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NatGeo Upgrades Genographic Consumer Genomics Service, Pledging Better Y, mtDNA Coverage

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NEW YORK (GenomeWeb) – National Geographic's Genographic Project this week introduced the next version of its SNP chip-based ancestry testing service.

Dubbed Geno 2.0: Next Generation, the new offering relies on a higher-density array containing five times as many markers as its previous Geno 2.0 service. The new service is currently priced at $199, and is available for order. National Geographic will commence shipment of kits for the new service in September.

Thanks to a new array, the project will now offer customers expanded Y chromosome and mitochondrial DNA analyses, setting it apart in a competitive consumer genomics market that includes offerings from Ancestry.com, 23andMe, and Family Tree DNA, according to Miguel Vilar, science manager at the Genographic Project.

"We were able to add a lot more Y and some more mtDNA than we did on Geno 2.0 with the new version of the chip," Vilar said. "That's where Genographic has stood out since the beginning, as the way to answer deep ancestry questions, to discover where we came from tens of thousands or hundreds of thousands of years go."  

National Geographic kicked off the Genographic Project in 2005, offering participants the possibility to learn more about their ancient ancestry by providing Y chromosome and mtDNA analysis using short-tandem-repeat testing and microsatellite genotyping to generate the results.

Since the Y chromosome is inherited patrilineally and mtDNA is passed on matrilineally, the project could assign a customer to a haplogroup based on that analyses, showing ancient migration patterns associated with such groups, as well as hinting at a region of origin for a person's deep paternal and maternal ancestry.

The Genographic Project's offering changed in 2012, when the endeavor introduced Geno 2.0, a custom, 130,000-marker Illumina HD iSelect BeadChip, which provided, in addition to Y and mtDNA haplogroup information, a regional breakdown of ancestry based on a customer's autosomal DNA, with additional percentages of how much Neanderthal or Denisovan ancestry a person might have. Neanderthals and Denisovans are hominids who split from humans around 500,000 years ago.

At the time of Geno 2.0's launch, about 520,000 people had already tested in the Genographic Project. According to National Geographic, about 705,000 people have now taken part in the project to date.

While Geno 2.0 was a significant technology upgrade from the earlier phase of the project, in terms of resolution, it was dwarfed by coverage offered by 23andMe, Ancestry.com, and Family Tree DNA's services, most of which rely on customized Illumina HumanOmniExpress BeadChips that contain more than 700,000 SNPs.

This difference in density also made it more difficult for Geno 2.0 customers to upload their data to third-party websites and to compare their results across platforms. For instance, GEDmatch, a third-party tool that allows users to upload their consumer genomics data and make use of a variety of free analysis tools, does not accept Geno 2.0 data.

It was for these reasons that National Geographic began building the next version of its service, according to Spencer Wells, who established and led the project for a decade, and who continues to act as its consultant.

"It is largely a decision we made based on compatibility issues," Wells said. "The GenoChip was great, but we were the only ones who were really using it," he said. "People want to be able to take their data [and] plug it into the databases to do searches."

Wells had discussed the idea of upgrading the service to a higher density chip already in 2013.

Wells noted that the focus of the Genographic Project has also changed recently, as the effort moved away from its early emphasis on genetic discovery and sampling indigenous populations toward "consolidating and analyzing existing data and selling the kits to get the citizen science angle up to speed." "Citizen science" is a term used in the consumer genomics arena to describe customers who download and share their data to conduct their own, independent research.

According to Vilar, in upgrading its service, National Geographic has also sought to provide similar features to competing offerings, by rolling out improved biogeographical analysis results and making it easier for customers to connect with genetic relatives.

In terms of biogeographical analysis, the Genographic Project had previously broken down customers' autosomal DNA results into nine regions of origin: Northeast Asian, Mediterranean, Southern African, Native American, Oceanian, Southeast Asian, Northern European, and Sub-Saharan African.

For Geno 2.0: Next Generation, the Genographic Project worked with partners at Family Tree DNA to break autosomal DNA results down into 18 different regions, according to Vilar. Family Tree DNA has processed the Genographic Project's array kits at its laboratories in Houston since they were launched. The Genographic Project itself is headquartered in Washington, DC. Vilar said that the Genographic Project is now using Family Tree DNA's algorithm to calculate regional percentages, but that it aims to expand beyond 18 regions during the next year.

"By incorporating more populations, we can separate North and South America into two different regional components," said Vilar. "We will also be able to incorporate other parts of the Pacific, to be able to break down Oceania into separate components," Vilar continued. "By incorporating more populations into the mix, the better we can break down percentages based on the data."

Ultimately, the Genographic Project might be able to break down customers' ancestry into somewhere between 20 and 25 regions, Vilar said.

One feature of Geno 2.0 that will continue in the next-generation service is the reporting of Neanderthal ancestry. It is estimated that most Europeans and Asians have between 1 and 4 percent Neanderthal ancestry. Geno 2.0 customers were able to learn if they were 1 percent Neanderthal or 4 percent Neanderthal, and the new chip contains markers to offer more precise results. "We will continue to do Neanderthal," said Vilar. "That was a big hit with Geno 2.0."

Connecting with genetic matches is another feature that Ancestry.com, Family Tree DNA, and 23andMe have been able to offer customers that the Genographic Project has been unable to do. Rather than build its own genetic relative matching database, the project has opted to enable customers to transfer their results into Family Tree DNA's Family Finder database instead.

"We will work with Family Tree DNA to create a flawless transfer system over to Family Tree DNA and anybody who wants to find genetic cousins will be able to do so very easily," said Vilar.

Customers will also be able to download their data via Family Tree DNA, enabling them at last to upload the results to third-party websites and conduct their own citizen science.

While Geno 2.0: Next Generation has become more similar to other consumer genomics offerings, Vilar noted that the what continues to set National Geographic apart is its focus on Y chromosome and mtDNA testing. He noted that where Geno 2.0 contained between 12,000 and 13,000 Y SNP markers, Geno 2.0: Next Generation contains closer to 20,000 Y markers. The new array also contains 4,000 mtDNA SNP markers, an increase from the 3,000 mtDNA SNPs offered on Geno 2.0.

"I think we will be able to provide the highest resolution mtDNA calls outside of doing complete mtDNA sequencing," said Avilar. "Y [chromosome testing] we will be improving significantly," he said. "As a single product, Geno 2.0: Next Generation will be the best Y chromosome calling, best mtDNA calling that you can get, other than whole-chromosome sequencing or mtDNA sequencing, in one analysis."

In terms of competition, Family Tree DNA offers an mtDNA sequencing test called mtDNA Full for $199, in addition to a Y chromosome next-generation sequencing service called Big Y for $575. Rockville, Md.-based Full Genomes also offers a Y chromosome sequencing service called Y Elite 2.0 for $750. Ancestry.com used to offer Y and mtDNA tests but discontinued that offering last year in order to focus exclusively on its array-based AncestryDNA service. 23andMe does provide customers with Y and mtDNA haplogroup information, but at a lower resolution than NatGeo will offer.

"As single product, we offer the best mtDNA and the best Y together," claimed Vilar. "We have more Y markers and more mtDNA markers and that translates to higher definition haplogroup calling," he said. The Genographic Project's user interface provides illustrations and video clips detailing the routes individuals with certain haplogroup-defining mutations followed. By fleshing out its Y and mtDNA results, the Genographic Project can therefore "tell more stories and break down the human family tree in higher detail" said Avilar.

He said that the project began adjusting its Y and mtDNA trees about six months ago, providing users with higher-resolution haplogroup calls based on existing Geno 2.0 chip data. "Now, with new markers available on the upgraded chip, we will have more markers which allows us to show more branches on the Y and mtDNA tree," he said.

That additional Y and mtDNA information does come at a higher price though, as the aforementioned competing services are all priced at $99.

"We are looking to play around with the price a bit, maybe in the fall; our biggest selling season is the holidays," Vilar said. "We will see how well it goes."

Some industry observers took a similar wait-and-see approach to the project's new offering.

"There were only 126,307 autosomal SNPs included in the old Geno 2.0 test, so the increase in the number of markers tested will put the test on par with its major competitors," said Tim Janzen, a genetic genealogy community leader and co-founder of the Institute for Genetic Genealogy. "We won't really know until they start delivering the results and we get access to the raw data files."  

Janzen also noted that the difference in price could slow adoption of Geno 2.0: Next Generation compared to other companies' services.

"The price is high relative to its primary competitors," said Janzen. "Based on the limited information available about this test, I would be willing to predict that it will not sell any more quickly than the old Geno 2.0 test has sold over the past three years."

Geno 2.0 has lagged the other firms in terms of adoption. For instance, while about 200,000 people have ordered Geno 2.0 since its debut in 2012, more than a million customers have opted to test with AncestryDNA, which launched at the same time. However, as project founder Spencer Wells has stated in the past, the Genographic Project is a scientific endeavor and is not a business venture like Ancestry.com, 23andMe, or Family Tree DNA's services.

Roberta Estes, author of the genetic genealogy blog DNAeXplained, said she was excited by National Geographic’s new service, especially because of the planned upgrades in biogeograhical analysis.

"I think this is an exciting offering with the potential to refine the autosomal ethnicity results we've all been craving," Estes said. "This could also be a really good step between standard STR and SNP testing and the Big Y type of tests,” she said. "We don't have any specifics yet on what is being included and I think we are all anxiously awaiting that information as NatGeo is always known for their innovation and quality products."

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