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University of Iowa Develops Genetic Diagnostic Test for Hearing Loss

By Bio-IT World Staff 

June 21, 2011 | University of Iowa researchers in the Molecular Otolaryngology and Renal Research Labs (MORL) are utilizing GenomeQuest’s clinical decision support system, GQ-Dx, to develop a first-of-its-kind molecular diagnostic test for individuals with hearing loss. GenomeQuest announced the clinical decision-support system for whole-genome diagnostics today.  

University of Iowa researchers are using GQ-Dx to compare a patient’s DNA with the human reference genome, known hearing loss mutations, and variations that are seen commonly in populations around the world. This will allow the MORL researchers to obtain a clinically relevant genetic blueprint of a patient’s specific cause of deafness and use that diagnostically.  

“To diagnose and treat genetic hearing loss until now has required sequencing of genes one-by-one. In many cases a diagnosis is not achieved because there are at least 66 genes implicated in deafness,” said Eliot Shearer, a NIDCD predoctoral research fellow and member of the MD/PhD program, at MORL. "If we’re to improve patient care by introducing personalized medicine, we need an analysis pipeline that provides one-click, streamlined data management to interrogate the sequence generated from these 66 deafness genes per patient." 

MORL’s approach leverages next-generation sequencing (NGS) gene panel diagnostics to pinpoint the cause of and treatment for this multi-gene disorder in one comprehensive test rather than multiple tests. Developed by MORL researchers and their colleagues at the Baylor College of Medicine, the OtoSCOPE test reduces their estimated cost of comprehensive diagnosis from $75,000 to just $2,000 and reduces the time for treatment decisions from one year to four weeks.  

“What we discovered is that GenomeQuest’s GQ-Dx processes patient data and integrates with multi-gene databases with greater speed and flexibility than other analysis pipelines,” Shearer added. “And the reporting capabilities allow us to generate high-quality molecular diagnostic results that can be easily interpreted by clinicians.”  

GQ-Dx runs on genome center-scale secure computational infrastructure housed and maintained by GenomeQuest. “Large-scale diagnosis of genetic deafness is not feasible for a laboratory without the infrastructure in place to support management of large volumes of genomic data,” said MORL’s Michael Hildebrand, a UI post-doctoral scientist also working on the project. “Diagnosing a single patient generates several gigabytes of data that must be processed, analyzed and stored. As a result the MORL would need to upgrade its data storage and processing infrastructure every six months. GQ-Dx’s clinical decision-support system will reduce or even eliminate MORL’s time and expenses involved with that infrastructure.” 

Inherited hearing loss affects 1 in 500 newborns. About 278 million people worldwide have moderate to severe hearing loss, and about two-thirds of hearing loss is inherited and can be caused by mutations in at least 66 different genes. “Our implementation of GQ-Dx at the University of Iowa in collaboration with GenomeQuest demonstrates that precise genome-based diagnostics are practical and affordable for diseases that involve multiple genes and multiple molecular pathways,” Hildebrand said. “MORL also intends to use GQ-Dx to develop a similar comprehensive molecular diagnostic platform for kidney disorders.”  

Multi-Gene Targets 

GenomeQuest believes that other multi-gene disorders that are ripe candidates for consolidated testing include HIV and hepatitis C, Alzheimer’s, cardiomyopathy, coronary artery disease, myocardial infarction and colon cancer. 

Gerry Higgins, GenomeQuest’s healthcare innovation officer added, "Whole-genome sequencing has placed us on an accelerated path to understanding the genetic drivers in complex diseases. I anticipate continued major progress in oncology as well as in cardiology, neurology, psychiatry, and other medical specialties. What is particularly fulfilling to me is to work with clinical research organizations that immediately translate discoveries into vastly improved health care—accurate diagnosis and, in many cases, targeted treatment for patients."  

The GQ-Dx product is based on the company's GQ-Engine, and provides comprehensive genomic information capabilities at clinical scale, including whole-genome, whole-exome, and gene panel processing; diagnostics reporting; and diagnostic research.  

“With whole-genome sequencing advancing to practical use, we see that the next roadblock is the effective clinical application of the emerging discoveries and vast amounts of data,” said Richard Resnick, GenomeQuest’s chief executive officer, in a press release. “GQ-Dx makes use of the aligned advancements in sequencing, bioinformatics, computing, and medicine to deliver whole-genome molecular diagnostics. Just as the industry has been able to reduce sequencing time and cost, GenomeQuest has addressed analysis time and cost so that researchers can finally take data from the bench and apply it at the bedside quickly and cost-effectively.”  

The service-based software option requires no capital or infrastructure investment and offers simple administration for diagnostic organizations. Optionally, customers can install GQ-Dx in their data center behind their firewall. Diagnostics users access all processing, reporting and research features via the Internet from their desktop or smart device.  

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