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Today, The Genographic Project officially announced the launch of their new Geno 2.0 project, a significant update to the type and quantity of genetic information that will be collected and analyzed by The Genographic Project.  The new project will use an entirely new SNP chip (the GenoChip) designed specifically for Geno 2.0 in order to provide the world’s most detailed information about Y-DNA and mtDNA haplogroups (using SNP information) as well as detailed biogeographical estimates and ancient population (Denisovan and Neanderthal) estimates.

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.