Children's Hospital Contributes to Genotyping Control Database

09/1/2007

The advanced automated technology from Illumina Inc. supports the Center for Applied Genomics (CAG) at Children's Hospital, the world's largest program for pediatric genotyping. Responding to a need by the life science community to access genotypic data from individuals that can be used as controls in case-control association studies, Illumina launched iControlDB, the first industry-hosted genotyping control repository available for immediate use by researchers conducting case-control whole-genome association studies.

Genetic case-control association studies, which compare groups of patients who already have a disease with a group of individuals without the disease to identify risk factors that may contribute to a medical condition, are becoming more widespread in the scientific community. Illumina created iControlDB to provide immediate access to data that would otherwise be more time-consuming, cumbersome, and costly to obtain. Illumina estimates that iControlDB will provide at least a 50 percent cost savings, in addition to halving the time necessary for processing samples.

"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, M.D., Ph.D., director of CAG. "Having this tool available allows researchers to significantly reduce both time and expenses in their genotyping studies. We hope this will facilitate collaborative interactions and advance our goal of building scientific foundations for developing successful treatments for childhood diseases."

Since its founding, CAG has generated genotypes on over 22,000 individuals and contributed 4,000 control samples from healthy individuals to iControlDB. This is the largest genotype donation by a single institute, and includes more than 2.5 times the number of genotypes released by the International HapMap Project, which took several years to generate by dozens of investigator sites.

Combined with the database of Genotype and Phenotype (dbGaP), the scientific community can now access nearly 10,000 control samples that have been donated by CAG and other leading genomics institutes using Illumina's technology for single-nucleotide polymorphism (SNP) genotyping.

All data uploaded to iControlDB are subject to Illumina's rigorous quality control process. To date, control samples uploaded to this database have an average call rate of 99.6 percent. By the end of 2007, samples in iControlDB are expected to reach more than 20,000.

In addition to controls deposited from the International HapMap Project, the database contains 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.