Press release from Family Tree DNA today:

Family Tree DNA’s Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

– By Offering Low Cost DNA Test, Family Tree DNA Aims to Expand Reach of DNA Testing to Encourage Further Exciting Discoveries About Human Origins –

[26-March-2013]

HOUSTON, March 26, 2013 /PRNewswire/ — Gene By Gene, Ltd., the Houston-based genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic’s Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years.  This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report “An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree” in The American Journal of Human Genetics earlier this month.  The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of the University of Arizona, who currently serves on Gene By Gene’s advisory board, and two of the company’s staff scientists, Drs.Thomas and Astrid-Maria Krahn.

The DNA sample had originally been submitted to National Geographic’s Genographic Project, the world’s largest “citizen science” genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA’s database for genealogical research.  Once in Family Tree DNA’s database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

“This whole discovery began, really, with a citizen scientist – someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products,” said Gene By Gene President Bennett Greenspan.  “While reviewing samples in our database, she recognized that this specific sample was unique and brought it to the attention of our scientists to do further testing.  The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution.”

The discovery took place at Family Tree DNA’s Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project.  Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company’s Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations.  Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

“Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago,” said Dr. Michael Hammer.  “Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade.  This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise.”

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%.  By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research.  They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd.

Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

Media Contacts:

Kate Croft

for Family Tree DNA and Gene By Gene, Ltd.

Casteel Schoenborn

888-609-8351

croft@csirfirm.com

SOURCE Gene By Gene, Ltd.

Web Site: http://www.genebygene.com

Earlier this week, Ancestry.com began releasing raw data to purchasers of the AncestryDNA autosomal DNA product.  Several others have written great articles on AncestryDNA’s new raw data, so I’ll point you to their articles instead of rehashing everything here:

• EDITED (03/24/2013) - Expect a post  on this subject very soon from CeCe Moore at Your Genetic Genealogist!

• “Downloading Ancestry’s Autosomal DNA Raw Data File” by Roberta Estes at DNAeXplained
• “AncestryDNA updates” by Debbie Kennett at Crewys news
• “The raw data at AncestryDNA” by Judy G. Russell at The Legal Genealogist

Within the next few weeks and months, you’ll be able to use the AncestryDNA raw data at places like Family Tree DNA and Gedmatch.com.

But note an issue that I first brought up on a mailing list last Thursday when the announcement came out.  The following language is found on the page after you click on the final download link:

The raw data is subject to the AncestryDNA Terms and Conditions and AncestryDNA Privacy Statement. You must not use the raw data in whole, in part and/or in combination with any other database for any discriminatory, breach of privacy or otherwise illegal activity (for example, to re-identify any anonymous donor or to make insurance or employment decisions).

Under “Rules of Conduct” in Section 5 of the Terms and Conditions, Ancestry.com states:

In addition, the following policies are part of this Agreement and must be followed anytime you access the AncestryDNA Website:

D. You must not use the information from the AncestryDNA website or DNA tests (including any downloaded raw DNA data) in whole, in part and/or in combination with any other database for any discriminatory, breach of privacy or otherwise illegal activity (for example, to re-identify any anonymous donor or to make insurance or employment decisions).

These Rules of Conduct are not exclusive. If we believe, in our sole discretion, that you are in breach of this Agreement, are acting inconsistently with the letter or spirit of this Agreement or otherwise interfering with the efficient management or delivery of the AncestryDNA Website, Service or Content, we may limit, suspend or terminate your access to our AncestryDNA Website. In such a case, no portion of your subscription payment will be refunded. Should we decide to suspend or terminate your access for any reason other than your actions or omissions which we believe to be inconsistent with this Agreement we will refund to you any unused portion of your payment, which will be your sole and exclusive remedy upon such a suspension.

Presumably “any anonymous donor” means someone who sent their DNA into AncestryDNA anonymously rather than, for example, a sperm donor, although the language is not clear.

It will be interested to see how this develops.  Stay tuned!

See what others have written about the sale:

• Family Tree DNA Lowers the Price of the 12-marker Y-DNA Test to $39 in Step Toward Universal Access
• 12 Marker Y DNA Test for $39

From the Press Release:

HOUSTON, Feb. 20, 2013 /PRNewswire/ – FamilyTreeDNA.com, the genetic genealogy arm of Gene By Gene, Ltd., is dramatically lowering the price of one of its basic Y-DNA tests to $39, making it the lowest-cost DNA test available on the market, in order to take a major step toward universal access by individuals to their personal genetic data.

By dropping the price of its basic Y-DNA test by 60 percent to $39, Family Tree DNA — the world’s largest processor of Y-DNA and full mitochondrial sequences — is working to eliminate cost as a barrier to individuals introducing themselves to the insights and knowledge to be gained from personal genetic and genomic research.

Family Tree DNA pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago, and has processed more than 5 million discrete tests for more than 700,000 individuals and organizations since it introduced its Y-DNA test in 2000.

The test investigates specific Y-DNA locations for males that provide individuals with their haplogroup, or the deep ancestral origin of the paternal line.  In addition, it can indicate if different individuals are likely to share a common male line.

Gene By Gene is also working to lower the cost of Family Tree DNA’s comparable mtDNA test, which would be applicable to both females and males and provides data on the direct maternal line.  The company expects to unveil new pricing for this test in spring 2013.

As the sponsor DNA Workshop of “Who Do You Think You Are – Live” in London this February, Family Tree DNA expects that the reduced price test will add a great number of individuals to its already large database – the largest of its kind in the world.

“We believe the first step to unearthing your personal and family history is to better understand your DNA,” Gene By Gene President Bennett Greenspan said.  “That’s why we are continuously investing in new technology and experienced scientists at our Genomics Research Center, enabling us to conduct tests more accurately, efficiently and at lower prices.  Our $39 Y-DNA test is just the latest example of how we are working to help individuals gain access to their genetic data.”

Customer Inquiries
Individuals interested in Family Tree DNA’s $39 Y-DNA test, or any of its ancestral testing products, can visit www.familytreedna.com for more information.

About Gene By Gene, Ltd.
Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests.  DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide.  Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

Media Contact:
Kate Croft
for Gene By Gene, Ltd.
Casteel Schoenborn
888-609-8351
croft@csirfirm.com

SOURCE Gene By Gene, Ltd.

RELATED LINKS
http://www.genebygene.com

Crowdfunding might be one way to do just that.  For those not familiar with “crowdfunding,” it is essentially a way for people to contribute a varying degree of money to a project they are interested in, usually in exchange for a special perk.  Wikipedia describes crowdfunding as:

Crowd funding or crowdfunding (alternately crowd financing, equity crowdfunding, or hyper funding) describes the collective effort of individuals who network and pool their money, usually via the Internet, to support efforts initiated by other people or organizations. Crowd funding is used in support of a wide variety of activities, including disaster relief, citizen journalism, support of artists by fans, political campaigns, startup company funding, movie or free software development, inventions development and scientific research.

Some of the more popular crowdfunding platforms already in existence are Kickstarter and indiegogo, among many others.  One of the advantages of crowdfunding is that contributions can be as low as $5 or as high as you want to contribute.

Rewards for contributing would be priority in receiving the results of the research, an advance copy of a funded documentary, free access to scanned records, and so on.

Here are just a few examples I came up with for projects that might be suitable for genealogy crowdfunding:

• Example 1 – A documentary about the War of 1812

For this project, the filmmakers might propose a documentary about Upstate New York in the War of 1812, including the towns of Oswego, Sackets Harbor, and Plattsburgh, NY.  The film might look at the lives of everyday citizens as they struggle through the war years, and could follow the stories of the war in this region (like “The Battle of Big Sandy and the Carrying of the Great Rope in 1814“).  This project might be of interest to people who live in these regions, or had ancestors in this region, including ancestors who fought or otherwise participated in the War of 1812 and may have been at these battles.

Funders could receive advance access to copies of the film, free copies of the film, special recognition in the credits, and so on.

• Example 2 – Research an early New England colonial family

For a project such as this one, a researcher or group of researchers would propose researching a particular family or individual from the colonial period.  The researcher(s) could briefly summarize the known facts and conclusions, and then set forth any hypotheses or goals they’d like to accomplish with the funding, such as identifying three generations of descendants, or finding a female surname, or uncovering the day-to-day facts of a certain key family.

One advantage of this project is that most early colonial families have hundreds of thousands of descendants and thus a large pool of genealogists who might be interested in funding the project.

As a reward for funding this project all funders might receive, for example, a free report of the research along with all discovered primary records, and/or special recognition in any publication that results from the project.

• Example 3 – The Colonial DNA Project

The Colonial DNA Project might seek to test descendants of colonials to identify shared DNA (autosomal, Y-DNA, and/or mtDNA).  For example, it could be descendants of a particular family, or a town, or a region.  A particularly ambitious project would be – as just one example – to characterize the Y-DNA and mtDNA profile of every individual living in Hebron in 1725.

Funders could receive advance or free access to research, results, summaries, and so on.

• Example 4 – Scan a historical society’s newspaper collection from the 1800s

For this project, a historical society might propose scanning their entire 1800s newspaper collection, which is currently degrading in the basement, into an electronic database.  This project might be particularly relevant to genealogists who have ancestors from that town or county in the 1800s, and would like to see these records.

People who helped fund the project might receive advance access to the database as the records are being scanned, or could receive free access to the database instead of paying a fee.

What are some other ideas or projects you would support?

Let’s Try It!

I’m interested in trying a project like one of the above on an existing crowdfunding platform such as indiegogo.  Do you have any proposals you’ve been kicking around?  Are you interested in giving this crowdfunding idea a shot?

If I received a suitable, affordable, and intriguing proposal that I thought the genealogy community could really get behind as a “kick start” for this concept, I would gladly promote that project here on my blog, Twitter, Facebook, and at presentations, for example.  And I’d also be happy to contribute to the funding of that project!

Specifically, Genetic Technologies has alleged that 23andMe and LabCorp infringe U.S. Patent No. 7,615,342, entitled “ACTN3 genotype screen for athletic performance.”  The complaint is available here.

ACTN3 (Alpha-actinin-3) is an actin-binding protein encoded by the ACTN3 gene.  A particular mutation in the ACTN3 gene (rs1815739; R577X) results in a deficiency of the ACTN3 protein.  The non-mutant version of the gene is associated with sprint performance, the mutant version is associated with endurance.

23andMe does analyze the rs1815739 SNP in their tests (see “Speed Gene: Fact or Fiction?”). My own rs1815739 SNP genotype, for example, is TT, meaning that I have no working copies of ACTN3 in my fast-twitch muscle fibers.  From the complaint:

23andMe’s marketing materials describe in detail the ACTN3 gene testing that LabCorp has and is performing for 23andMe. More specifically, those marketing materials indicate that LabCorp analyzes and detects the single nucleotide polymorphism rs1815739, which is also referred to as R577X, in the ACTN3 gene. The rs1815739 polymorphism alters position 577 of the α-actinin-3 protein. The marketing materials also indicate that the Defendants associate athletic performance with the ACTN3 gene, which is “turned on in a type of muscle fiber used for power-based sports.” The testing method includes analyzing a sample obtained from a human for the presence of one or more genetic variations in the ACTN3 gene and detecting the presence of two 577R alleles (i.e., rs1815739(C,C)) at the loci encoding amino acid number 577 of the ACTN3 protein.  Defendants then use the presence of two 577R alleles to predict the potential sprinting, strength, or power performance of the human because the presence of two copies of the 577R allele is positively associated with potential sprinting, strength, or power performance. Thus, Defendants’ ACTN3 testing directly infringes upon one or more claims of the ’342 Patent.

Although Genetic Technologies did not identify which claims of the ‘342 patent it is asserting against 23andMe and LabCorp, only claims 1-8 are specifically genetic testing claims.  For example, claim 1 of the patent is a method claim:

1. A method to predict potential sprinting, strength, or power performance in a human comprising:

a)      analyzing a sample obtained from the human for the presence of one or more genetic variations in α-actinin-3 (ACTN3) gene;

b)      detecting the presence of two 577R alleles at the loci encoding amino acid number 577 of the α-actinin-3 (ACTN3) protein; and

c)      predicting the potential sprinting, strength, or power performance of the human, wherein the presence of two copies of the 577R allele is positively associated with potential sprinting, strength, or power performance.

The patent lists Kathryn Nance North (see here and here) as the sole inventor of this method.  The 2003 study that reported a link between ACTN3 and athletic performance (full text online here) lists six authors along with Professor North, including genetics blogger Daniel MacArthur.  Daniel wrote about ACTN3 a few years ago at Genetic Future.

What Now?

If the case isn’t immediately settled, then 23andMe and LabCorp will likely challenge the validity of the ‘342 patent on various grounds.  A quick review of the prosecution history (the back-and-forth with the patent office before the application issued as a granted patent) reveals that the patent application had very few prior art issues during prosecution, being challenged primarily by North’s earlier paper on ACTN3, instead encountering challenges under 35 U.S.C. 112 (enablement).

It is also likely that this patent will be challenged under the Mayo v. Prometheus holding, in which the Court held that not only is a law of nature itself unpatentable under 35 U.S.C. 101, but so is the application of that law of nature if the application merely relies upon elements already known in the art. In Mayo, the law of nature was the relationship between “concentrations of certain metabolites in the blood and the likelihood that a dosage of a thiopurine drug will prove ineffective or cause harm.”  Undoubtedly this case will examine whether the natural relationship between genetic variations in ACTN3 gene and the “potential sprinting, strength, or power performance” of a human is a similar law of nature.  If so, the question then becomes whether the claim of the ‘342 patent recites more than just that law of nature and the general instruction to apply it.  Based on the claim set forth above, this will be a significant challenge for the ‘342 patent.

Even more interesting is my paternal haplogroup designation.  The NatGeo tests lists the terminal SNP instead of a haplogroup that will typically encompass multiple SNPs.  I am listed as R-Z306, which is R1b1a2a1a1a3a1 on the current ISOGG Y-DNA tree.  However, my results indicate that I am L1+, which is associated with Null439 (I previously knew I was null439).  Many believe that L1+ is downstream of Z306+, but these types of questions are exactly what the NatGeo 2.0 test will help determine.

I immediately transferred my results to FTDNA, and if you go to the public null439 Y-SNP results page (here), for example, you’ll see that under my results are listed all SNPs for which I am derived, including L1, Z306, etc.  It’s truly an incredible list, and the real power of the results will come from comparing them to many other people.

As you can see, NatGeo estimates 3.2% Neanderthal (23andMe predicted 2.7%), and 3.3% Denisovan.  I’m not completely up on my Denisovan research, but I wonder if I am enriched for Denisovan because of my Native American ancestry.

Lastly, the NatGeo results report 2% Native American, directly in line with other tests.  23andMe, for example, has consistently reported 2-3%.

Disclosure: I received a complementary test kit from National Genographic for analysis purposes. My analysis, however, is based on my own opinions of the product and the results.

Many genetic genealogists are already familiar with Richard Hill and his website DNA-Testing-Adviser.com, where he shares information about using genetic genealogy to learn about your family, especially for adoptees and birth parents.  You may also be familiar with Mr. Hill through the front-page 2009 Wall Street Journal article detailing his search for his family, or from the 2009 article in the Grand Rapids Press (“Rockford man uses DNA testing, Internet searches to find his birth father“).

Finding Family

Mr. Hill’s fascinating new page-turner describes his 30-year search for his birth patents.  Although he was quickly able to identify his birth mother, the search for his birth father took much, much longer.  As the author writes:

Finding Family: My Search for Roots and the Secrets in My DNA is Richard Hill’s true and intensely personal story of how he pieced together the long-kept secret of his own origins. This highly suspenseful book is a page-turning saga of personal detective work that will appeal to anyone who loves a good mystery.

I found this 260-page book waiting for me in my mailbox on Friday evening after work, and before 24 hours had passed I finished the last page.  I was completely unable to put it down, anxious to discover the conclusion of Mr. Hill’s decades-long search (even though I knew how it ended!).

Highly Recommended!

I highly recommend this book to anyone interested in genealogy, family secrets, genetic genealogy, or mystery in general.  The book is a complete and entertaining saga from A to Z.  Although it was occasionally challenging to follow the considerable cast of characters, I think this serves to emphasize how meticulous Mr. Hill must have been in his research and record-taking.  Without good notes and research ability, it might have taken Mr. Hill much longer to complete his search.

Mr. Hill’s story also shows the power of genetic genealogy, especially for adoptees and birth parents.  However, the story also shows that DNA alone is not a magic tool; as I’ve argued for many years now, DNA is a tool that supplements traditional research.  Genetic genealogy is at its best when combined with a well-researched paper trail.  In the case of adoptees with no hope of a paper trail, DNA might provide clues that will help point you toward the paper trail.

You can get more information about using genetic genealogy to supplement your search by reading Finding Family: My Search for Roots and the Secrets in My DNA, or my visiting Mr. Hill’s great website at DNA-Testing-Adviser.com.

I met Dick in the fall of 2011 at the Family Tree DNA administrator’s meeting, although we had corresponded several times prior to meeting in person.  Dick was warm and inviting, and it clearly shows in his book.  He has connected with innumerable people in his search for family, and by reading his book I now count myself among them.

Disclosure: I received a free copy of Mr. Hill’s book to review for The Genetic Genealogist. However, this review reflects my honest thoughts about the book.

As of today you can pre-order a Geno 2.0 kit, which is expected to ship no later than October 30th (although you can probably expect it earlier than that).

Once again Family Tree DNA will perform all the testing, and The Genographic Project has worked very closely with FTDNA to design, troubleshoot, and use the GenoChip.  FTDNA will perform both the Family Finder and the Geno 2.0 test.

Overview of Geno 2.0

The new Geno 2.0 SNP chip contains roughly the following SNPs:

• ~3,200 mtDNA SNPs
• ~12,000 Y-DNA SNPs
• ~130,000 autosomal and X-chromosomal AIMs (including ~30,000 SNPs from candidate regions of interbreeding between extinct hominins (Denisovan and Neanderthal) and modern humans)

The AIMs (Ancestry Informative Markers) were derived from roughly 450 populations around the globe, including many that are unique to the Genographic project and many that have never been previously searched for AIMs.  The SNPs in regions believed to represent Denisovan and Neanderthal interbreeding will be used to detect and study DNA flow between humans and these extinct populations.

Overview of Results

So what do you get when you order a Geno 2.0 test? Via the new user interface (some of which you can see below), you will receive the following:

• A deep-clade Y-DNA haplogroup assignment;
• A deep-clade mtDNA haplogroup assignment;
• Information about the history and migration of mtDNA and Y-DNA haplogroups;
• A biogeographical (ethnicity) estimate; and
• An ancient population (Denisovan and Neanderthal) estimate.

What Geno 2.0 does NOT do:

• Geno 2.0 does not reveal medically-relevant information (but note that medical/health/trait information can sometimes be revealed unintentionally as new health associations are discovered, for example).  NG went to great lengths to prevent medical/health/trait information from being detected by the Geno 2.0 chip.  For example, the team selected only non-coding SNPs with no known functional association, and filtered all selected SNPs against a 1.5 million SNP database (which they constructed from numerous sources) containing all SNPs known or believed to be associated with disease or health. The team also removed all SNPs with a high association with medically-relevant SNPs (which you might be familiar with b/c of Dr. Watson and his APOE status).

• Identify genetic cousins with autosomal DNA.  The Geno 2.0 product is not intended to identify close genetic relatives based on autosomal DNA, and thus does not have that functionality.  I’m guessing that it will be possible for third-party sites to glean some information about relatedness from the data, however.  Note that relatedness through the Y-DNA or mtDNA based on haplogroup information is a part of the functionality of Geno 2.0, as can be seen in the screenshots below.

FTDNA (Deep Clade Testing; Integration of Genographic Results)

One interesting aspect of the new Geno 2.0 chip is that it will completely replace the deep-clade analysis performed at FTDNA.  With this one test, all SNPs currently analyzed by FTDNA in all of its different deep-clade analyses are analyzed in their entirety.

Another great benefit of the Geno 2.0 test is that Genographic will allow the test-taker to upload/transfer their results back into FTDNA, and neither Genographic or FTDNA will charge a fee for this transfer.  This means that Project Administrators will be able to work within the FTDNA system to analyze results of their project members rather than having to rely on collecting data from project members outside the system (thereby potentially increasing participation and results).

Validation of the GenoChip

The designed GenoChip has undergone significant validation (including the use of  about 400 known Y-DNA and mtDNA samples, and as many as 650 samples from various populations around the world).  Following this validation process (which will continue for at least the foreseeable future), the validated GenoChip SNPs are as follows:

• ~12,000 Y-DNA SNPs
• ~3,200 mtDNA SNPs
• ~130,000 autosomal and X-chromosomal SNPs which include the following SNPs:
• 23,692 Neanderthal
• 1,357 Denisovan
• 12,027 Aboriginal
• 10,159 Eskimo Saqqaq
• 998 Chimpanzee

Downloadable Raw Data: Treasure for Third-Party Analysis and Apps

The test-taker’s raw data will be available for download by the test-taker.  This has happily become the norm for most genetic genealogy companies, and NG will follow suit.  It’s not clear at this point whether that will be an immediate functionality (although I’m guessing it will be), or whether it will be in the near future.

Interestingly, the ability to download raw data opens the door for third-party analysis.  For example, I data from the Geno 2.o chip will lead to significant new mtDNA and Y-DNA discoveries (using the user-fueled Y-Chromosome Genome Comparison project, for example).

Consent

During a presentation put on by Spencer Wells and FTDNA a few weeks ago describing the new Geno 2.0 project, I and several other DNA bloggers were able to ask questions about the new chip and the project.  I and a few others asked questions about consent, which is of course an important aspect of any research project involving human samples.

Specifically, I asked whether all test-takers are automatically participants in the research aspect of the new Geno 2.0 project.  Dr. Wells responded that test-takers must opt into research; they are not automatically research participants.  Accordingly, people who are interested in the new test but have concerns about participating in research can do so.

The Geno 2.o Terms and Conditions are here.

Miscellaneous

A few miscellaneous points:

• As of the recent presentation, Genographic was not yet certain if they will be storing DNA samples after they are tested.  They are considering doing so, but of course there are significant costs associated with long-term storage of tens of thousands of DNA samples.
• Testing will take approximately 4-6 weeks once the system is in full swing (but I’m guessing there might be some delays in the beginning with an initial influx of orders).
• You will eventually be able to order the Geno 2.0 test directly through the FTDNA website.
• Although not completely reflected in the screenshots below, the new project allows for much greater participant involvement and interaction.  For example, test-takers are encouraged to share their stories after receiving their results.

For More Information:

Several other bloggers will be writing about today’s launch, and I will update this post to include links to those reviews.  Also, since I will be taking the Geno 2.0 test in the near future, stay tuned for my review and results.

• National Geographic and Family Tree DNA Announce Geno 2.0 – at Your Genetic Genealogist (CeCe Moore)
• Geno 2.0 launches! – at The Legal Genealogist (Judy G. Russell)
• The Genographic Project: onto the autosome! - at Gene Expression (Razib Khan)
• National Geographic – Geno 2.0 Announcement – The Human Story – at DNAeXplained (Roberta Estes)
• National Geographic Announces New DNA Test - DNA – Genealem’s Genetic Genealogy (Emily Aulicino)

Screenshots

Below are a series of screenshots from the new Geno 2.0 project and test results, provided by National Genographic:

The complete kit (collection is by cheek swab):

Introduction Page:

Overview Page:

An mtDNA haplogroup and heat map (showing modern-day locations and frequencies of the haplogroup):

The “Your Story” main page:

An example of more information at the “Your Story” page:

The “Your Map” page (showing an mtDNA map):

More of the “Your Map” page (showing an mtDNA map):

NOTE: much of this information is based on preliminary information about the GenoChip and Geno 2.0 project.  Accordingly, the information is subject to change. Check The National Genographic website for the latest information.

I’ve received a number of emails and comments (see, e.g., here) complaining about Ancestry.com’s new test, AncestryDNA.  Specifically, several test-takers believe that the Genetic Ethnicity Prediction provided by Ancestry.com does not reflect the numbers that they expected based on their own research.

For example:

“I just got my DNA test results back from Ancestry.com and I am concerned. I was born in England and I have gone back many generations and have found that all my ancestors as far back as the 1600′s in most cases are English.  According to the results I have no British Isles DNA. It states that I have 60% Central Europe, 30% Scandinavian and 7% Southern Europe. I also have 3% unknown. How can this be?”

“Just received my results: 21% Southern European and 79% Central European which doesn’t follow years of work on my family history.”

Do these comments reflect errors in AncestryDNA’s Genetic Ethnicity Prediction, or are there other factors at play?

Caveats

Although I am not privy to the ‘behind-the-scenes’ at Ancestry.com, I don’t believe that there are serious issues with AncestryDNA’s Genetic Ethnicity Prediction.  Ancestry.com’s DNA arm has a solid scientific team and a large and valuable reference database.

Indeed, Ancestry.com is well aware of the limitations and challenges that their Genetic Ethnicity Prediction brings:

We use cutting-edge science as a base for our predictions, but that comes with its own inherent challenges. It’s an emerging field with exciting new discoveries and developments constantly changing the landscape. Right now, your genetic ethnicity may not look quite right, with some ethnicities under or over-represented. As scientists gain a deeper understanding of the data, our prediction models will evolve to provide you with more accurate and relevant information about your family history.

It’s important to understand that biogeographical estimates, which are still relatively new, are notoriously difficult and complicated.  Ten different researchers analyzing the same genome can come up with ten different estimates based on a number of different factors, including their algorithm, the reference populations used for comparison, and many others.

Here are just a few factors that can influence a biogeographical estimate, and any one or more of these may be the reason that your Genetic Ethnicity Prediction does not match estimates you make based on your paper trail.

• Different Reference Populations and Algorithms

As I suggested above, different companies use different reference populations and algorithms to create a biogeographical estimate, which can result in varying estimates.

For example, in my previous review of AncestryDNA’s Genetic Ethnicity Prediction, I compared my genetic ethnicity results from three companies (Ancestry.com, 23andMe, and FTDNA), and found that their results varied considerably.  I’m not surprised by this, but I do expect that over time – as the industry arrives at more standard reference populations and algorithms (which the cheap whole-genome sequencing revolution will enable) – that estimates from different companies will align much more closely.  Be patient and enjoy being a pioneer.

• You Have TWO Family Trees!

Remember that “Everyone Has Two Family Trees – A Genealogical Tree and a Genetic Tree.” Your Genealogical Tree is the tree containing ALL of your ancestors.  However, only a tiny subset of these individuals actually (randomly) contributed DNA to the genome that you walk around with today.  These ancestors are the only individuals in your Genetic Tree.  It has been estimated, for example, that at 10 generations, only about 10-12% of ancestors in your Genealogical Tree are actually in your Genetic Tree!

Accordingly, even if a decent percentage of your ancestors at 10 generations originated in the British Isles, there is possibility that your DNA – and thus your Genetic Ethnicity Prediction – could include very little or absolutely no British Isles ancestry, simply because of the rules of genetics.

Ancestry.com tries to explain this as well (I’m biased, but I think my “Everyone Has Two Trees” explanation is a little clearer; I’ve had great luck explaining this to newbies):

So if you look at your family tree, it may indicate a pedigree-based ethnicity of 30% English, 20% Scandinavian, and 50% Italian (based on birth locations of your great-great-great grandparents). While this is one valid way to look at ethnicity (and in fact has been the only way until recently), DNA analysis can reveal the actual percentage of your DNA that is reflected by these ethnic groups. So your genetic-based ethnicity might reveal you are 40% British Isles, 15% Scandinavian, and 45% Southern European. Both measures are accurate and informative—but they are measuring different things.

• Misleading Labels

Another issue with any biogeographical estimate is the labels used to describe a population.  For example, what does “Scandinavian” or “Central European” really mean?  Does “Scandinavian” mean that great-grandpa must have been a Swede, or does it mean something else?

Ancestry.com defines the “Scandinavian” with the modern day locations of Norway, Sweden, Denmark, but explains in their FAQ that it can mean much, much more:

Ethnic groups moved around. Because people move over time, (and when they do they take their DNA with them), a group may contribute DNA to other groups at different times. So ethnic groups can be defined by time and place—not just location. For example, if you have German or British ancestors in your family tree, it’s a possibility that your genetic ethnicity may be partly Scandinavian. The Viking invasions and conquests about a thousand years ago are likely responsible for occurrences of Scandinavian ethnicity throughout other regions. And there are similar examples for other ethnicities. With your results, we provide historical information describing migrations to and from the regions to give you a broader picture of the origins of your DNA.

Similarly, the “Central European” label is defined to include the enormous swath of land in Europe including the modern day locations of Austria, Belgium, France, Germany, Netherlands, Switzerland, Slovenia, Czech Republic, Luxembourg, and Liechtenstein.

I certainly don’t think of France as being “Central Europe,” which shows that a test-taker shouldn’t rely on the labels alone. Dig a little deeper.

• Non-Paternal Events (NPEs)

I won’t dwell on non-paternal events, because I believe they have become too much of a scapegoat.  Non-paternal events, or NPEs, can be broadly defined as secret or unknown breaks in your Genealogical Tree (adoption, infidelity, etc.).  At some point every single Genealogical Tree has an NPE, although current estimates vary widely.  Consider the possibility of a break in your tree, but focus on the other factors presented here as the more likely explanation for your unexpected results.

Reviewing My Genetic Ethnicity Prediction

I have a fairly well-documented Genealogical Tree.  My documented ancestors were mostly from the British Isles (England and Ireland) and France, with far fewer ancestors from Germany, and Central America.  Years ago, based on my paper trail, I might have predicted 65% British Isles, 20% Irish, 15% French, and 5% German.

In light of the above, let’s review my AncestryDNA Genetic Ethnicity Prediction:

• Scandinavian – 78%
• Central European – 12%
• Uncertain – 10%

At first glance and without any of the knowledge above, these numbers seem way out of whack.  I don’t have a single document ancestor from Scandinavia or the area I think of as “Central Europe.”

However, when I learn that “Central Europe” includes France and Germany, a contribution of 12% “Central European” doesn’t seem far-fetched.  Further, considering that ancestry in the British Isles can include “Scandinavian” ancestors as a result of relatively recent Viking conquests (on a genetic timescale), perhaps the 78% Scandinavian isn’t so far-fetched either.

While I am still surprised that I don’t report any British Isles DNA, that could simply be because of difficulties in deciphering between Scandinavian and British Isles, or perhaps because of the random inheritance of DNA from those ancestors rather than others.

Lastly, where’s my confirmed Native American and African DNA?  Well, these percentages are rather small (­~ or <5% each) and I’m sure they’re contained within the “Uncertain” category.

In any event, I’m not discouraged by my results, and I fully expect my results to change over time.

Conclusions

Lastly, as Ancestry.com has warned, don’t forget that your results are subject to change with revisions of their algorithms and new discoveries.  And if Ancestry.com is dedicated to the best and latest results, your results almost certainly will and should change.

Your Turn

What are your percentages?  Do they match your expected percentages?  If you were unhappy with your AncestryDNA Genetic Ethnicity Prediction, does any of the above change your view?

(A similar tool was previously created by David Pike at http://www.math.mun.ca/~dapike/FF23utils/; with David’s tool, users receive their results directly and do not need to upload their DNA test results; accordingly, users have a variety of options depending on their privacy tolerance).

What the Heck is “Phasing”?

Currently, SNP chip testing performed by 23andMe or Family Tree DNA is unable to attribute a test result to either one of your parents.  For example, if your results for SNP rs00000 are “AG,” the test alone cannot determine whether the “A” came from your mother or father.

“Phasing” refers to the process of separating the mixed DNA results (the “AG”) into the DNA obtained from your mother (the “A”) and the DNA obtained from your father (the “G”).  This is typically done by comparing your results to your parents’ results and determining which parent could have and/or must have contributed each SNP.

For example, if mother’s results are “AA” at rs00000, and father’s results are “GA” at rs0000, then the data can be phased into “A” from mom and “G” from dad (since only dad could have contributed the “G”).  Every once in a while, the data can’t be phased, however (say you’re “AG,” mom is “AG,” and dad is “AG”).

What Good is Phasing?

Many genealogists are using phased data to identify which DNA came from individual grandparents, great-grandparents, and beyond.  I won’t get into that in detail now, but hope to at some point in the future (and eventually in the book I’m working on!).

As another example of using phased data, I used the new GEDmatch.com tool to phase my data.  Both my parents and I had previously uploaded our 23andMe and FTDNA data into GEDmatch.  I then performed some admixture analysis to compare unphased v. phased data.

Here is my unphased chromosome painting (Dodecad World9):

For comparison, here is my chromosome painting using the DNA I obtained from my father (same settings):

And here is my chromosome painting using the DNA I obtained from my mother (same settings):

Note that since this is so early I can’t say for certain whether using phased data creates some unwanted effects on the analysis (I’d love some input on that).  It is interesting, however, to compare the results of phased v. unphased data.

What uses will you put your phased data to?