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 … Click to read more!
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.”
You can buy the full article for .99 cents at MATTER. You can also get the … Click to read more!
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.
The … Click to read more!
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.
- David Pike’s Utilities (http://www.math.mun.ca/~dapike/FF23utils) (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.
- DNAGedcom (http://www.dnagedcom.com) (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.
- DNAMatch4iPad (http://www.dnamatch4ipad.com) ($) – A app for the iPad that is an “alternative to the use of conventional spreadsheets for the processing of autosomal DNA data.” Users download their match data from one of the testing companies in the form of a .CSV file and upload it to DNAMatch4iPad.
- GEDmatch (http://gedmatch.com/) (FREE) – A powerful suite of tools for 23andMe, AncestryDNA, and Family Tree DNA raw data. Users can compare their DNA to everyone else in the database or to a specific individual in the database, or perform numerous admixture analyses, phase their DNA, and much more.
- Genes & Us (http://www.genesand.us) (FREE) – A website for 23andMe users to “combine their genomes in order to better understand what disease risks most affect their family.” For example, a mother and father can link their 23andMe accounts to the site and determine the possible combinations for their children’s DNA. Appears to work with 23andMe’s new API offering.
- Genetic Genealogy Tools (http://www.y-str.org) (FREE) – An impressive and ever-growing list of advanced tools for analyzing raw data, including an X-DNA Relationship Path Finder, Ancestral Cousin Marriages, Autosomal Segment Analyzer, a DNA Cleaner, a SNP Extractor, My-Health, and many more! A terrific resource from Felix Jeyareuben Chandrakumar, an Australian software professional.
- Genetic Genie (http://geneticgenie.org/) (FREE) – A tool that analyzes your 23andMe results to perform a methylation gene analysis (“Methylation Analysis”). The site also provides a tool for a “Detox Profile” which looks for defects in the Cytochrome P450 detox enzymes. The site uses the 23andme API, so users can link their 23andMe account to the service.
- Genetrainer (https://www.genetrainer.com/) ($) – Users of 23andMe and Family Tree DNA can link their results to the Genetrainer service, which will then provide you with training plans and exercises personalized to the user.
- HIR Search (http://hirs.snpology.com) (FREE) – Once your raw data is entered in the database, you can find HIRs (half-identical regions) that you share with others in the database.
- Imputation Tools (http://mathgen.stats.ox.ac.uk/impute/impute_v2.html) and (http://faculty.washington.edu/browning/beagle/b4.html) (FREE) – Sometimes you find a SNP in the literature that isn’t tested by any of the big testing companies. Imputation allows you to determine the most probable genotype for that SNP based on the surrounding SNPs and a database of known sequencing results (such as the 1000 Genomes data). IMPUTE2, for example, is a computer program for phasing observed genotypes and imputing missing genotypes. See more about IMPUTE2 here, including a link to a script to convert your 23andMe raw data to a useable form. BEAGLE4 is similarly performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Learn how to use BEAGLE4 here.
- Interpretome (http://esquilax.stanford.edu/) (FREE) – A collection of tools for analyzing 23andMe raw data using only a web browser (i.e., raw data is not uploaded). The tools include an admixture analysis, health information, and a Neanderthal calculator.
- Minor Allele Program (http://www.ianlogan.co.uk/23andme/23andMe_index2.htm) (FREE) – A tool to identify rare SNPs in your 23andMe or Family Tree DNA raw data. My own results are available here.
- mtDNA Haplogroup Analysis (http://dna.jameslick.com/mthap/) (FREE) – A terrific tool for predicting your maternal haplogroup using a variety of formats, including 23andMe raw data.
- NAT2PRED (http://nat2pred.rit.albany.edu) (FREE) – a tool for inferring human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype. In other words, a tool for predicting the function of your NAT2 enzyme (either slow, rapid, or intermediate) based on your DNA. The NAT2 enzyme is involved in activating and deactivating arylamine and hydrazine drugs and carcinogens, among other things.
- Promethease (https://promethease.com/ondemand) ($5) – Analyze your 23andMe, Family Tree DNA, or AncestryDNA raw data and build a report based on SNPedia. Reports contain information about health and ancestry as well as several other new options. A sample report is here.
- Segment Mapper (http://kittymunson.com/dna/SegmentMapper.php) (FREE) – A tool to show specific DNA segments in a graphic chromosome-style chart. This is a clever and powerful “mapping” tool. Learn more about the tool here.
- SNPTips (http://snptips.5amsolutions.com/) (FREE) – A Firefox browser extension that allows 23andMe customers to access their SNP genotype information without logging into their 23andMe account or leave the webpage they are browsing. Users can simply hover their mouse cursor over a SNP RSID on a webpage and, if that was tested by 23andMe, the SNPTips extension will provide a popup with the user’s genotype and some relevant links.
- SPA (http://genetics.cs.ucla.edu/spa/index.html) (FREE) – Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual’s DNA. 23andMe users can download the software and analyze their results with this admixture tool.
- The 23andMe Gene App at Livewello (https://livewello.com/23andme) ($19.95) – a Variance Report Software analyzes 23andMe Raw Data are reports on 300 SNPs for things like “Methylation Detox, Immune Factors, IgE, IgG disorders and much more.” Livewello is a Social Health Management Platform with customized App.
Did I miss anything? Do you have any suggestions or comments regarding the programs listed above? Feel free to let me know in the comments … Click to read more!
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 … Click to read more!
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 … Click to read more!
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 … Click to read more!
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 … Click to read more!
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 … Click to read more!
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.”
It sounds as though … Click to read more!