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Family Tree DNA Expands beyond Array-based Offerings with New Y Chromosome Sequencing Service

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As the consumer genomics market continues to grow, driven in part by the low cost of microarray-based ancestry testing, next-generation sequencing-based services targeted to "hardcore genealogists" are beginning to pop up.

Family Tree DNA this week launched a Y chromosome sequencing service with an introductory sale price of $495 per sample. Called the Big Y DNA Test, Family Tree DNA claims that its new product allows users to explore at least 10-million-base-pairs of the Y chromosome, including 25,000 known SNPs, at an average coverage of 60X. The test, the company notes on its website, is intended for customers interested in exploring their deep paternal ancestry. Family Tree DNA also believes the service will yield new, undiscovered SNPs that will allow users to place themselves specifically within certain lineages.

According to David Mittelman, chief scientific officer of Gene By Gene, of which Family Tree DNA is a subdivision, the new Big Y DNA Test is intended to do just that.

"There is a market for people who want to dissect all variation on their Y chromosome," Mittelman told BioArray News. "An array is not going to be able to do that," he said. "So, if you are a hardcore genealogist and you want to discover sequences unique to you, or new SNPs, this is a great research product."

Houston-based Family Tree DNA is not the first company to see a business opportunity in making Y chromosome sequencing available as a service. Earlier this year, Full Genomes, a privately held Rockville, Md.-based firm introduced "comprehensive Y chromosome sequencing" for a price of $1,250 (BAN 10/1/2013).

Consumer genomics players reacted differently to Full Genomes' launch. While representatives for Ancestry.com and National Geographic's Genographic Project said they had no plans to introduce sequencing-based services, 23andMe and Family Tree DNA confirmed that they were interested in developing products based on the technology.

Full Genomes' Greg Magoon, the company's Y chromosome data analysis consultant, told BioArray News this week that the company believes its offering is more comprehensive.

At the same time, he was reluctant to compare the services, citing a lack of information on Family Tree DNA's service.

"It seems the biggest differences are likely to be the breadth of coverage and in the analysis of results, but unfortunately there doesn't yet seem to be any example data to compare against," Magoon said.

And while Family Tree DNA's Big Y DNA Test, which will retail at $695 starting in January, costs less than Full Genomes' test, Mittelman stressed that his company's goal is "not to compete with Full Genomes or another product" but to empower its user community. To do that, he said, the company built the assay to target regions of the chromosome that are accessible by short reads and contain the most useful information, and to keep the service as affordable as possible.

Customers can submit saliva samples to Family Tree DNA by mail, and the company will analyze the samples in its Houston laboratories using the Illumina HiSeq2000 platform, Mittelman said. Turnaround time is between 10 weeks and 12 weeks.

He noted that Family Tree DNA already offers microsatellite-based genotyping services that allow customers to test themselves for specific SNPs, as well as an array-based autosomal DNA testing service that captures between 10,000 and 15,000 known SNPs.

"The idea behind Big Y is to get the most data available to the community as possible to help accelerate genetic genealogy," said Mittelman.

'The thrill of discovery'

It's a concept that resonates with some industry observers. CeCe Moore, a professional genetic genealogist and author of the blog Your Genetic Genealogist, told BioArray News that the demand for products like Family Tree DNA and Full Genomes' Y chromosome sequencing tests is coming from so-called citizen scientists, customers of such services that use the data to further both population genetics and genealogical research.

"We have been working with limited Y-DNA data for well over a decade," Moore said. "Up to this point, the Y-SNPs that we have been utilizing have been exclusively informative of deep ancestry and, with these type of new tests, there is the potential for Y-SNPs to become genealogically relevant," she said.

"What drives this advanced user market," she added, "is the thrill of discovery – literally charting unknown territory – with the hope of meaningful application to our family trees."

Another industry observer who shares Moore's enthusiasm is Doug McDonald, a professor of chemistry at the University of Illinois, who is the data curator for the Clan Donald Y-Chromosome Project.

McDonald told BioArray News last month that for a price tag of less than $1,000, Clan Donald will likely organize sequencing-based ancestry tests for around 100 participants.

"We are somewhat unique, but this is finally allowing us to assign people to clan septs," McDonald said. He noted 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 (BAN 10/1/2013).

Moore this week agreed that it was likely that such sequencing-based services would inform future microsatellite or array-based products.

"The market for these [sequencing-based] tests is only a small subset of the [direct-to-consumer] demographic," she said. "However, the results will inform and drive a much wider audience toward complementary products, for example, individual SNP orders and future arrays."

Mittelman acknowledged that Family Tree DNA has no plans to migrate its array services to next-generation sequencing.

"I don't think arrays are going to be retired any time soon," Mittelman said. "There is a lot of value to arrays, they provide high throughput and cost-effective ways to survey variation across the entire genome," he said. As such, Family Tree DNA will "continue to invest in the next-gen space – arrays and sequencing," Mittelman added.

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