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Ancestry.com to Discontinue Y, mtDNA Testing in Favor of Array-based Genetic Genealogy Service

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NEW YORK (GenomeWeb) — Ancestry.com announced earlier this month that it will soon retire its mitochondrial DNA and Y chromosome testing services in order to focus exclusively on its microarray-based AncestryDNA offering.

While Ancestry.com's decision did not surprise industry observers, who see Family Tree DNA as the leading provider of mtDNA and Y chromosome testing, Ancestry.com's intentions to shutter the website that allows its mtDNA and Y test customers to compare results, as well as to destroy all samples submitted for such testing has created some controversy. Concerned customers have even created an online petition that urges the genealogy giant to reconsider its plans and to maintain the website and DNA samples associated with the services.

The move has also raised questions about the future of sequencing-based mtDNA and Y testing as array-based autosomal DNA services continue to gain in popularity, with Ancestry.com announcing in May that it has genotyped more than 400,000 samples since it introduced its service two years ago.

"My perspective on Ancestry.com's decision is that autosomal DNA is clearly becoming the giant in terms of the DNA test of choice for the vast majority of genetic genealogists," Tim Janzen, a genetic genealogist, told BioArray News this week. "As the atDNA databases grow, atDNA testing becomes more and more valuable."

'Not an easy decision'

Y chromosome and mtDNA tests provide genetic genealogists with different kinds of information. As the Y chromosome is inherited paternally from father to son, a Y test performed using short tandem repeat analysis can lead to a haplogroup assignment, from which a region of origin can typically be inferred. For example, the paternal ancestor of a person belonging to haplogroup E1a is likely to have come from West Africa, where that haplogroup is most abundant, whereas haplogroup R1b occurs with the greatest frequency in Western Europe. This also allows genetic genealogists to answer questions about descent, as two men who supposedly share a common paternal ancestor should belong to the same haplogroup.

As mtDNA is passed down maternally, from mother to both son and daughter, the test, which is carried out using microsatellites, allows genetic genealogists to answer similar questions about maternal family origins and descent.

In contrast, the array-based atDNA services look at up to 900,000 SNPs and compare them to reference genomes for various populations in order to deliver to customers a biogeographical analysis, where they are informed of how much of their genome comes from different regions of the world. For example, a client of Ancestry.com's AncestryDNA service might be informed that 60 percent of her genome is Eastern European and the remaining 40 percent is Finnish and Northwestern Russian.

In some cases, such as National Geographic's Genographic Project, the arrays have been designed with the intent of reporting Y and mtDNA haplogroups back to participants. Still, biogeographical analysis and matching with relatives through provider or third party websites seem to be the most popular atDNA applications, and Ancestry.com currently does not report back Y chromosome and mtDNA haplogroups to AncestryDNA customers.

Prior to the advent of array-based atDNA testing, both mtDNA and Y tests were the flagship offerings of companies and organizations that offer ancestry testing. Ancestry.com began offering its Y chromosome and mtDNA offerings, marketed as its Paternal and Maternal Lineage Tests, in 2007. However, the apparent shift in favor of atDNA testing prompted the firm earlier this month to announce that it would retire its Y and mtDNA offerings.

On June 4, Ancestry.com's Eric Shoup wrote on the company's blog that as of Sept. 5, 2014, Ancestry.com would no longer offer access to its mtDNA and Y testing services, including the website that allowed participants to network with other matches, as part of an effort to "focus our efforts in a way that provide the most impact." Shoup acknowledged that retiring the offers "wasn't an easy decision" for Ancestry.com to make, but that "in the end, it came down to priorities and we think our core offerings are a great place to spend our time and resources."

As part of its discontinuation of the services, Ancestry.com also stated that it would destroy any remaining samples associated with its Y and mtDNA offerings, a decision that provoked some criticism in the genetic genealogy community.

In a June 8 post on her blog The Legal Genealogist, Judy Russell noted that "DNA is a finite item," and that by destroying its collection of samples, which may have belonged to individuals who have since died, Ancestry.com "may well destroy evidence of lineages that can't be reconstructed," as those persons can no longer take an atDNA test or other genetic genealogy tests offered by Ancestry.com's rivals.

"What about the family that tested the grandfather who was the last living representative of a male line that is now gone? The grandmother whose genes contained the last direct evidence of a female line?" Russell wrote. "It certainly isn't Ancestry's fault if we and our families lose genetic evidence because we dilly-dallied around and didn't get the testing done when it could have been done," she continued, "but it's different where there is a sample that exists right now that could be used."

Russell told BioArray News that these issues probably affect a small subset of customers who ordered Y chromosome or mtDNA tests through Ancestry.com. "Still, if there is an individual situation where the sample still exists and is viable, to say across the board, 'we're going to destroy it, no matter what' is unconscionable," she said. "We can't deal with an irretrievable loss of genetic lineage because an existing sample is destroyed," Russell added.

"I think what they are doing is utterly unconscionable," Roberta Estes, author of the genetic genealogy blog DNAeXplained, told BioArray News. According to Estes, she has two issues with Ancestry.com's decision: the destruction of the DNA samples and the deletion of the database. "It would cost them literally nothing to maintain the database for people to search in its current format," she said. "It's akin to throwing away irreplaceable records."

That sentiment is evidently shared by other people. A Change.org petition urging Ancestry.com to reconsider its decision to destroy the samples has already garnered close to 900 supporters.

On June 12, AncestryDNA General Manager Ken Chahine authored a follow-up post on the company's blog that defended the company's decisions.

"While the Y-DNA and mtDNA tests launched genetic genealogy and led to many great discoveries, the autosomal test has opened even more possibilities for family history research," Chahine wrote. "Therefore, our decision to retire the Y-DNA and mtDNA tests is a deliberate attempt to focus our resources on providing powerful family history research tools that use autosomal testing."

With regards to the destruction of existing samples, Chahine lamented the lack of a legal framework to retest samples submitted for Y or mtDNA testing using its AncestryDNA array, or to transfer them to participants or next of kin.

Russell, who is a lawyer, raised questions about Chahine's explanation though. "The legal considerations include difficulty not insurmountability," she said, adding, "This is a business decision, not a legal decision."

Still, Chahine also stated that many of the samples are no longer usable, making retesting or return a non-issue.

"Many of the swabs were exhausted of genetic material during our testing or the sample may be past its shelf life," wrote Chahine. "In the end we made the difficult decision to destroy the samples and are committed to trying to find solutions to these roadblocks for future products."

An Ancestry.com DNA spokesperson declined to provide further comment on the company's decisions, including alternatives to destroying the samples, as well as any future plans to add mtDNA and Y chromosome haplogroup assignment to its service.

'Ceding the market'

While the momentum in the ancestry testing market seems to be on the side of array-based atDNA testing, some questioned if Ancestry.com's decision signals the end for mtDNA and Y chromosome testing services across the industry.

According to Janzen, who co-directs the Institute for Genetic Genealogy, Family Tree DNA is "clearly dominating in the Y and mtDNA arenas" and by shuttering its services, Ancestry.com is "essentially ceding the market to FTDNA in this area." He noted that Ancestry.com already last year "hid the webpages where one could order Y and mtDNA tests on their website," and said that he is "not particularly surprised" that Ancestry.com decided to stop selling the tests altogether.

Despite this, Janzen maintained that there will continue to be "significant interest" in the Y chromosome, and said that while mtDNA is the "poor stepchild" of ancestry testing, in terms of there being more limited interest in the test compared to Y chromosome and atDNA analysis services, it is "still a nice test for people to do."

Over at Family Tree DNA, a business unit of Houston, Texas-based Gene by Gene, there is no apparent slowdown in demand for Y chromosome and mtDNA testing. "We have offered Y and mtDNA testing for almost 15 years and since the introduction of atDNA testing we still have strong interest for the Y and mtDNA testing products," Elliott Greenspan, laboratory information systems lead at Gene by Gene, told BioArray News. "It's unlikely atDNA will replace these products, and they will become increasingly valuable for customers working to build their family trees," he said.

CSO David Mittelman told BioArray News that the company will help Ancestry.com customers who have until Sept. 5 to download their test data before it is deleted forever. He noted that Family Tree DNA accepts data transfers into its database, which he claimed is the largest genetic database containing Y chromosome and mtDNA test results in the world.

CeCe Moore, a professional genetic genealogist who together with Janzen co-directs the IGG, said that she has been urging Ancestry.com customers to do just that.

"Although the destruction of the DNA samples is a significant and understandably upsetting loss for the people who cannot retest a deceased family member, from my perspective the tragedy that will most impact the entire community and future research opportunities is the elimination of the database with approximately 70,000 records – many unique and irreplaceable," Moore told BioArray News.

"We are doing our best to get the word out and encourage these testers to transfer to the Family Tree DNA database or upload to the free Ysearch site, but it will be impossible to reach everyone and, ultimately, only a fraction will remain for future research," she said.

While Family Tree DNA continues to offer Y chromosome, mtDNA, and array-based atDNA testing, the company has also introduced a next-generation sequencing-based Y chromosome service called Big Y that allows users to explore up to 13 million base pairs of the Y chromosome, including 30,000 known SNPs, at an average coverage of between 55X and 80X. The company also just released a new matching feature for BigY customers to compare their results against others.

Though the $695 price tag is seven times the cost of its $99 Family Finder atDNA offering, Janzen noted that the cost of next-generation sequencing continues to drop, and speculated that Ancestry.com might in the future return to the Y chromosome testing market with a NGS-based offering.

"It is possible that when complete genome sequencing becomes affordable, Ancestry.com will introduce a product that incorporates full genome data," said Janzen. "Until that time, I suspect that they will simply stick with their current atDNA test," he said.

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