The Illumina system will be housed at the hospital's Center for Applied Genomics and will provide a core capability for the Center's research goal of ultimately genotyping over 100,000 children.
The knowledge gained from these studies is expected to provide significant insight into the genetic basis of common childhood disease, linking genetic variations called SNPs with specific illnesses.
Including arrays and reagents for the first 30,000 samples, the initial value of the agreement is expected to exceed $25 million.
The Center for Applied Genomics will focus on some of the most prevalent diseases of childhood - asthma, obesity, diabetes and cancer among others - all of which are thought to involve the contributions of multiple, interacting genes.
The Center's researchers will then work to translate the genetic knowledge into targeted treatments for the diseases in question, customizing treatments to a child's genetic profile.
The genotyping studies will be guided by Hakon Hakonarson, M.D., Ph.D., a Director at the Center.
"We will be tracing the major underlying genetic component of disease-related genes while discovering the biological pathways involved in disease development," Dr. Hakonarson explained.
"For instance, a specific cholesterol receptor may be dysregulated because of genetics, or the pathway may also be dysregulated because of an unhealthy diet."
"If we can identify key bottlenecks for dysregulation, we may able to treat not only the five percent of people with a particular gene variant for a disease, but also the larger percentage who suffer the disease without having that variant."
The ultimate aim of the Center's investigators is to enable tailoring of treatments to patients' individual profiles, formally introducing into the clinic a personalized approach to medicine with the intent of improving outcomes while creating a model for clinical practice around the world.
"We are following a trail blazed by the Human Genome and HapMap Projects, but tailoring our approach to children," said Philip R. Johnson, M.D., chief scientific officer at The Children's Hospital of Philadelphia.
"As one of the world's largest and most comprehensive pediatric networks, we have a sizable base of patients and families from which to collect data."
"This focused effort in genomics reaffirms that we are absolutely committed to finding cures for childhood diseases."
When installed, the system will be capable of producing 150 million genotypes per day, all extracted from blood samples.
To accommodate its sample analysis objectives, patients at Children's Hospital and throughout its network of pediatricians' offices and satellite centers will be asked to contribute blood samples.
For those who agree, a sophisticated information management system will track the samples and store medical records information in an encrypted form to preserve patient confidentiality.
Clinicians will also ask the children's parents to contribute blood samples and divulge medical information to further strengthen the project's base of information.
"Our sample size will be large enough to provide great statistical power to our research," added Dr. Hakonarson.
"We will be able to characterize genotypes and health conditions over a sizable population of children."
"This project will help to set the standard for identifying biological links to childhood diseases."
Dr. Hakonarson and his colleagues will first conduct whole-genome genotyping using Sentrix® HumanHap550 BeadChips, each of which can analyze over 550,000 single nucleotide polymorphism loci with per-sample genomic coverage and data quality.
Subsequent phases will use Illumina arrays and reagents to study focused sets of SNPs thought to be implicated in disease cause and progression.
While focused initially on SNP genotyping, the Center's research teams expect to use the BeadLab for a range of integrated genetic studies, including but not limited to whole-genome and focused gene expression to characterize certain diseases and analyze biological pathways, discover and validate disease-related biomarkers, and understand interactions between human genes and environmental exposures.
The system installation will be centered around Illumina's BeadLab with a substantial number of additional scanner and automation components.
"The whole-genome genotyping market continues to grow rapidly as investigators design exciting studies and build capacity to generate and analyze the genetic information necessary to help understand the molecular basis of disease," stated Jay Flatley, Illumina President and CEO.
"The Center for Applied Genomics will benefit from a facility that is unrivaled in the world of disease research."
"We're gratified to be able to contribute so meaningfully to the Hospital's exciting research agenda with our flagship HumanHap550 product."
"More broadly, our agreement with Children's Hospital is another dramatic step in the evolution of the genotyping market, setting the stage for what we believe will be routine application in the fast-emerging field of predictive diagnostics."