Genomic Research Projects Exemplify CHOP Research's Stimulus Grant Success


The American Recovery and Reinvestment Act (ARRA), commonly known as the Stimulus Bill, provided the National Institutes of Health with $10.4 billion it was required to allocate for grants and other projects by the end of September 2010. The CHOP Research Institute worked rapidly and diligently to take advantage of the unprecedented opportunities for the advancement of research and education that the Stimulus Bill presented. CHOP Research submitted more than 220 ARRA proposals and received more than $45 million in stimulus funding.

Hakon Hakonarson, M.D., Ph.D., provides a snapshot of the success that CHOP Research investigators achieved in securing grant funding from the NIH’s stimulus allocation. Dr. Hakonarson, who directs the Center for Applied Genomics (CAG), was listed as the principal investigator on three grants awarded from the NIH’s stimulus funding. Totaling $22.2 million, and focused on epilepsy, juvenile idiopathic arthritis, and mental illness, the grants seek to enhance the understanding of genetic factors that contribute to these disorders in order to facilitate the development of more effective diagnoses and treatments.

The projects hinge on the genomic expertise at CAG, which performs genome-wide association studies (GWAS) to examine genetic variations across an individual’s entire genome and compare variations between groups affected and unaffected by a disease. GWAS identify copy number variations (CNVs), segments of DNA consisting of deleted, duplicated, or rearranged genetic material, and single nucleotide polymorphisms (SNPs), single base pair differences between the DNA of two individuals in the population. Identifying the location of an SNP or CNV that is significantly more frequent in a patient group than in controls points investigators toward a segment of DNA that might play a role in the disease being studied.

Under the stimulus funding for the epilepsy project, Dr. Hakonarson and his team are using a whole genome association approach to uncover genes and genetic variants that predispose individuals to common forms of epilepsy. Epilepsy, which affects approximately one in every 100 children, is among the most common causes of childhood disability. Many epilepsy patients treated with existing therapies continue to experience seizures and new treatments are limited by a lack of understanding of the neurobiological mechanisms that produce recurrent seizures, the hallmark of epilepsy.

The epilepsy study team will genotype DNA from an existing cohort of 2,000 epilepsy patients and 4,000 healthy individuals to identify genetic variants that associate with epilepsy. The team will subsequently test the variants in an independent, newly recruited cohort of 1,000 epilepsy patients and 1,000 unrelated healthy patients to confirm the roles the identified variants play in epilepsy. As the team recruits the independent cohort, they will also conduct a fine-mapping analysis of the five most compelling biological candidates in DNA from 400 parent-child trios within the original cohort.

To further validate and refine the findings in the first stages of the study, the team will genotype 10 to 20 candidate SNPs in DNA samples from 250 African-American epilepsy patients and 1,000 African-American controls, a population of different genetic background. After using this approach to help pinpoint the key disease genes, the team will complete a fine-mapping analysis of the variants found to be significant. Additionally, they will resequence the three most significant and biologically relevant candidate genes in a group of 100 epilepsy patients and 100 healthy individuals. By identifying variants that are most significant and affect genes that have a compelling biological role in epilepsy, the investigators are prioritizing genes with variants that will be further evaluated as targets for new therapies.

Dr. Hakonarson’s second stimulus grant is a collaborative effort that focuses on juvenile idiopathic arthritis (JIA), one of the most common chronic diseases of childhood and the number one cause of acquired disability in children. Previous studies of JIA identified genetic variants that are common in multiple subtypes of adult and pediatric inflammatory arthritis by looking at candidate genes suspected to play a role in the JIA based their role in its pathological mechanism. However, because the pathophysiological mechanisms underlying JIA are unknown, continued use of the candidate gene approach is likely to miss many important genetic risk factors for the disease.

Addressing the need for a more comprehensive strategy, the JIA study team will conduct a whole genome scan to look at gene regions likely to be associated with JIA. They will genotype DNA already collected from 1,500 JIA patients whose symptoms are well described and DNA from at least 4,000 healthy patients with rates of non-disease causing SNPs that are similar to the JIA patients, known as matched controls.

In an approach similar to that used in the epilepsy study, the team will validate the disease genes identified in an independent cohort of 1,000 JIA patients and 2,000 controls to ensure the genes identified are causative of JIA. This research is expected to identify 10 to 20 candidate genomic regions that predispose patients to JIA and should be evaluated further in studies aimed at developing new treatment approaches.

The third, and largest, project funded by a stimulus grant to Dr. Hakonarson focuses on mental illnesses, which emerge in more than 4 million children and adolescents as a result of an interplay between epigenetic and environmental processes in genetically susceptible individuals. A lack of information pertinent to mental illness in medical records and the complexity of behavior in the brain have made it difficult for genetic research efforts to link genetics, behavior, and brain function to improve diagnosis and treatment.

The research team will evaluate disease characteristics of 10,000 children and adolescents and assess behavioral dimensions – such as anxiety, mood, and substance abuse – to identify which factors indicate vulnerability to mental illness. These 10,000 children, who have already been genotyped by CAG, will undergo a comprehensive neurocognitive assessment through a battery of computerized tests to determine which genes play a key role in normal development and how mutations in these genes may lead to disease. These children will also undergo neuroimaging to look at brain structure, white matter connectivity, cerebral blood flow, and cerebral activation of neural circuits implicated in major mental illnesses. To identify gene networks underlying neuronal vulnerabilities that lead to mental disorders, the team will conduct genome-wide studies that assess methylation, a DNA modification that alters the expression of genes, in the patients who underwent neuroimaging.

A database combining the collected data on neuroimaging, neurocognitive assessment, and genotyping will link genetics and epigenetics with brain systems that regulate behavior and psychopathology. The database, which will be available to the scientific community at large, will provide the scaffolding for future research that will elucidate processes through which mental illnesses are expressed.

“The state-of-the-art genomic resources at CAG and the funding provided by the stimulus grants are acting together to fuel projects that will have lasting effects on these areas of research and will stimulate future research with regional and national impact,” says Dr. Hakonarson. “We expect that these pioneering studies will bring us a few steps closer to our goal of developing better ways to diagnose pediatric diseases and develop new and better treatments.”