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Illumina takes the controls -- iControlDB makes data of 10,000 genotyping control samples available to researchers
SAN DIEGO—Looking to help drive sales of its high-density microarrays and to potentially provide its customers with significant savings in time and money in their whole-genome association studies, Illumina Inc. announced last month iControlDB, a company-hosted genotyping repository that contains data from nearly 10,000 control samples.
"In general, we see this as a benefit to the research community," says Carsten Rosenow, DNA analysis senior marketing manager with Illumina. "Having immediate access to this database will save researchers from doing the time-consuming work on their own controls and could provide as much as a 50 percent savings in the cost of their work, not including the time they would save not having to process their own control samples."
To help assemble the database, Illumina turned to customers at research centers that would be willing to upload their control data to Illumina. Early contributors to iControlDB include The Children's Hospital of Philadelphia (CHOP) and the Robert S. Boas Center for Genomics and Human Genetics at the Feinstein Institute for Medical Research, which contributed more than 6,000 samples between them. The data also includes controls from the International HapMap Project.
"This database will benefit the research community at large by providing investigators with an extensive set of control samples to validate their genetic studies," says Hakon Hakonarson, director of the Center for Applied Genomics at CHOP. "We hope this will facilitate collaborative interactions and advance our goal of building scientific foundations for developing successful treatments for childhood diseases."
In order to use—or submit data to—the control database, researchers must be registered Illumina customers with password-protected access to Illumina web services called iCom. "One reason researchers need to be registered with us is due to HIPAA regulations," explains Rosenow. "We need to show for these rules an identifier of the individual and that this person is qualified to use this data."
In order to continue to build the data in iControlDB, Illumina is encouraging its customers to upload control data to the site, activity which will help to broaden the diversity of the data set. By year-end, the company anticipates these contributions from researchers will help build the database to more than 20,000 control samples.
Researchers only need the bare minimum phenotype information of age, gender and ethnicity to upload sample information, but can also provide much more information per sample if they so chose. Likewise, researchers who want to avail themselves of the control data can be as broad or as specific as their studies require.
Rosenow is particularly happy with the diversity of the control samples which currently includes samples from Caucasian, African, African American, African-American mixed-descent, Chinese, Japanese, Korean, Native Hawaiian/Pacific Islander, Hispanic, Hispanic mixed-descent, Indian and Vietnamese populations.
"One of our strengths is that we already have 2,000 African American and mixed-ethnicity samples," says Rosenow. "And we encourage those in the community to help us build these sets. We also have strength in samples from Asian populations."
All data uploaded to iControlDB are subject to Illumina's quality control standards. According to information supplied by the company, samples uploaded to the database have an average call rate of 99.6 percent.