Bringing Advanced Genomic Sequencing In-house

Bringing Advanced Genomic Sequencing In-house
New lab will aid diagnosis, research for genetically inherited conditions.

The recent launch of a Clinical Genomics Laboratory to provide specialized diagnostic testing for genetic conditions using whole exome sequencing (WES) makes Vanderbilt University Medical Center one of the few academic medical centers nationally to offer WES in-house.

Thomas Stricker, M.D., medical director of the laboratory, says that performing the sequencing on-site saves considerable time and enhances security and control over quality and gene panel selection. It also allows Vanderbilt to amass a large, de-identified database of whole exomes for research.

“With their consent, patients’ clinical sequencing data will be linked to the EHR data. This union of clinical and genomic data will augment BioVU and other clinical genomic initiatives at Vanderbilt, and drive improvements in medicine for our patients,” Stricker said.

Panel Offerings

The laboratory’s initial focus is pediatric services, where demand is highest. “Mostly, we are testing children with confounding symptoms that have eluded diagnosis through smaller genetic panels,” Stricker said. “We have already had some early successes in helping clinicians finally solve what is often a diagnostic odyssey for the family.”

“We have already had some early successes in helping clinicians finally solve what is often a diagnostic odyssey for the family.”

By year-end, Vanderbilt hopes to offer disease-specific panels for pediatric and adult patients, with the menu growing over the next few years. These will test for variants associated with the most widespread genetically inherited diseases, such as cancer, cardiomyopathy, arrhythmia, epilepsy and intellectual disability.

Only specific genes on each panel will be analyzed and reported to the physician and patient. The rest of the exome will be available for both research and additional clinical testing, if necessary.

Up and Running

The process of getting a genomics lab up and running is actually more complicated than the work of analyzing the exome, Stricker says. “Launching this laboratory has been a combined effort between pathology, finance, pediatric genetics, health IT and others, with a lot of planning tools, meetings and conversations to design a system that works for us.”

The workflow must account for many components: placing orders, linking to the EHR, navigating insurance preauthorizations, maintaining privacy, and establishing a fail-safe consent process. All of these depend on multiple units merging their expertise and providing ongoing support. The consent process and preauthorization can be challenging, Stricker says. “This level of diagnostic work is a leap ahead of coding and insurance company practices, so approvals are on a case-by-case basis.”

Administrative challenges met, the laboratory is only as good as the sequencing instrument itself, says Adam Seegmiller, M.D., vice chair of clinical pathology. Seegmiller calls Vanderbilt’s WES system “one of the most advanced on the market today, with a high-throughput and capacity that we anticipate needing as our services expand.”

Services and Safeguards

Vanderbilt’s genetic counselors play a crucial role in guiding referring physicians and patients through the testing decision process, reviewing privacy safeguards and explaining how consent to share sequencing data may have the added benefit of advancing population health goals. Besides offering rich data for use in genetic disease research, testing enables a physician to later order different panels derived from the patient’s already sequenced exome.

Stricker foresees a time when sequence data will be further integrated with the EHR to help improve pharmacogenetic and other treatment decisions in real-time. “I think at Vanderbilt we have the best EHR that exists today, but advances in integration and decision support are needed,” he said.

“Vanderbilt is a leader in this integration of genomic data into clinical medicine, and I hope the Clinical Genomics Laboratory will play an important role in this endeavor,” he added.