the type of technology described in the patent, but he thinks it’s important to be realistic about what’s even possible.
Indeed, in 2009 I wrote a paper entitled “The Potential Impact of Preimplantation Genetic Diagnosis on Discrimination of the Disabled: Analysis of Mitigating Factors,” in which I argue that although parents will eventually have the ability to screen embryos based on thousands of tested traits, the science simply prevents preimplantation screening based on more than a tiny handful of traits.
For example, if I only have a small number of viable embryos that I can screen, there will only a very limited number of possible combinations. I would need hundreds or thousands of embryos to positively select for a large number of traits. The paper provides an example of a three-trait cross, in which just 1 of 16 embryos will statistically satisfy the requirements for all three traits. However, fertility centers only harvest an average of 6 to 15 eggs for in vitro fertilization.
The 23andMe patent describes a method for calculating the possible traits of a child and lets the user select a donor based on those calculations. In my opinion, the only difference between this method and using education or health history to screen donors is the involvement of DNA. How you come out on this issue is likely a strong predictor, I would imagine, of your opinion of genetic exceptionalism.