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Affymetrix Plans to Debut Chinese Population-Specific Genotyping Array this Year

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This story has been updated to include comments from Affymetrix officials.

By Justin Petrone

Affymetrix this week said it will launch later this year a new array for genome-wide association studies on Chinese populations.

The planned offering, called the Axiom Genome-Wide CHB Array, is part of a suite of population-specific chips the array vendor intends to release in the future. Content for the chip is being selected from Affy's internally developed Axiom Genomic Database, which includes data from the 1000 Genomes Project as well as Han Chinese data made available through the International HapMap Project, the company said.

In addition to supporting GWAS, customers will also be able to conduct population-specific replication, fine mapping, and candidate gene studies on the array, Affy said.

The Santa Clara, Calif.-based vendor is developing its CHB Array with customers in China, including Lin He, a genomic researcher at Shanghai Jiao Tong and Fudan Universities and a member of the Chinese Academy of Sciences, and Dongfeng Gu of Beijing Fuwai Hospital. Lin He plans to use the new array to study schizophrenia, while Dongfeng Gu will use the chip to study hypertension in the Chinese population, Affy said.

"Expanding our Axiom family of genotyping products to cover the Chinese population comes in response to Dr. He's scientific insights on genotyping study design," Jay Kaufman, vice president of DNA product marketing at Affymetrix, said in a statement. "Our customers in China … called for more focused, Chinese-specific content to give them greater genetic coverage and thus more power."

Kaufman told BioArray News this week that the firm's suite of population-specific arrays should "better facilitate GWAS in diverse populations." Affy's strategy is "based on the research community’s need for more effective genomic tools to study complex, common diseases, such as cardiovascular disease, diabetes, and cancer; communicable diseases; and biological process, such as drug metabolism in African, Asian, and Latino populations," Kaufman said.

To accomplish this, Affy is partnering with the scientific community to use its Axiom Genomic Database to generate predesigned and custom arrays. Indeed, the firm said last week that it intends to enable researchers to design in the "near future" custom arrays containing 5 million markers (BAN 7/27/2010). Using its database, Affy customers can currently create custom arrays containing between 50,000 and 2.6 million SNPs.

Kaufman said that Affy has seen interest for population-optimized arrays from two fronts in the research community: those studying traditionally homogeneous populations with deep ancient ancestry as well as populations with diverse, mixed ancestry. He said this interest springs from the fact that "previous commercial arrays did not provide sufficient coverage and heterozygosity for non-European cohorts, nor are they well-suited for studies in individuals of mixed ancestries."

By combining on its arrays new sequencing data, including data from the 1000 Genomes Project, Affy's goal is to "generate a more complete collection of genetic markers ... for both predesigned and custom arrays," Kaufman said. "This content can be leveraged for projects focusing on disease risk factors in inherited and communicable diseases in a variety of populations," he added.

A Legal Entity

In addition to announcing the coming release of its Axiom Genome-Wide CHB Array last week, the company also disclosed that it has opened a foreign-investment commercial enterprise in Shanghai.

Affy had maintained for several years a representative office in China, which under Chinese law enabled the firm to conduct market research and liaison with Chinese business partners, but not to directly import and resell its products to Chinese customers.

Chris Barbazette, Affy's senior director and general manager of the Asia-Pacific region, told BioArray News this week that this new legal status gives the firm the option of "speaking directly to customers and converting our consultants and contractors to Affymetrix employees."

Barbazette said that Affy chose to expand its presence in China "based on the fact that the business in China is strong and continues to grow at a very rapid pace."

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