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At RootsTech, Consumer Genomics Players, Observers Discuss New Trends, Tools, and Chips

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RootsTech is a family history conference held each year in Salt Lake City. While the conference has had a technology focus since its inception four years ago, the most recent conference, which occurred earlier this month, had a special focus on genetic genealogy and ancestry testing.

In talks from Spencer Wells, director of National Geographic's Genographic Project, Ken Chahine, general manager of Ancestry.com's AncestryDNA business, Gene by Gene CEO Bennett Greenspan, professional genetic genealogists Tim Janzen and CeCe Moore, and many others, attendees heard not only about the growing popularity of microarray-based autosomal DNA testing, but also about new features that consumer genomics providers are planning for the coming year.

Among the major themes that emerged during the three-day event were an appeal for consumer genomics customers to test themselves at more than one company, a desire to see higher-resolution arrays implemented in genetic testing services, a discussion of new ethnicity analysis tools that will soon launch, and predictions about future expansion of testing, both in the US and abroad.

Once, twice, three times ...

Currently, consumer genomics customers can choose from a number of different autosomal DNA testing services offered separately by Ancestry.com, Gene by Gene's Family Tree DNA business, NatGeo's Genographic Project, and 23andMe. ScotlandsDNA, a UK-based consumer genomics firm, has also recently introduced an array-based autosomal DNA test. Each one of these companies and organizations relies on a different Illumina-manufactured genotyping array.

Both Ancestry.com and Family Tree DNA use 24-sample HumanOmniExpress BeadChips, which feature about 750,000 markers per array. NatGeo and 23andMe, meantime, provide their services using lower-density, custom chips with different focuses. While 23andMe's new array contains health-informative content, NatGeo built its Geno 2.0 array to provide insight into a customer's deep ancestry.

All providers allow customers to download their data so that they can upload it to third-party websites that provide do-it-yourself data analysis tools, such as GEDmatch. Family Tree DNA also accepts data uploads from other providers for a fee, although, since 23andMe's newest array is significantly different from Family Tree DNA's, the Houston, Texas-based company is at the moment does not accept data uploads from 23andMe customers who have tested with its new, version 4 chip. Still, according to several industry observers, testing at, say, Ancestry.com, and uploading one's data to Family Tree DNA is not enough. Instead, they recommend testing at all of the major providers in order to gain access to new tools and to make connections with other customers.

"The tools are different, the databases are different," said Kitty Cooper, author of a popular blog about genetic genealogy. Another issue is a person's ancestry, she told BioArray News at the conference. According to Cooper, "many people with Ashkenazi Jewish ancestry" have tested at Family Tree DNA, while 23andMe "has a lot of Scandinavian customers," since its service is available internationally.

Cooper noted that 23andMe customers also get to take advantage of the "best tools," because the Mountain View, Calif.-based company allows users to compare matching chromosomal segments with multiple participants. At the same time, she noted that some 23andMe customers have a limited interest in ancestry testing, having opted for the firm's service because of its health interpretations. The firm suspended the health component of its Personal Genome Service in December after it received a letter from the US Food and Drug Administration instructing it to discontinue marketing the service until it receives authorization from the agency. However, customers who tested with 23andMe prior to December still have access to their personal health interpretations.

Cooper maintained that by testing at multiple firms and uploading data to Family Tree DNA or third-party sites like GEDmatch, consumer genomics customers' experiences will improve. "The more people test, the better the accuracy is going to be," she said.

And while testing at multiple firms might seem costly for some consumers, given the price tag of between $99 and $199 for most services, genetic genealogist Tim Janzen estimated that interested customers could have their samples analyzed at Ancestry.com, Family Tree DNA, and 23andMe – the three firms that offer kinship analysis tools – for just $300.

Going higher

All four major providers of autosomal DNA testing in the US offer their services using arrays that contain less than a million SNPs. Yet Illumina, the vendor that manufactures all of their arrays, and even runs Ancestry.com's AncestryDNA service in its own laboratories, offers higher-resolution microarrays for genome-wide association studies, such as its HumanOmni5-Quad BeadChip, which contains 4.3 million markers that target variants down to 1 percent minor allele frequency.

During a genetic genealogy roundtable at the conference, Gene by Gene's Greenspan hinted that the decreasing prices of both whole-genome array-based genotyping and sequencing could lead to the use of higher-resolution arrays, on par with the Omni5 in terms of content, in the future.

"I think that as time goes on, there is going to be demand for higher quality, higher resolution testing that requires changing platforms to autosomal chips that look at 2.5 million or 5 million bases," Greenspan said during the roundtable. "The lower cost of genome sequencing equals a qualitative gain," he noted.

"We will be looking at singleton familial autosomal SNPs that occurred 500 years ago and tracking those over time," said Janzen about the opportunity of using higher-density arrays. "We will be looking at shorter and shorter genotypes, small haploblocks of genetic material, and we will be tracking those back through time and linking those to specific ancestors," he said. "The more density we have in terms of SNP coverage, the more specifically we can look at these small haplotypes of genetic data."

Of course, price would be a factor in companies' ability to introduce higher-resolution testing. Illumina's highest resolution chips are more affordable than they have ever been, but still are more expensive than the arrays used in consumer genomics firms' services. In October, the San Diego vendor reduced the price per sample of its Omni5 BeadChip to $273 from $399, and Omni2.5 BeadChip to $172 from $349.

Ethnicity predictors

Both Ancestry.com and Family Tree DNA discussed plans to improve the biogeographical analysis (BGA) components of their services, which predict the regions of the world a person's ancestors come from and can also estimate proportions of particular ancestries.

Greenspan said that within the next six to eight weeks, Family Tree DNA will introduce a new version of its Population Finder BGA tool, which he described to BioArray News as a new "graphic or interface that will explain someone's cornucopia of ancestry with more specificity." Greenspan said that the company will be "adding more underlying populations to the database, which should ultimately give customers a more nuanced view of their ancestry," but did not elaborate.

Janzen welcomed the news, calling the current version of Family Tree DNA's Population Finder the "least informative of BGA tools" available. "They all have some issues, but Population Finder is the least specific of all of them," he said, adding that he was "eager to see what they come up with."

Ancestry.com's Chahine similarly told BioArray News that the firm would soon upgrade its BGA tool to be more specific, including offering subcontinental predictions of customers' ancestral components (see related Q&A, this issue). He attributed Ancestry.com's ability to offer that kind of fine detail to the greater amount of samples genotyped with its chip.

"If I had told you a few years ago that we are going to get this resolution from an Illumina OmniExpress chip, which has the most common variations in the human population, I would have thought, 'Not a chance,'" said Chahine. "What has helped is the numbers, and the scale," he said. "The number of people has demonstrated that even though these alleles are some of the more commonly found ones, with scale, we start seeing separation of the populations that I don't think we would have predicted."

The beginning of the 'S curve'

In his keynote talk and during the roundtbale, NatGeo's Wells told attendees that while it had taken the industry 11 years – since the launch of genetic testing services more than a decade ago – to reach the millionth person tested last year, it was possible that the second millionth person will be tested by the end of 2014 most likely via an array-based autosomal DNA testing service, a trend that he saw as beneficial both for genetic genealogists and the aims of the Genographic Project, which aims to track mankind's ancient migration using DNA testing.

"As the number of people tested goes up, DNA becomes much more valuable as a tool for doing genealogy," said Wells during the roundtable. "For us on the deep ancestry side, it gives us more data to deal with," he said. "I think that trend is going to continue," Wells added, "[and] more and more people will get themselves tested."

Ancestry.com's Chahine said that he agreed with Wells' prediction.

"I predict that we are at the very early part of the S curve," Chahine told BioArray News. "I think we are just getting past the early adopters, we are just barely going mainstream, and I don't think we have hit that massive inflection point," he said. "There is no question in my mind, that in a couple years, we could be sitting here talking about doing a million samples a year."

Janzen, however, expressed some doubt about Wells' predictions, arguing that 23andMe's cessation of health interpretations had likely cost the firm some business. "The number of matches I am getting through 23andMe has dropped," said Janzen. "Prior to November, I was getting about 50 matches a week and now I am getting between 10 and 15 a week," he said.

He noted that Ancestry.com will not begin selling its kits outside the US until 2015, which could also limit growth this year. "I would be a little surprised if we get to 2 million this year," Janzen said.

CeCe Moore said that she agreed with Wells and Chahine's projections.

"I think we are already extremely close to that number if not already past it, especially if we include Y-DNA and mtDNA tests," Moore told BioArray News. She estimated that the four major providers may have already run more than 2 million tests, although some may have been customers ordering multiple assays. "This is also not including Britain's DNA, Full Genomes, GeneTree, GeneBase, Oxford Ancestors, and other lesser-known companies," said Moore. "Some of us have tested at more than one company, but the vast majority are unique to each company's database, which is also one of the main reasons that I advise testing at all three of the major companies," she added.

Janzen and Moore are organizing a conference specifically focused on genetic genealogy through the Institute of Genetic Genealogy, a new nonprofit they founded together with Rachel Janzen, Tim Janzen's wife. According to Moore, the event will be held in Washington, DC, on Aug. 16 and 17, and NatGeo's Wells will be the keynote speaker.

Moore expressed to BioArray News the need for more genealogists, such as the estimated 10,000 people who attended RootsTech, to get tested and to get involved in genetic genealogy.

"We need to get this community, which has good paper records, to test, because that is how we are going to make progress," Moore said. "This is really the market that we want to pull people in from," she said. "It's important for us to be here, but it is also important for us to have a meeting for specialists, that traditional genealogists might not be interested in."

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