Affymetrix Control Program Advances Association Studies

Affymetrix Inc. has announced that it is collaborating with leading researchers around the world as part of the Affymetrix Control Program.

The program will provide free, public access to control cohort data for whole-genome association studies using Affymetrix GeneChip^® genotyping arrays.

Participating organizations include GlaxoSmithKline, the National Genome Research Network (NGFN) in Germany, Erasmus MC in the Netherlands, the Karolinska Institute in Sweden, the Centre National de Genotypage in France and the Wellcome Trust Case Control Consortium (WTCCC) in the UK.

Genotype data from 12,000 samples is in the process of being committed to this unique project, which will make this the world's largest population genetics resource.

Use of appropriate control data can reduce the number of control samples required.

Researchers can also add age- and sex-matched controls from similar ethnic backgrounds as their cases to increase the genetic power of their current studies.

The data on 9,000 samples will be released through the National Center for Biotechnology Information (NCBI) over the next few months to qualified scientific investigators.

In addition, control data from 1,500 samples from the 1958 British Birth Cohort and 1,500 consented blood donors of the UK Blood Services will be released by the WTCCC to qualified scientific investigators. The WTCCC data will be linked to and from the NCBI database.

"The NCBI's mission is to serve as a public repository for data to help advance scientific research," said Steve Sherry, Ph.D., staff scientist at NCBI.

"We are pleased to partner in this program, to not only to distribute the data, but more importantly, to help ensure that they are as useful as possible in benefiting the public health."

"The database will enable researchers from both academia and the pharmaceutical industry to gain a better understanding of population stratification, and how to correct for it when performing large-scale association studies or pharmacogenomics studies," said Professor Stefan Schreiber M.D., one of the two speakers of the NGFN in Germany and researcher from the Christian-Albrechts-University in Kiel, Germany.

The NGFN will provide almost 3,000 control datasets with the two population collections, popgen and KORA-gen.

A multinational team of researchers, organized by Professor Michael Krawczak, Ph.D., and his University colleague Professor Schreiber, are collaborating to create a genetic map of Europe as part of the Affymetrix Control Program.

The group is analyzing data to discover markers that could be used to identify different genetic sub-populations on the continent.

To watch a two-part Affymetrix UserForum interview with Professors Schreiber and Krawczak, visit Company website. 

"We have almost finished typing 1,800 samples from the KORA-gen population that will go into the Affymetrix Control Database," said Professor Thomas Meitinger, M.D., director of the Institute of Human Genetics at the GSF - Forschungszentrum fur Umwelt und Gesundheit and member of the NGFN in Germany.

"We have started genotyping cases from several diseases for investigators who will use the KORA-gen data as controls."

"We plan to also make our control sample from KORA-gen available in association with P3G, the public population project in genomics," said Professor Erich Wichmann, M.D., Ph.D., GSF Institute of Epidemiology and head of the KORA study.

Affymetrix continues to look for eligible samples and anticipates that an additional 5,000 to 10,000 samples will be added to this control program over the next year.

A sample will be eligible for the controls program if it represents the general population or a control population, and was not selected for having a particular disease phenotype.

"We plan on expanding the Affymetrix control program to include data from populations around the world to better support the broad spectrum of sample types used for genetic studies," said Tom Willis, Ph.D., vice president, DNA Marketing at Affymetrix.

"This program, which consists of half a million SNPs across thousands of individuals, will complement the database constructed by the International HapMap Project that included four million SNPs across 210 individuals."

"It will serve to increase the genetic discovery power for all customers using our whole-genome association products."

To watch the two-part UserForum interview featuring Greg Marcus, Ph.D., senior product manager, DNA Analysis at Affymetrix, visit Company website.