R&D Update: Nov. 20, 2007

Development of the AutChip: Early Clinical Diagnostic Testing for Autism

 Autistic spectrum disorders (ASDs) are complex, behaviorally defined neuro-developmental disorders characterized by qualitative impairment in social interaction and communication, as well as restricted, repetitive and stereotypic patterns of behavior, interests and activities. The national prevalence rate of ASDs is 1/150, although recent surveys in New Jersey suggest the prevalence is 1/96. Although ASDs are multi-factorial with substantial differences in presentation of the disease, 15% to 20% percent of cases are thought to be attributable to an underlying genetic cause as shown by recent studies using a novel high-resolution genome analysis technique called array-based comparative genomic hybridization (array-CGH). Array-CGH is used for identification of copy number variations (CNV) that reflect deletions and amplifications in the human genome. Our goal is to develop an ASD-specific array for CGH called the AutChip which targets only genomic regions that include a critical genes or CNVs that are reported to be causative of ASDs. The AutChip will reduce false positives that lead to parental testing and will substantially decrease the cost of diagnostic testing of ASDs with array-CGH to under $500/test.

Cost Effective Genetic Screening for Hypertrophic Cardiomyopathy

 Hypertrophic Cardiomyopathy (HCM), an often fatal but manageable disease with an incidence of 1/400, is the most common monogenic cardiac disorder in the US . In addition, it is the most frequent cause of unexpected sudden death in teenagers and young adults. Genetic studies have defined HCM as a disease of the contractile proteins in heart muscle cells caused by mutations in 11 genes. Currently, only two laboratories offer HCM diagnostic testing, both of which are based on DNA sequencing of eight of these genes at a cost of more than $4,000. This high cost has been a major impediment to genetic diagnosis. Interestingly, 180 of the 434 known HCM-associated mutations are recurrent, suggesting that the catch rate of a low cost test that interrogates recurrent mutations will identify greater than 60% of the patients at risk. We are currently developing a new $350 clinical diagnostic test that probes all of the 180 recurrent mutations to catch over 60% of HCM patients.

Identification of Risk Alleles for Multiple Sclerosis

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system (CNS) that leads to degeneration of central axons. S everal studies have shown an association of MS with the HLA class II gene, DR15 DQ6, though there is no convincing evidence pointing to a common single susceptibility gene. We identified a variant of the disialoganglioside 3 (GD3) synthase gene (SIAT8A) that appears to be associated with disruption of the ganglioside pathway and leads to MS. If confirmed, this gene along HLA DR15 DQ6, may form the basis of a new two gene clinical diagnostic test that predicts MS risk. Defining gene variants that confer MS susceptibility may identify pathways that can be targeted by immunomodulatory agents to guide novel therapeutic selection strategies for individual patients. A second potential diagnostic application may involve monitoring the GD3 synthase protein and enzymatic analysis on fresh white blood cells using an antibody.

Mental Retardation/Developmental Delay Diagnosis Using Chip-based Comparative Genomic Hybridization

A customized version of Agilent Technology's 44K CGH platform was developed by our staff that permits comprehensive whole genome screening for deletions, duplications, trisomies and other quantitative changes in the genome that are associated with mental retardation/developmental delay (American Journal of Medical Genetics, 143A: 824-829, 2007). We introduced our chip into clinical practice in July 2008 and in addition to providing a screening service to NJ hospitals, we have also provided the chip to out-of state testing labs. Our current efforts are aimed towards replacing the first generation chip with one that provides triple the resolution at the same cost.

Clinical Introduction of an Automated Proteomic Diagnostic System

The Intrinsic Bioprobes Mass Spectrometry Immunoassay (MSIA) is an automated robotic system that can perform single and/or multiplexed immunoassays in 1 hr detecting up to six analytes/sample with high sensitivity (in the femtomolar range). We are the first academic lab in the world to offer this type of service, providing 25 clinical proteomic assays to NJ hospitals in 2008. MSIA technology couples antibody affinity capture to mass spectrometry allowing determination in one platform of both sensitive quantification as well as qualitative changes in proteins arising from amino acid substitutions, RNA splice variants, posttranslational modifications, and proteolytic processing.

Innovative Technologies to Discovery Blood Proteins for Early Detection of Any Cancer

It is postulated that every gene product eventually gets into the blood stream, either by an active secretion/transport mechanism or as passive tissue leakage proteins after cell death. This implies that an ultra sensitive and accurate technology may be able to detect any biomarker in blood, including tumor specific proteins that are shed at the earliest stages of cancer. A wealth of potential cancer biomarkers have been implicated by DNA chip/microarray experiments that revealed differentially expressed RNA transcripts in cancer cells. However, early detection of the proteins encoded by these transcripts in blood has been elusive due to both the lack of ultra sensitive protein detection techniques and the known fact that a hand full of extremely abundant proteins such as albumin, that account for the bulk of the protein mass in blood, tend to sequester less abundant proteins and prevent their detection. The IGM in collaboration with George Mason University are collaborating to unite two novel technologies that may solve these problems and open a new era in targeted biomarker discovery. In combination, these two technologies permit the release of scarce proteins that are trapped by abundant proteins using size tunable nanoparticles that act as molecular sieves, and their eventual detection using the MSIA technology described in the previous section.

Identification of Human Biomarkers Indicative of Bioterrorism

Utilizing an in vitro model system for infection of lymphocytes, researchers at the IGM and the Center for Biodefense are identifying biomarkers of potential infections caused by acts of bioterrorism. This involves DNA chip/microarray expression and polymorphic variant analysis in population studies and identification of disease specific markers by examining infected blood cells.

Development of Smartpin Technology

SmartPin™ technology, conceived and developed by IGM researchers and their collaborators at the New Jersey Institute of Technology, is a computer-controlled liquid handling system that allows the dispensing of tiny spots of liquid, in desired volumes, on any surface. The technology can be applied to any liquid-handling application including high-throughput drug screening, in which large amounts of data is collected, the production of DNA and protein chips, and clinical diagnostic testing. It also has potential application in the manufacturing of semiconductor components such as in the printing of molecular nanotube transistors. This technology is described in a patent issued in 2006 and was awarded the 2007 Thomas Alva Edison Patent of the Year Award, (emerging technologies category), from the Research and Development Council of New Jersey. A prototype system has been built and proof of concept experiments have been completed. The next phase of this work is to develop a commercial unit that can be manufactured for widespread use.

Development of Hydrogel Nanoarrays