The Genetic Genealogist

A few days ago I wrote about John Reid’s “Where Has Your DNA Been” post at Anglo-Connections a few days ago. This is similar to another meme which has been circulating the genealogy blogosphere for a few weeks now, including “Where was your family in 1908?” at 100 Years in America and “Where was your family 200 years ago?” at What’s Past is Prologue. Steve at Steve’s Genealogy Blog has also given the ‘Map Your DNA’ meme a try. I thought it was a fun idea, and had a number of potentially interesting applications, if I were a programmer and if I had any free time. Absent that, I thought I would at least try to replicate John’s idea by mapping my location in 2008 versus the locations of my Y-DNA and mtDNA in 1808, 200 years ago.

First, my Y-DNA. The blue dot on the following map of New York State is the location of my great-great-great-great-great-grandfather in 1808, and the yellow dot is me in 2008. The two dots are only 11 miles apart!! So, my Y-DNA has traveled at an average speed of just 0.05 miles per year! My Y-DNA appears to be a little lazy.

Next, my mtDNA. The blue dot on the Cayman Islands is the location of my great-great-great-great-great-great-grandmother in 1808, and the yellow dot is me in 2008. The distance between the two locations is 1664 miles, for a average traveling speed of 8.3 miles per year! Now that’s more like it!

Where was YOUR mtDNA and Y-DNA in 1808?

January 2008 has been another interesting and busy month for genetic genealogy and personal genomics. Keeping track of the latest developments can be a challenge, so I thought I’d do a brief round-up of some of the headlines that I thought were particularly interesting. Happy reading!

• Hsien at Eye on DNA discusses the use of DNAWitness, a Bio-Geographical Ancestry analysis, to narrow the pool of potential suspects in a crime. This hotly debated test has been used in over 200 crimes. And am I the only one who thinks that DNAPrint Genomics needs to invest a little money to upgrade its web design? Hsien also highlights the genetic genealogy pages of Kevin Duerink, pages that I myself have found to be quite useful.

• DNAdirect mentioned a recent study in the New York Times that examined the ancestry of Pacific Islanders. According to the study, “each individual was originally genotyped for 751 microsatellite and 481 insertion/deletion autosomal polymorphisms.” That’s a lot of genetic genealogy! Similar studies include autosomal analysis of Polynesian DNA (abstract here, Yann Klimentidis’ discussion here) and a recent paper that identified 300 informative autosomal markers that delineate types of European ancestry (paper here, Henry’s discussion here). What a great time to be either an anthropologist or a genetic genealogist. As more genomes become available, these types of studies will be easier to conduct.

• After winning the recent contest here at TGG, Jasia of Creative Gene was “Excited“, and then had to choose between an mtDNA and Y-DNA test. She ultimately chose the mtDNA test, and the DNA collection kit has already arrived and been mailed back.

• The New York Times has launched The Root, which is “an online magazine primarily for a black audience, with news and commentary on politics and culture, and tools for readers to research their family histories.” Epidemix recently discussed The Root as well. According to an announcement in the NYT:
  • “The third major part of the new site, titled “Roots,” will have online tools for people to build their family trees, link to or add information to other people’s trees and construct maps showing their ancestral trails. It will also urge people to have DNA testing, which can help them trace their backgrounds to specific ethnic groups and parts of the world. It will offer links to companies that do the testing.”

• VentureBeat:life sciences discusses deCODEme’s science and 23andMe’s recent “European vacation” (more about that at TechCrunch). Genetic Future, a new member of the DNA Network, discusses genetic genealogist Ann Turner’s response to the VentureBeat deCODEme piece. Over at a great post on Eye on DNA, Ann Turner shared some thoughts about whole genome testing.

• And finally, John Reid at Anglo-Celtic Connections writes “Where Has Your DNA Been?” He uses Google maps to pinpoint the locations of his Y-DNA and mtDNA in 1808 and 1908. What a great idea! I can picture entire applications where users enter the locations of the Y-DNA or mtDNA ancestors at certain points in time (perhaps lining up with census information) to get a “DNA Trail.” Then maybe you could line up with other users to create DNA migration patterns for haplogroups, haplotypes, or surnames. For instance, how did the Smith Y-DNA modal haplotype distribute throughout the United States and the world? I guess this would just be a microcosm for the Genographic Project, but it would still be interesting.

As I recently mentioned, SeqWright has launched a new Personal Genomics Service. Using a saliva sample, this service will analyze 930,000 SNPs from a customer’s genome using the Affymetrix 6.0 Human SNP Genotyping microarray. SeqWright will then report information back to the customer about “Genetic Health,” “Ancestral Origins,” and “Genealogy.” The cost of the service is $998. According to the website, they “will begin accepting orders for Genetic Profiling Services on Monday January 28 2008.” The official press release is available here.

From the consent form available on the SeqWright website:

“SeqWright will generate its client’s personal genomic data on the Affymetrix 6.0 Human SNP Genotyping microarray. This Array is capable of recognizing approximately 930,000 unique human SNP’s. However, due to individual sample and test variation the number of SNP genotypes that SeqWright will report for a given individual will be a fraction of those SNP’s.”

The SNPs that SeqWright will report are those that are believed to be associated with disease:

“SeqWright will only report SNP’s which we have deemed, through the analysis of publications with significant statistical size and power, to have an established association with a disease state or trait.”

SeqWright provides the usual and very necessary disclaimer that their information is NOT to be used as a substitute for medical information:

“This service cannot be used for medical diagnostic purposes. The state, and dynamic nature, of scientific understanding within this field precludes the use of SNP’s as definitive predictors of disease. Therefore, it is of paramount importance that clients do not use the information provided by SeqWright’s Personal Genomic service as a substitute for a clinical diagnosis or medical advice. Clients with concerns related to the information provided through this service as it pertains to an increased or decreased likelihood of developing a particular disease state, are encouraged to seek medical advice.”

SeqWright joins 23andMe, deCODEme, Navigenics, and Knome in the field of personal genomics, although Navigenics has not officially launched.

A potentially very useful new tool for mitochondrial DNA sequences has just launched. The mitoWheel, announced today on Attila Csordás’ blog “Pimm – Partial immortalization” is a web-based graphical interface to visualize mtDNA. Attila is actually a member of the developing team for this project. According to the mitoWheel website:

“The mitoWheel is a graphical representation of the human mitochondrial genome. Use the left and right arrows to start browsing the sequence. You can also search for a nucleotide position, a gene, or a sequence motif by clicking in the search field, typing a term and pressing ENTER. Be sure to return soon for updates introducing further tools.”

According to Attila, “The sequence used is the standard Revised Cambridge Reference Sequence.” Here is a small screenshot of the tool:

As you can see, the CRS sequence is listed along the front of the interface, and is scrollable:

While I was exploring the new tool, I thought of a few (genetic genealogy-related) features that I would love to see:

1. 1. Ability to upload an entire sequence or list of mutations to be translated into your own personal graphical representation (with changes from the CRS highlighted, maybe even with annotated information about those mutations);
   2. Ability to compare to sequences side-by-side (your sequence v. the CRS, or your sequence v. your 4th cousins’, for example).

This is a very interesting tool, and hopefully will be updated with new features, so stay tuned.

The DNA Network was full of news about 23andMe, Knome, and the newly-announced 1000 Genomes Project, which plans to sequence (can you guess?) 1,000 genomes from around the world. The 1GP will “receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute (BGI) Shenzhen, China and the National Human Genome Research Institute (NHGRI), part of the U.S. National Institutes of Health (NIH).” Source.

Here’s a brief roundup of all the latest regarding the 1GP:

• Forbes.com, “Project Will Map Genomes of 1,000 People Worldwide.“
• Genetic Future, “1000 Genomes Project launched.”
• Cosmic Log, “Let a thousand genomes bloom.”

New information about 23andMe, including the launch of their new blog, the spittoon:

• 23andMe now available in Canada and Europe (press release).
• Scienceroll, “23andMe in Europe: Donation Makes Sense!” And speaking of donations: Buzzyeah, “$1,000 Raised! Just Ordered My 23andMe DNA Kit.”
• Eye on DNA, “Latest Launches at 23andMe.“
• Microarray Blog, “The 1000 Genomes Project to Study Human Genetic Variation to Support Disease Studies.”
• Genetic Future, “UK Controversy over 23andMe.”

Other stuff:

• Scienceroll, “Knome Begins Sequencing First Clients.” Remember that Knome is currently charging customers $350,000 to have their entire genome privately sequenced. As I recently commented at Eye on DNA, I think the price tag is too high in light of recent developments in technology. This is actually amazing, considering that $350,000 would have been a bargain in January 2007. Companies hoping to make money from sequencing are going to learn to act quickly and adapt even faster.
• SEQanswers.com, “deCODEme opens sample data set, check it out!“

And last but not least, are you worried about hair loss? A new company called HairDX offers a test that will examine SNP(s) on the X-chromosome, but the specifics are extremely vague at the moment, including a lack of information on their website. For more information, see My Biotech Life, “HairDX – the genetic test for hair loss” and Eye on DNA, “HairDX – Genetic Test for Male Pattern Baldness (be sure to read the comments to see information from Dr. Ann Turner).”

Jasia of Creative Gene! Jasia’s winning entry was from a post she wrote about the contest. If Jasia accepts the prize, she will discuss her testing experience or her results either on her blog or here at The Genetic Genealogist, which should be a lot of fun and will help genetic genealogy newbies gain some insight into testing. Congratulations Jasia!

If Jasia doesn’t claim the prize, or decides she doesn’t want it, the runner-up for this contest is Yann of Yann Klimentidis’ Weblog.

Thank you to everyone who wrote about the contest on their blog, subscribed to my feed, subscribed to my mailing list, or left a comment at the original post. Overall, 34 people entered the contest with a total of 117 entries! I met some new readers and read some fantastic posts about the blog. At the end of this post is a list of all the blogs that mentioned the contest.

I wish I could afford tests for everyone that entered! However, don’t be too discouraged that you didn’t win, as I will be doing this contest again in the very near future!!!

I would like to extend a huge thank you to DNA Heritage, who sponsored this contest.

Here is a shot of the randomizer results:

Before obtaining the random numbers, I randomized the Excel spreadsheet. Going back to the list armed with the winning numbers, I found the winner (surrounding names removed for privacy):

And the runner-up, who happened to be the last entry on the list:

Thank you again to everyone that entered, and to the following list of blogs that mentioned the contest:

• Becky at kinexxions
• Lori at Smoky Mountain Family Historian
• Matt at Contest Beat
• Corey at Perusing Aardvarks
• Jessica at Jessica’s Genejournal
• Randy at Genea-Musings
• Lee at The I Seek Dead People Blog
• Jasia at Creative Gene
• Rhonda at Rhonda’s Ponderings and Aussie Rhonda’s Genealogy
• Lisa at 100 Years in America, Small-leaved Shamrock, and A Light That Shines Again
• Yann at Yann Klimentidis’ Weblog
• Terry at Desktop Genealogist
• Jean-Yves at Geneasofts

Here are few of the latest sources of information or discussion about 23andMe:

Mark Fletcher at Wingedpig.com writes about some “23andMe Updates.” Fletcher notes that Andrew Scheidecker has written a program that will extract and download your own raw SNP data from 23andMe (http://www.scheidecker.net/personal-genome-explorer/). Scheidecker writes that the program doesn’t violate 23andMe’s terms of service, but I recommend confirming that for yourself before you use this program. Fletcher also links to Kevin Kelly at the Quantified Self, who writes “23andMe, Alzheimer’s disease, and ApoE.” Kelly notes (as has Fletcher) that the rs1702 and rs4420638 SNPs tested by 23andMe are resulting in “no call” for many individuals. These two SNPs are believed to be associated with Alzheimer’s disease.

HT & the Sheriff has decided to order a test at “Me, Me, Me (and 23).” Stay tuned for the results.

Jay Cross at Internet Time Blog writes “The Jay DNA” and ” The Jay DNA 2.0.” Cross recently ordered a 23andMe test and discusses his reactions to his results. He concludes: “Do I recommend 23andMe? Not yet. Wait a while.”

Jennifer Lahl at the Human Future writes “The Human Genome is Out of the Bottle” in which she creates a great list of questions that “we must ask ourselves.” Unfortunately, Lahl does not give any substantive analysis and merely cites the recent NEJM article (which, as you’ll recall, was not about genetic genealogy).

Canada’s Globeandmail.com presents “Goodbye Facebook, hello cheek swabs.” The article discusses the creation of social networks based on genetic relationships and mentions companies like 23andMe, GeneTree.com, and Canada’s DNA Ancestry Project (which was the subject of great controversy recently). This type of networking is new but is being pursued by many companies, including dna.ancestry.com, which compares your DNA tests results to their database to find and display your closest connections. I’m not crazy about this article, as it is a little weak on the science side.

As always, these links do not constitute a “promotion” of 23andMe, as one reader previously suggested. This post is merely a compilation of sites that contain information about 23andMe’s products and services to allow readers to do their own research and come to their own conclusions.

This is just a last reminder that my contest to give away a free genetic genealogy test ends tonight at 11:59PM (EST). The contest rules are here. Don’t forget that you can enter multiples times by:

1. Leaving a comment on the original contest post (here), or;
2. Write a short review of the blog or the contest with a link to http://www.thegeneticgenealogist.com using the anchor text “genetic genealogy” and then leave a comment here with a link to the review, or;
3. Subscribe to my feed and then email me (blaine_5 at hotmail.com) your name and the secret password found in the feed, or;
4. Subscribe to my blog by email using the form in the far right sidebar.

I will announce the winner and the runner-up tomorrow, along with a list of every blog review or blogger that commented! I would like to thank everyone who has already written a review, subscribed to my blog, or left a comment. This contest has been a lot of fun, and I look forward to learning more about the winner’s experience with genetic genealogy. Good luck!

Kimberly Powell of About.com:Genealogy recently posted “10 Genealogy Blogs Worth Reading.” I was honored to see that I was included as one of those blogs, along with some outstanding company. The others are:

1. Genea-Musings – “Randy’s musings bring out the genealogist in all of us…”

2. The Genealogue – “His unique brand of genealogy humor puts a special spin on just about everything genealogy…” I was saddened to hear that The Genealogue is on temporary hiatus as the author deals with a family situation. I wish Chris and his family all the best and look forward to his return.

3. Ancestry Insider – “…provides the “insider” point of view you won’t easily find elsewhere.”

4. Creative Genealogy – “Through this blog she brings something new to family history enthusiasts…”

5. Genealogy Blog – “Topics run the gamut from genealogy news, press releases and new products, to research techniques and highlights from other blog posts around the Internet.:

6. Think Genealogy – “His blog is an interesting, thought provoking outlet for his thinking about genealogy and genealogy software.”

7. The Practical Archivist – “She writes about archival-safe products and organizing family photos and memorabilia, with plenty of random research and preservation tips sprinkled in.”

8. Eastman’s Online Genealogy Newsletter – “News, reviews and a wealth of insightful commentary on various technologies as they relate to genealogy are the hallmark of Dick Eastman’s blog, read regularly by almost every genealogist I know.”

9. Boston 1775 – “The eclectic content covers New England during the time just before, during and after the Revolutionary War…”

The article also mentioned a number of other fantastic blogs, almost all of which I read on a regular basis (and more that I will probably be adding soon)! They include:

• Dear Myrtle by Pat Richley.
• 24-7 Family History Circle featuring Juliana Smith, Michael John Neill and Maureen Taylor.
• Geneablogie by Craig Mason.
• Rootdig by Michael John Neill.
• Family Oral History Using Digital Tools by Susan Kitchens.
• Walking the Berkshires by Tim Abbott.
• Genealogy Reviews Online by Tim Agazio.
• Hill Country of Monroe County, Mississippi by Terry Thornton.
• AnceStories by Miriam Robbins. Family Matters by Denise Olson.
• Tracing the Tribe by Shelly Talalay Dardashti.

As many of you know, I am currently a second-year law student preparing for a career in intellectual property. Last semester, I began work as a research assistant for one of my first-year professors. The project we worked on, examining portrayals of the United States patent system in the newspaper media, turned into two papers. Naturally I think the papers are great and it was interesting to see the results, especially considering all the attention the patent system has received lately.

1. Dolak, Lisa A. and Bettinger, Blaine T., “The United States Patent System in the Media Mirror.” Syracuse Law Review, Forthcoming. Available at SSRN: http://ssrn.com/abstract=1084420.
2. Dolak, Lisa A. and Bettinger, Blaine T., “Ebay and the Blackberry®: A Media Coverage Case Study” (December 11, 2007). Available at SSRN: http://ssrn.com/abstract=1082220.