Better Genomic Diagnostics for Alabama

By Christina Crowe

QIAGEN QIASYMPHONY SP Sample Preparation/DNA RNA PurificationGenomic diagnostics are poised to play an increased role in precision medicine at UAB and throughout the state, if Alexander “Craig” Mackinnon, M.D., Ph.D., division director, Genomic Diagnostics and Bioinformatics has anything to say about it. Last year we brought you the story of how Mackinnon joined the Department of Pathology and under the leadership of George Netto, M.D., Robert and Ruth Anderson Endowed Chair, outlined several initiatives for 2020, including the creation of a precision diagnostics laboratory. That plan was part of Netto’s vision for the department when he came to serve as chair four years ago.

At the start of 2020, those plans were coming together with an expansion of laboratory space in West Pavilion underway and a signed agreement between several departments and UAB Hospital to support the creation of a larger, freestanding space.

Then COVID hit, and everyone’s priorities shifted. The Division of Genomic Diagnostics pivoted to assist the department’s and institution’s efforts to provide COVID testing by identifying information technology support for the GuideSafe program. With funding from the CARES (Coronavirus Aid, Relief and Economic Security) Act, the department and other hospital labs purchased a laboratory information management system (LIMS) and several instruments to allow for DNA/RNA extraction and high-throughput testing of biological samples, which Pathology’s faculty and staff helped take online (see sidebar).

“As much as the lab work is so crucial, managing the work flow is another component of successfully handling the large volumes of tests that we continue to do at UAB,” Mackinnon says. He and colleagues Shuko Harada, M.D., professor, Diana Morlote, M.D., assistant professor, GDB, and Sixto Leal, M.D., Ph.D., helped design programs and processes to take these new machines live and coordinate the dozens of laboratory staff running them. This includes informatics support by joint faculty member Elizabeth Worthey, Ph.D., associate professor and Informatics section head, Pathology and Pediatrics.

"You can generate a lot of data that will live in Alabama, rather than sending the work out of state to third-party reference labs."

 

The acquisition of these instruments will allow UAB to become a so-called “COVID Center of Excellence,” Mackinnon says, which will have the capacity to avoid issues such as the complete cessation of work due to a supply issue, such as a plastic tube shortage, for example. “These machines allow for a great deal of testing for Alabama,” he says, “and the sequencing machines can do rapid COVID sequencing.”

What does this mean? Mackinnon offers the example of a nurse working in a pediatric intensive care unit where a COVID outbreak affects the patients and nursing staff. “If the patient transmitted COVID to the nurse, this would indicate the unit’s preventative measures are failing,” he states. Alternatively, the individuals could be independently infected.

“You need to know the difference. By having COVID sequencing capabilities at UAB, we are able to sequence the COVID viral genome in both patients and compare the sequencing results. I think that has a huge benefit for managing outbreak.”

The instruments do not work exclusively on COVID, of course, but for any type of viral infection or other diseases. “From a molecular genetics standpoint, what’s cool about viruses and other infectious organisms,” Mackinnon says, “is that you can identify the organism by the sequencing, and then work to pinpoint its origin and isolate it.”

The sequencers UAB has acquired allow for fast turnaround times delivering results in 24-36 hours rather than the standard, which can be up to 7 days. This benefits the entire state, he argues. “Alabama has long been an underserved state with populations that can be hard to reach. Now with GuideSafe in place, combined with these test capabilities and instrumentation, we have the capacity to become a regional genomic diagnostic center,” he says.

Returning to the shared vision of a freestanding Genomic Diagnostics Laboratory (GDL), Mackinnon praises institution and hospital leadership for allowing for the renovation of 1,000 square feet in West Pavilion this year, and the acquisition of two pieces of equipment that will help promote tumor cancer genetics and pharmacogenomics. Staff are also being hired to help with this expansion, which Mackinnon calls, “a bridge- but it’s short term.”

The longer-term goal is a freestanding GDL in the former Southern Research building purchased by UAB Health System in February, as part of a block of properties along University Boulevard between 22^nd Street and 23^rd Street South. Mackinnon is working on approval to make this multimillion-dollar renovation to a 24,000-square-foot space a reality.

“What we’re doing with molecular medicine is important for the state because 1) it keeps us relevant with the high cancer and disease burden we have in our patient population, and 2) it can create added benefits for the state through commercialization of intellectual property, collaborations with drug companies on clinical trials, and partnerships with UAB affiliates. You can generate a lot of data that will live in Alabama, rather than sending the work out of state to third-party reference labs.”

The plan is to integrate efforts from the departments of Pathology, Genetics, Pediatrics, and the UAB Hospital, Mackinnon says. Pathology would occupy space in a newly designed clinical genetics lab to do molecular oncology (tumor testing); molecular microbiology (including continued COVID testing); pharmacogenomics, which look at how a patient’s genetic makeup influences how he or she metabolizes drugs; and bioinformatics.

A key to success for this collaboration will be a strategy for reimbursement for the testing, Mackinnon says, but to stay competitive with other healthcare systems nationwide, this next generation of tools is a must.

“This is not just another lab test,” he says. “We can take this testing and identify how to impact and improve patient care.”

 The New Tools

These instruments were acquired by UAB Pathology and UAB Hospital Labs during 2020 with funding support from the CARES Act.

Janis G3 Primary Sample

Provides safe and traceable barcode scanning and reformatting of up to 192 input biological samples from nasoparyngeal, oropharungeal, and anterior nasal swabs into various destination labware to support viral nucleic acid extraction. 

JANUS 3G qPCR Workstation

Enables traceable and reproducible real-time PCR sample preparation for high-throughput SARS-CoV-2 detection. This automated workstation offers walkaway PCR sample prep while reducing the risk of hands-on errors. 

Chemagic 360

An innovative system with a small footprint that can be adapted to fit most nucleaic acid purification needs. Provides high yields of ultra-pure nucleic acids suitable for a wide range of downstream applications, such as NGS, MLPA, genotyping, and PCR. 

ZEPHYR G3 NGS

A compact, cost-effective multi-channel liquid handler ideal for key applications in compound management, HTS, genomics, proteomics, and bioanalytical assays. 

QUANTSTUDIO DX 96W FAST

A real-time PCR platform that offers flexibility, expandability, and high performance standards. 

GENEXUS SEQ System Instrument

The first turnkey next-generation sequencing (NGS) solution that automates the specimen-to-report workflow and delivers same-day results with just two user touchpoints. It makes it easy for your clinical research or testing lab to bring NGS in-house, regardless of expertise.