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National Geographic Considering Move to New SNP Chip for Genographic Project

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National Geographic may adopt another genotyping platform for use in its Genographic Project as soon as next year.

The second phase of the project, dubbed Geno 2.0, has relied on a custom, 130,000-marker Illumina HD iSelect BeadChip since last year (BAN 7/31/2012). Prior to that, since its inception in 2005, the earlier phase of the Genographic Project had relied on microsatellite genotyping.

Though National Geographic's current platform has been available for just a year, the company is already looking to "update its genotyping technology," Spencer Wells, the project's director, told BioArray News last week. He said that National Geographic could potentially use a different chip or supplement its existing platform with new content.

"In part, it's driven by wanting to add new features, get more info out of the SNPs, and also the price [of genotyping arrays] has dropped over the past few years," Wells said.

Ideally, National Geographic would like to have its new array available to Geno 2.0 participants next year, Wells said. He confirmed that it would be a genotyping microarray, rather than some other genotyping technology.

National Geographic collaborated with Johns Hopkins University, Family Tree DNA, and Illumina, to select ancestry-informative markers from more than 450 worldwide populations for use in the Genographic Project, which is dedicated to mapping the migratory history of humans by analyzing DNA samples from hundreds of thousands of people from around the world.

At the time of the chip's launch, Wells noted that NatGeo had removed all medically relevant markers and designed an array of autosomal and X-chromosomal SNPs with an average spacing of one SNP per 100 kilobases across 92 percent of the human genome. These included 25,000 SNPs from candidate regions of interbreeding with Neanderthals and Denisovans, hominids who split from humans around 500,000 years ago, as well as coverage of ancestry-informative Y chromosome and mtDNA SNPs.

While Wells noted that Geno 2.0 is a project, not a business venture, it does appeal to the same target audience as Family Tree DNA, Ancestry.com, and 23andMe. All four offerings rely on Illumina arrays, but these other services rely on different designs.

For example, both Ancestry.com's AncestryDNA service and Family Tree DNA's Family Finder service rely on Illumina HumanOmniExpress BeadChips that contain more than 700,000 SNPs (BAN 5/29/2012). And 23andMe offers an even higher-density array in its service, relying on a million-marker, HumanOmniExpress Plus BeadChip, according to its website.

Illumina has benefited from its array sales to National Geographic, 23andMe, Family Tree DNA, and Ancestry.com. During the firm's recent second quarter earnings call, CEO Jay Flatley said the company expects to generate $50 million in consumer-related revenues this year.

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