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With Sequencing Ancestry Test Launch, Startup Full Genomes Enters Array-Dominated Market

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Ancestry testing, or genetic genealogy, is arguably the largest component of the direct-to-consumer genomics market, and is dominated by four companies and organizations with microarray-based offerings: 23andMe, Ancestry.com, Family Tree DNA, and National Geographic.

A new company, though, recently introduced a next-generation-sequencing-based service into the mix.

Since January, Full Genomes, a privately held Rockville, Md.-based firm, has been offering "comprehensive Y chromosome sequencing," for a price tag of $1,250.

As advertised on its website, the full Y sequencing service traces the "DNA you inherit from your father and his father and so on, back in time." Full Genomes provides information that allows customers to determine the SNPs and short tandem repeats they have in common with other family members, the company claims.

While the price of Full Genomes' service is about ten times that of current ancestry testing services — which in general cost between $99 and $199 — it provides information that the other DTC services do not provide, CEO Justin Loe told BioArray News.

He said that Full Genomes' product provides customers with between 300 and 400 short tandem repeats and about 28,000 SNPs, "of which 20 or more may be private to that individual."

Loe said that other ancestry-testing companies are providing "incomplete" coverage of the Y chromosome by relying on microarrays or microsatellite-based genotyping. But given the comprehensiveness of its test, Full Genomes aims to provide its customers with "essentially the last paternal line ancestry test that they will need."

Full Genomes' Y service offers 50x coverage with 100-base-pair reads. Loe said that the company outsources its sequencing to BGI or the University of California, Los Angeles. He confirmed that suppliers charge $1,000 for the raw data, and that the company has a margin of 25 percent for its services. Data is secured on Full Genomes' website and "accessed only by a small amount of people."

He declined to provide information on the company's investors or financing.

Loe acknowledged that Full Genomes' overall focus is "unexploited biotech markets and niches," noting that the firm has tried to woo foreign customers by making its website available in 10 languages. However, the company will compete more directly with established ancestry-testing services in the future.

According to Loe, the company is planning a sequencing-based autosomal DNA service. Existing providers of autosomal DNA testing enable customers to learn, in general, from what regions of the world their ancestors originated. Loe said that Full Genomes' autosomal DNA testing service would be "similar to, but with better coverage than the 23andMe-type microarray being marketed." Other potential genetic genealogy tests in the firm's pipeline include another Y chromosome sequencing service with lower coverage.

"Our first goal was to address this vacuum in the market in terms of Y chromosome testing for genealogy," said Loe, adding that the company aims to offer the market "products that are slightly different but of higher quality for genetic genealogy."

Full Genomes has separate technology development programs underway, Loe said. The firm's biotech R&D arm has a "distinct mission for medical testing" that would distinguish the company from others who rely on external parties to perform the sequencing component of their services. While this biotech program "has even better potential" than Full Genomes' genetic genealogy offerings, Loe declined to provide additional information, stating that the technology is being validated ahead of a filing with the US Patent and Trademark Office.

Evolving technologies

It is unclear to what extent sequencing may displace array or microsatellite-based genotyping in the ancestry-testing market, though some of the entrenched players have shown interest in applying the technology.

In August, Houston-based Gene by Gene, the parent company of Family Tree DNA, acquired Arpeggi, a provider of genome sequencing, data management, and computational analysis. Gene by Gene already offers exome sequencing services via a division it founded last year called DNA Traits. However, in April Gene by Gene CEO Bennett Greenspan told BioArray News that the firm had not seen any exome sequencing orders connected with genetic genealogy (BAN 4/9/2013).

David Mittelman, Gene by Gene's chief scientific officer, told BioArray News this week that his company is "actively looking into how to best capture the maximum information from the Y chromosome," and that the company's recent acquisition of Arpeggi has "shifted a lot of our attention to the best ways to exploit NGS to solve these sorts of problems."

He also noted that Gene by Gene offers a "pretty extensive catalog of SNP and STR tests," and that the firm offers 80X exome sequencing for $899, about $350 less than Full Genomes' 50X sequencing.

Other ancestry test providers seemed less interested in adding sequencing to their offerings. An Ancestry.com spokesperson declined to comment on Full Genomes' offering, saying that sequencing-based ancestry testing is "not a part of the market we have looked at much."

Spencer Wells, director of National Geographic's Genographic Project, seemed similarly unconcerned by Full Genomes' market entry.

"The market for this kind of testing is pretty tiny at the moment," Wells told BioArray News, adding that it "caters to a select group of people … interested in enough in their Y chromosome that they are willing to pay that much" for such a test.

Wells noted that the Genographic Project's chip contains 20,000 SNPs covering the Y chromosome, which he said is "plenty" to establish the Y-chromosome haplotype of an individual. While he said that sequencing-based Y testing will likely get bigger, it is not something that National Geographic is considering at this time.

The view from Mountain View, Calif., is somewhat different: 23andMe spokesperson Catherine Afarian said that the DTC firm has "always believed that our entire service will eventually move to full sequencing versus genotyping." She noted that 23andMe has "regularly done full sequencing as part of various research projects," and carried out an exome sequencing pilot program two years ago.

At the same time, she said that 23andMe's customer base has more than doubled since it lowered its price to $99 from $299 last December. While the firm will "continue to stay on top of evolving technologies," she said that "for now, genotyping remains the most effective and efficient technology platform for a consumer-facing service."

The way of the future?

One industry observer who is interested in sequencing-based ancestry testing is Doug McDonald, a professor of chemistry at the University of Illinois who offers biogeographical ancestry analysis to DTC customers who wish to have their raw data reanalyzed. He is also the data curator for the Clan Donald Y-Chromosome Project.

"I think they are the cat's meow," McDonald told BioArray News when asked for his opinion of sequencing-based ancestry tests. McDonald said that Clan Donald will likely organize sequencing-based ancestry tests for "at least 15 people" participating in the project. And if the price tag for sequencing-based ancestry-testing services drops below $1,000, Clan Donald may try to have as many as 100 participants sequenced, he added.

"We are somewhat unique, but this is finally allowing us to assign people to clan septs," he said. He added that once Clan Donald "figures things out" with regards to its lineage, "only a few chip-based SNPs will do the job" of allowing a participant to place himself on the clan's genetically reconstructed family tree.

Genetic genealogy consultant Roberta Estes said she was "very excited" about applying next-generation sequencing. Estes is the founder of DNAExplain, a company that helps ancestry-testing customers analyze and interpret their data results.

But Estes also told BioArray News that there is a need for a comparison database to aid in interpreting one's test results.

"I think [sequencing-based ancestry testing] would be much more useful if it were simply incorporated into an existing database," like Family Tree DNA's, Estes said. "I also think that until the price point falls to about half of [$1,250], there won't be enough people to take the test to create that comparative database, if that is being considered," she said.

Estes also raised questions about data privacy, noting that the SNPs and STRs that have been included on current array and microsatellite-based genotyping tests have been selected to minimize the risk of one's personal medical information becoming public.

Still, she said that tests such as Full Genomes' offering are the "way of the future," and that, by combining one's sequencing results with STR data, ancestry-testing companies will eventually be able to construct a "very personal" genetic story for their customers.

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