Friday, December 31, 2010

2010 in Review at "Your Genetic Genealogist"

I have been blogging just over six months and, during this time, I have been amazed at the response. I could never have imagined the kind of readership and encouragement that I would receive in such a short time. I am a simple layman, not a scientist, writing about what I love - genetic genealogy, yet I have been welcomed and encouraged by those in the forefront of personal genomics. I am deeply honored to have the opportunity to participate in this incredibly exciting emerging field of research.

In particular, I would like to thank Daniel MacArthur of Genetic Future and Genomes Unzipped, Dan Vorhaus of Genomics Law Report and Genomes Unzipped, Blaine Bettinger of The Genetic Genealogist and Katherine Hope Borges, Director of ISOGG.

I installed Google Analytics on July 18th, so I have about five and a half months of stats. Since then, I have had 7,580 visits to my blog, resulting from only 32 posts. Of these visits, about 40% came directly to my site. Approximately 20% came from Google and the rest came from 261 different referral paths - including Discover Magazine Blogs, Science Blogs, Newsweek, Facebook, Twitter, Genetic Future, Genomes Unzipped, Genomics Law Report, Blogger, LinkedIn, SNPedia, DNA Forums, Cyndi's List, Rootsweb, Fatwallet, and CNN's Paging Dr. Gupta.

My post from November 23rd entitled, "News from 23andMe: Consolidated Offerings, Personal Genome Service, Upgraded Chip and Possible Sale" was the most visited with 843 views. This coincided with my biggest single day of 468 visits on November 24th. Thanks to many referrals, including Genomes Unzipped, "Ashkenazi and Me: A Case for EuroDNA Calculator Application Using Ancestry Analysis Tools from 23andMe" came in second. Third was "Washington Post - Can We Take The Higher Road?" dealing with the 23andMe sample mix-up. The fourth most read was "Sale and New Personal Genome Service Subscription at 23andMe." Rounding out the top five was my post from July clarifying the confusion over mtDNA testing vs. X-Chromosome testing.

What most amazed me is the type of readership that I have enjoyed this year. My readers come from 73 different countries - originating from top universities, research hospitals, pharmaceutical companies, the national news media, genomic sequencing/research/testing companies, venture capitalists and governments - as well as the expected genealogy enthusiasts. These include visitors from Stanford, Harvard, Yale, Princeton, MIT, Oxford, Cambridge, Columbia, Duke, Georgetown, Tokyo Institute of Technology, University of Sydney, Hebrew University of Jerusalem, Israel Interuniversity Computation Center, Danish Network for Research and Education, Wageningen University and Research Centre, Johns Hopkins Medical Institutes, Albert Einstein College of Medicine, Mayo Clinic, St Jude's Children's Research Hospital, Vanderbilt University Medical Center, King's College London, Royal Berkshire Hospital, Fred Hutchinson Cancer Research Center, Wellcome Trust Sanger Institute, Eurac, Russian Academy of Sciences, SMGF, Lawrence Berkeley National Lab, P4MI, Broad Institute, NASA, US Senate, US State Department, US Department of Foreign Affairs, US Department of Veterans' Affairs, US Department of Energy, Democratic National Committee, National Institutes of Health, FCC, Library of Congress, EPA, Social Security Administration, NHS Trust (UK), Commonwealth Department of Foreign Affairs and Trade (Australia), Department of Foreign Affairs (Canada), Illumina, Genentech, Eli Lilly, Counsyl, Siemens, IBM, Boeing, Google Inc, NY Times and USA Today.

This has demonstrated to me quite clearly the power and importance of personal genomics in our society. It has also proven to me that any of us can play a part in this emerging science. Scientists and hobbyists can work together and, it seems, our contributions are welcome.

I look forward to the exciting discoveries that 2011 will, no doubt, bring.

My Full Mitochondrial Sequence, Heteroplasmy and Comparing mtDNA designations at FTDNA and 23andMe

I received my Full Mitochondrial Sequence (FMS) results from FTDNA last week. FTDNA lists my mtDNA haplogroup as U5b1, while 23andMe reports it as U5b1b2. I am fortunate in that I have four exact matches in the FTDNA database, including a close relative of Dave Dowell of Dr D Digs Up Ancestors.
Often mtDNA testing is not especially meaningful genealogically, but in my case it is more so because this subclade does seem to be predominantly Finnish, which matches my paper trail perfectly. My matrilineal great grandmother Mathilda Huhtala (1878-1950)  immigrated to the United States from the South Ostrobothnia area of Finland in 1902. Thanks to my wonderful Finnish friends, including one of my early high resolution mtDNA matches, I have a pretty solid paper trail back to Margaretta Mattsdotter Kauppi Storstraka Taipale born 21 July 1712 in Härmä, Lansi-Suomen Laani, Finland. Margaretta is my sixth great grandmother and from the same area of Finland as Mathilda.
I have ten High Resolution (HRV1 + HRV2) mtDNA matches. Eight of these are Finnish and two suspect Finnish ancestry. Eight of the ten have done the FMS test and, of those, I match four. I'd say that I got pretty lucky since so many people have no matches to their FMS in the database so far. There seems to be quite a lot of interest in DNA testing among my subclade. Perhaps this is because Finns have an unusually high participation rate in DNA testing overall compared to other countries outside of the US.

I asked Dr. Ann Turner to review my results. She was especially interested in comparing the mtDNA sequences recorded by FTDNA to my 23andMe raw data. She found 34 no-calls in my 23andMe mtDNA data, including one at 6260 where, according to FTDNA, I have a heteroplasmy (notated by a "R"). She checked my mother's 23andMe data and discovered that she also showed a no-call there. Dr. Turner noted that no-calls are usually not significant, but in this case, she theorized that my mother may also have a heteroplasmy at that location, resulting in the shared no-call.

(Note on heteroplasmy- Funny how a concept becomes so much clearer when you learn that it affects you personally.)

From my custom report prepared by Dr. Turner:
You have the mutations that define superhaplogroup UK (11467G, 12308G, and 12372A)...U5 splits off with 3197C, 9477A, and 13617. U5 in turn is divided into smaller groups, with 7768G and 14182C defining U5b, 5656G defining U5b1, and 12618A defining U5b1b. Somewhat unusually, a mutation in HVR2, 217C, defines the deepest level, U5b1b2.
...the most recent mutations (are) the ones that have not been observed often enough to be formally recognized as a subhaplogroup. Population geneticists sometimes call these “private” mutations, using the word in the sense of “confined to particular persons or groups.” Private mutations may in fact be very recent or quite old, but regardless of their absolute age, they are the ones that narrow down the pool of matrilineal relatives to your closest cousins. Not everyone will even have a private mutation. Your private mutation is 6260R.

Interestingly at 23andMe where I have tested ten close matrilineal relatives so far, one of my first cousin's mtDNA haplogroup is designated as U5b, while the rest of us are U5b1b2. Dr. Turner investigated this difference by checking my cousin's raw data for no-calls. As she suspected, my cousin has a no-call at a defining SNP, thus causing the different designation. She also noted that this cousin does not share my heteroplasmy at 6260, adding, "That's a good illustration of how heteroplasmy levels can vary within a family."

Since Dr. Turner confirmed that there are no known medical implications to my mtDNA results, I am sharing them here for anyone who is interested:
HVR1 differences from CRS
16189C, 16192T, 16270T

HVR2 differences from CRS
73G, 150T, 217C, 263G, 309.1C, 315.1C, 573.1C, 573.2C

CR differences from CRS
750G, 1438G, 2706G, 3197C, 4769G, 5656G, 6260R, 7028T, 7768G, 8860G, 9477A, 11467G, 11719A, 12308G, 12372A, 12618A, 13617C, 14182C, 14766T, 15326G

I am in the process of submitting my results to GenBank. It is a bit complicated, so I am including links and helpful instructions I received from Ian below.

If you are looking for your FASTA file to submit to Ian Logan for GenBank, it has been moved. Here is what you do:
Login to your FTDNA account.
Go to the mtDNA -> Print Certificate/Report/Data page.
Look for where it says:
mtDNA Results
Click on the FASTA File link to download your FASTA file. Further submission instructions are here.

[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I receive no other compensation in relation to any of the companies or products referenced in my blog.]

Sunday, December 26, 2010

23andMe's "New Low Price for All!"

The holiday sale has ended, but it appears that 23andMe has lowered their regular price to $199 (from $499) plus $5 per month for their PGS. This is a fantastic every day price point to entice more people into their database. I am very happy to see that they are staying competitive and making their service affordable to a large demographic. Hopefully, this will result in continuing advancement of our collective knowledge of the human genome.

Wednesday, December 1, 2010

End of the Year Sale at FTDNA

Family Tree DNA, the most trusted company in genetic genealogy, just announced their annual end of the year promotion. Starting tonight, there are great prices on the most popular products, including Family Finder (autosomal DNA test), Y-DNA testing and mtDNA testing. The regular prices are listed below with the sale prices in bold.

Price for NEW KITS: Regular Price Promotional Price
YDNA37 $149 $119
YDNA67 $239 $199
mtDNAPlus $159 $129
Family Finder $289 $249
Price for UPGRADE:
Family Finder $289 $229
Orders must be in and paid for by Dec. 31, 2010, to receive this offer.

I don't want to be the blogger who just reports on sales, however I do want as many people to get tested as possible. The more the databases grow, the more our success rate will increase in scaling those genealogical brickwalls and learning more about our ancestry. With that goal in mind, I encourage everyone to take advantage of, at least, one of the current holiday sales and get that DNA tested that you have been wondering about!

[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I receive no other compensation in relation to any of the companies or products referenced in my blog.]