Illumina, Inc. has announced a large-scale collaboration with the Institute of Translational Medicine and Therapeutics (ITMAT) at the University of Pennsylvania (Penn), the Broad Institute, and the National Heart, Lung, and Blood Institute's (NHLBI) Candidate-gene Association REsource (CARe) Consortium to develop a customized chip for vascular disease.
Called the IBC (ITMAT, Broad, CARe) chip, this array will be developed to analyze more than 55,000 single-nucleotide polymorphisms (SNPs) in candidate genes selected for cardiovascular and other associated phenotypes.
Employing Illumina's iSelect Custom Genotyping BeadChip, researchers will assess the genetic diversity within pathways of approximately 2,100 genes believed to underpin primary and secondary vascular disease processes, such as blood pressure, myocardial infarction, heart failure, stroke, insulin resistance, metabolic disorders, dyslipidemia (changes in lipid levels in the blood), and inflammation.
At the study's completion, more than 120,000 samples from large population studies and clinical trials will be analyzed for genetic links to vascular disease.
Vascular disease refers to any condition that affects the circulatory system. This ranges from diseases of the arteries, veins, and lymph vessels to blood disorders that affect circulation. It is the leading cause of death and disability in the United States, Japan, and Europe, and a rapidly increasing cause of death and disability elsewhere in the world.
The content for the custom array was chosen based on published scientific literature, cardiovascular disease (CVD) pathway analysis, and recent whole-genome analysis data sets. Some of the cohorts to be interrogated using the 55,000+ SNPs include nine NHLBI epidemiologic cohorts that compose the CARe study, the Diabetes Reduction Assessment with Ramipril and Rosiglitazone Medication trial (DREAM), EpiDREAM (an observational sub-study of DREAM), the Chronic Renal Insufficiency Cohort (CRIC), and a University of Pennsylvania consortium of CVD studies that includes PennCATH.
"Our team opted to work with Illumina's iSelect Custom Genotyping array because the technology has proven to be extremely flexible and provides us with highly-robust data, making it an optimal platform for a study of this magnitude," said Garret FitzGerald, M.D., McNeil Professor of Translational Medicine and Therapeutics and Director of ITMAT.
The collaboration, led by the University of Pennsylvania, the Broad Institute and the CARe Consortium is the first major cardiovascular initiative to use the iSelect Infinium Custom Genotyping array. iSelect custom panels enable researchers to focus on specific disease-related or pathway-related SNPs.
The multi-sample BeadChip format increases throughput and shortens sample processing time. iSelect Infinium Custom Genotyping offers the same benefits as standard Infinium products, including the ability to access SNPs across the entire genome, industry-leading data quality, reproducibility, and call rates greater than 99 percent.
"With Illumina's assistance, we worked together to build a comprehensive, focused vascular disease panel. This panel will allow us to quickly genotype thousands of patients across thousands of genes to identify genetic risk factors underlying vascular diseases and other complex genetic traits," said Joel Hirschhorn, M.D., Ph.D, Associate Member, and Coordinator of Metabolism Initiative at the Broad Institute.
"The ability to choose any SNP we desire gives us great confidence that we will develop an accurate and high-quality panel for clinical diagnosis," Hirschhorn said.
To select SNPs in candidate genes, the group's approach was to find the union of tagging SNPs from the four HapMap populations and SeattleSNPs resequencing data.
"The University of Pennsylvania's interest in customizing this genotyping panel to tackle vascular-disease research underscores the creative ways the research community is working with Illumina to unravel the complexities of human disease," said Jay Flatley, President and Chief Executive Officer of Illumina.
"Our whole-genome genotyping technology continues to raise industry standards by delivering unparalleled data quality, format and content flexibility, and cost-effectiveness. This is helping researchers accelerate discoveries that will help us better understand, cure, and ultimately prevent disease," Flatley added.