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”).
Published today at MATTER is “Uprooted,” an in-depth look at genetic genealogy and DNA testing. The article contains numerous quotes from several names you’ll recognize, including CeCe Moore and me. Much of the story focuses on genealogist Cheryl Whittle and her roller-coaster quest to find her biological roots using DNA testing. From the preview of the roughly 10,000 word article:
“In Issue 11 of MATTER, award-winning writer Virginia Hughes tells Cheryl’s story, and describes how the twin revolutions of the internet and DNA testing have turned genealogy into a privacy minefield. After all, your genetic code is as personal as it gets — yet thanks to the web, you are no longer the only person who gets to control it.”
Imagine the following scenario:
- You’ve just received an email that your DNA test results are ready, and you log into your account. The welcome screen guides you through a tutorial and presents you with several tabs to choose from.
- You click the first tab which reads “Your Ancestors.” The page shares information about 35 of your ancestors from the past 300 years, identified because you have inherited some of their DNA, although you have not yet provided any genealogical information to the testing company. Each of these ancestors has their own profile page complete with dates, family members, and other information such as computer-generated images and a health report which are based on a genome reconstructed entirely from modern-day descendants.
- You then click on the tab that reads “Your Reverse Family Tree,” which contains a partial family tree that has been constructed by the testing company. Based on extensive and well-documented genealogies, there is likely only one way in which the 35 identified ancestors can fit together in a tree (although other possible combinations are provided along with statistical probabilities). There are a considerable gaps, especially on your recent immigrant grandmother’s line, but the tree appears to be entirely consistent with your many years of traditional genealogical research. Well, except for the family of John G. Rogers from the 1850’s; you’d copied that off the Internet years ago and never confirmed for yourself anyway.
- Next you click on “Your Cousins,” which contains numerous close and distant relatives in the database. Some of these cousins are Genetic Cousins (with whom you share DNA), and some of whom are Genealogical Cousins (with whom you share a genealogical relationship based on your generated family tree). There are numerous 2nd and 3rd cousins matches. There are also pending offers to join several citizen science and family research groups, including the “Descendants of Calvin Lane of Old Lyme, Connecticut” group, the “Family of German Immigrant Johann Kehl” group and the “Relatives of the American Franklin Family” group, each of which has a slightly different research goal.
- Lastly, you click on “Your Memberships,” which offers – among other things – a discount membership to the Daughters of the American Revolution based on your predicted descendancy from Revolutionary War veteran Jedidiah Johnson (although you don’t happen to share any of Jedidiah Johnson’s DNA, he’s in your generated family tree with an extremely high probability (95%)).
While the scenario I described above may sound like science fiction, it’s the inevitable future of genetic genealogy and is much, much closer than you might think (okay, maybe not the DAR offer!).
Next month at the American Society of Human Genetics 2013 meeting, researchers from AncestryDNA will present their work detailing the reconstruction of portions of the genomes of an 18th-century couple using detailed genealogical information and Identity-by-Descent (“IBD”) DNA segments from several hundred descendants of the couple in the AncestryDNA database. In other words, researchers identified several hundred descendants of a certain couple living in the 1700s and then used the DNA shared by those descendants to recreate as much of the couples’ genomes as possible.
In addition to the information you received from 23andMe, Family Tree DNA, or AncestryDNA about your ancestry, there is a wealth of additional information still within in your DNA. Below (in alphabetical order) are some of the most popular and well-known tools for wringing every last bit of information out of your raw data, and maximizing the cost of your DNA test. Please note that I have not used or verified all of these apps; always use caution when providing information to an unknown recipient.
Apps, Extensions, Programs, and Websites:
- 23++ (http://23pp.david-web.co.uk/about/) (FREE) – An extension for the Google Chrome web browser that adds additional functionality to the 23andMe website. The extension especially adds a number of features to Relative Finder.
- 529andYou (http://goo.gl/FQSiwW) (FREE) – An extension for the Google Chrome web browser that works with 23andMe’s Family Inheritance: Advanced tool (found under Ancestry Labs or, in the new beta website design, under My Results, Ancestry Tools) to collect information about DNA matches. The information, which includes shared segment data, is stored in a local database on your computer.
) (FREE) – A comprehesive suite of tools for analyzing raw data, including searching for Runs of Homozygosity (ROHs), searching for shared DNA in two files, and several advanced phasing tools.
) (FREE) – A suite of tools for 23andMe and Family Tree DNA customers. Users can download their matches, shared segments, and other data into a handy spreadsheet for further analysis.
23andMe and Udacity today announced a new online course entitled “Tales from the Genome: Adventures in DNA, Identity, and Health,” a Massive Open Online Course (“MOOC”) directed at genetics. According to the website, students will learn about “fundamental principles of inheritance, gene expression, mutation and variation, development of simple and complex biological traits, human ancestry and evolution, and the acquisition of personal genetic information.” The class is labeled as being aimed at beginners.
Although not announced on the Udacity website, the course will be available beginning on September 30, 2013.
The “Tales from the Genome” class will be taught by Matthew Cook, Lauren Castellano, Joanna Mountain (of 23andMe), and Uta Francke (also of 23andMe). For more information, see the press release at Market Watch (“23andMe and Udacity Launch Introductory Human Genetics Course“).
At Salon, an article entitled “The college class that could reveal your real father” by Katya Cengel discusses a course at Stanford called “Genetics 210.” The class uses [entirely optional] 23andme testing to explore the many issues associated with genetic testing. Although the class is offered to both graduate and undergraduate students, the class is filled with mostly graduate students.
All students go through the informed consent process carefully, and have access to a genetic counselor and a psychiatrist (although according to the report not a single student has contacted the psychiatrist in the four semesters the course has been offered, and only two have contacted the genetic counselor).
The most interesting aspect of the article, to me, was the complication that identical twins pose to genetic testing. Epigenetic differences aside (which are currently NOT tested), a genetic test for one will directly apply to the other. So what happens when one twin wants to know and the other doesn’t?
There has been much discussion (see here and here for a few examples) of the so-called “Scandinavian Problem” with AncestryDNA‘s ethnicity estimate, in which certain populations appeared to be over-represented in the reference panel utilized by Ancestry.com. I, for example, have no documented Scandinavian ancestry, but had 78% Scandinavian. Many others experienced the same issue.
The AncestryDNA team were well aware of the issues, and have been working on an update to their ethnicity algorithm, reference panel, and user interface. Indeed, at “The First DNA Day at the Southern California Genealogy Society Jamboree” in June of this year, Ken Chahine (Senior Vice President and General Manager, DNA) gave a presentation in which he announced that the ethnicity calculations at AncestryDNA were undergoing a complete overhaul and a major update would be provided to all customers later this year.
Family Tree DNA has announced yet another new sale, with the popular Family Finder being available for only $99 for a limited time:
Dear Valued Customer,
Summer is once again upon us and it is time for our Sizzling Summer event! Our successful summers over the last two years have led us to offer you great values again this year.
We have been working with Illumina to offer our Family Finder autosomal test for only $99 during our summer event. In fact, if we receive enough orders at $99, Illumina may be able to help us keep it at this extremely low of rate of $99!
As you take advantage of our summer event, remember that the permanency of the $99 Family Finder test is actually in your hands!
Beginning on Thursday, June 27, 2013 and running until Friday, July 26, 2013, we will offer the following:
Yesterday, AncestryDNA announced on the Ancestry.com Facebook page the launch of a long-awaited search function for surnames and locations of genetic matches.
The top bar of the AncestryDNA Member Matches section now looks like this:
Clicking in the “Search matches” box causes the box to expand and reveal the new search boxes:
Both seem to work well, and I suggest you use the search feature to mine your matches. For example, I found a number of matches for several unique surnames and locations in my tree that I had missed in the flood of matches over the past six months.
New Ethnicity Estimates Coming Soon
At “The First DNA Day at the Southern California Genealogy Society Jamboree,” I discussed the changes to the ethnicity algorithms and reference populations that AncestryDNA was planning to implement by the end of 2013:
For the next week or so, 23andMe is pausing updates to the DNA Relatives feature. This feature provides a list of genetic matches and estimates the range of relationship.
According to this week’s 23andMe update entitled “Release Notes: 7 June 2013,” (you must log in to view), “The computation time for DNA Relatives and Ancestry Composition has been growing.”
Going into greater detail at “DNA Relatives computations temporarily on hold,” 23andMe explains that due to the increased computational time, and in an effort to reduce the time it takes to generate DNA Relatives matches, updates are paused. Accordingly, “[t]his means that you won’t be receiving new matches to your existing DNA Relatives list, and if you haven’t received your matches yet there may be some additional waiting time.”