Vanderbilt University Medical Center has opened a Clinical Genomics Laboratory to provide diagnostic testing for genetic disorders.
In its initial phase, the laboratory is offering whole exome sequencing, a technology that provides a “read-out” of all the pieces of DNA that provide instructions for making proteins. VUMC is one of only a handful of academic medical centers to offer the specialized testing; previously, samples were sent to outside vendors for analysis.
“Having the data here will be a huge advantage in terms of patient care and decision support,” said Thomas Stricker, MD, PhD, assistant professor of Pathology, Microbiology and Immunology, and medical director of the Clinical Genomics Laboratory.
The laboratory will also be moving toward offering other germline genetic testing, for example for inherited mutations in genes associated with cancer, cardiomyopathy, arrhythmia, epilepsy and intellectual disability.
Such testing usually involves sequencing a specific set of genes, a so-called gene “panel.” VUMC plans to perform whole exome sequencing and then use bioinformatics tools to analyze specific gene panels within the data.
“The technology for sequencing has advanced to the point where it’s considerably less expensive and time consuming to do the sequencing than it once was,” said Adam Seegmiller, MD, PhD, professor of Pathology, Microbiology and Immunology and vice chair for Clinical Pathology. “VUMC has provided the funding to purchase one of the most advanced sequencing instruments on the market today, with the high-throughput and capacity that we anticipate needing as our services expand.”
Whole exome sequencing is particularly useful for individuals in which there is a strong suspicion of an inherited disorder, “but we haven’t been able to identify what that is through all the usual testing we do,” Seegmiller said. “By looking globally at the entire (protein coding) genome, we can potentially identify unexpected or previously unknown variants.”
“An increasing number of diseases are genetically mediated, and the decisions for how to treat those patients are dependent on the diagnosis,” added Mary Zutter, MD, Vice President for Integrative Diagnostics at VUMC.
Whole exome sequencing will initially be used mostly for pediatric patients. The typical patient is a child with multiple symptoms, perhaps including global developmental delay, intellectual disability and cardiac and other abnormalities.
“They’ve usually been on a diagnostic odyssey that may have lasted for years trying to find the cause of the illness,” Stricker said.
Whole exome sequencing has been ordered for five patients since the Clinical Genomics Laboratory opened in late December.
“We see complex patients who get complicated genetic testing, and having this capability in-house will give us better quality control, faster results and improved access to the data,” said Rizwan Hamid, MD, PhD, Dorothy Overall Wells Professor of Pediatrics and director of the Division of Pediatric Medical Genetics and Genomic Medicine.
“Setting up this laboratory has been a herculean task,” Hamid said. “Everyone who will utilize this service, which will be most physicians at Vanderbilt as genetic testing increases in future years, should be extremely thankful to this team and to Dr. Jeff Balser and the institutional leadership who had the vision to bring this service to VUMC.”
Hamid and his team have been important partners in developing processes for ordering the testing, Seegmiller said.
In addition to improving the quality and speed of genetic testing, having clinical genomics capabilities at VUMC will ensure that genomic data is fully available for patient care and for future research.
“All the data that could have been going into BioVU (Vanderbilt’s DNA biobank and database of de-identified electronic health records) and that we could be using for research is lost to other vendors,” Zutter said.
“I refer to it as data mineral rights,” Stricker said. “By doing whole exome sequencing in-house, we’ll have all the data. As we move forward, we will be learning how to leverage this deep genetic data for clinical decision-making and for research opportunities.”
Neil Patel, MD, MPH, Chief Informatics Officer for VUMC HealthIT, and his team are developing systems to make the whole exome sequencing data available for both research and operations, for example for identifying known pharmacogenomic variants that affect response to medications.
“This is where genomic medicine is heading, and VUMC needs to be part of building these systems and processes,” Zutter said.
The operational team includes the Clinical Genomics Laboratory group (Stricker, Emily Schwedler and Ping Mayo), Hamid and Patel and their groups, genetic counselors to aid with interpreting results and communicating with clinicians and patients, and financial counselors to facilitate the authorization process for expensive genetic testing.
