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1000 Genomes Data Submission a 'Milestone' for Affymetrix, Official Says


This story has been updated from a previous version to clarify that Affymetrix is now a participant in the 1000 Genomes Project. It has also been updated to include new comments from a company official.

By Justin Petrone

Affymetrix could benefit from its decision to contribute genotyping data to the 1000 Genomes Project, according to a company official.

The firm has announced that it will submit to the effort data for a large set of validated rare and common genomic variants, including genotyping information from more than 2 million SNPs and insertions/deletions that were not previously available from any source.

"We have deposited a large amount of data into the public domain, and we have really advanced the project," said Andy Last, the Santa Clara, Calif.-based company's chief commercial officer. "Public access to that data will give people a better understanding of what we can run on our platform," Last added.

Last spoke to BioArray News following a presentation at the American Society of Human Genetics annual meeting, held in Washington, DC, earlier this month. During his talk, Last called the data contribution to 1000 Genomes a "milestone" for the company.

In addition, Jay Kaufman, vice president of strategic marketing for DNA applications at the Santa Clara, Calif.-based company, said this week that participating in the project was in line with the firm's "corporate goal of keeping Affymetrix at the forefront of influential scientific endeavors." He told BioArray News that the firm will also "gain the opportunity to engage on a scientific and technical level more formally with key thought leaders in the field in the pursuit of common goals."

Additionally, the company will benefit from "being closer to the sequencing activities and the output of those efforts, which to date has led to the discovery of approximately 25 million novel variants that are now publicly available," Kaufman said.

Up until joining last week, Affy was not an official participant in the 1000 Genomes Project, though some of its rivals, such as Illumina, Life Technologies, and Roche, have been taking part since the project kicked off nearly three years ago, as their sequencing platforms are being used to generate the data. Affy is now an official participant in the project. Both Affy and Illumina have been using data from 1000 Genomes to build next-generation whole-genome genotyping arrays for use in association studies.

According to Affy, its contribution to 1000 Genomes includes common and rare variants genotyped on the four major HapMap populations: Caucasian, Yoruba, Chinese, and Japanese, as well as on the larger HapMap Phase 3 sample-set. The data will be incorporated into the 1000 Genomes public data repository and will be freely available, according to the company.

1000 Genomes co-chair David Altschuler said in a statement that the large data set would "complement existing genotyping data in the public domain," and that Affy's data will "be of interest to the project's participants, as well as to the broader research community."

As a project participant, Kaufman said the company will assist by "generating genotyping data and related information on the entire set of 1000 Genomes samples across relevant subsets of SNPs" that have been discovered by the project. "This will lead to the creation of resources in the form of data and information we will leverage to create new genotyping arrays for a variety of purposes," Kaufman said.

In addition to its 1000 Genomes participation, Affy said it will by year end release on its website a larger data set of approximately 5 million variants. The new data includes approximately 3 million human SNPs discovered by the 1000 Genomes Project that were not found in the HapMap Project or the National Center for Biotechnology Information's dbSNP database.

Affy generated the data using its Axiom genotyping platform, and said the availability of the data will allow its clients to create customized Axiom genotyping arrays containing 50,000 to as many as 2.6 million markers. Kaufman said that the database will grow in coming months to contain between 8 million and 9 million variants by early next year.

Carlos Bustamante, a professor of genetics at Stanford University, said in a statement that the availability of the new data will benefit ongoing work at Stanford in "enabling multi- and trans-ethnic genome-wide association and medical resequencing studies."

Affy said its Axiom Genome Screening Service will also allow researchers to screen their populations and cohorts of interest against approximately 5 million of the validated Axiom markers. Last told BioArray News that the firm is considering making a 5-million catalog product available, but that it has not decided if or when such a tool will be commercialized.

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.