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February 11th, 2016

Next-Generation Sequencing: Targeted Panels Versus Whole Exome Sequencing

By Jeff Briggs

 

Two DNA StrandsNext-generation sequencing is becoming more prominent in the clinical laboratory, something we reported on recently on the Center for Individualized Medicine blog. With its unprecedented throughput, scalability, and speed, next-generation sequencing enables researchers to study biological systems at a level never before possible. Today's complex genomic research questions demand a depth of information beyond the capacity of traditional DNA sequencing technologies. Next-generation sequencing has filled that gap and become an everyday research tool to address these questions.

Now, we’re starting to see differences developing between its use when there is a defined phenotype, as with hereditary oncology syndromes or hereditary cardiovascular disorders, and its use in diagnosing hereditary developmental disorders. For example, in oncology, targeted panels remain the optimal mode of application, while in medical genetics, next-generation sequencing is moving beyond panels to whole exome sequencing and even to whole genome sequencing.

CAP TODAY reported on a recent Association for Molecular Pathology workshop, which compared the clinical utility of genomes versus exomes versus targeted panels and how decisions are being made for one or the other in diagnosing inherited disorders.

Brian Dawson, Ph.D., co-director of Mayo Clinic’s molecular genetics laboratory and an associate professor of laboratory medicine and pathology and medical genetics, was the workshop organizer. According to Dr. Dawson, the speakers “presented strengths and weaknesses of both approaches” — which is helpful to hear for those who are just getting into whole exome sequencing or targeted panels using next-generation sequencing.

Currently, Mayo Clinic is mainly developing targeted panels for a variety of disorders. Mayo offers whole exome sequencing through the Center for Individualized Medicine but is preparing to offer whole exome sequencing in the Department of Laboratory Medicine and Pathology through the efforts of a team led by genomic scientist Matthew Ferber, Ph.D., associate director at the Center for Individualized Medicine, and Eric Klee, Ph.D., co-director of Mayo Clinic's clinical next-generation sequencing laboratory.

Dr. Brian Dawson

Dr. Brian Dawson

“We will start with trio analysis, mainly for diagnostic odyssey cases,” Dr. Dawson says. “We have looked at trying to develop panels out of whole exome sequencing. We were not really happy with the depth of coverage.”

He says there may be a way to do that down the line.

In Mayo’s molecular genetics laboratory, a minimum coverage of 100× is currently the goal for inherited disease target panels. “If we go lower than 100×,” Dr. Dawson says, “we need to be transparent about that to our clinicians. Some of the literature suggests that in some cases even small insertions and deletions need depth of coverage greater than 100× to detect them routinely.”

Commenting on cost, Dr. Dawson says, “Certainly with large panels we know exactly what genes we will be looking at, and we know the cost of the bioinformatic component up front.” With whole exome sequencing, that can change during the investigation. Then, too, “Some targeted panels are getting CPT codes. In that situation certain genes must be included, so hopefully you know about that ahead of time.”

“CPT codes” is a common term in the lab for Current Procedural Terminology codes, which are medical codes used to report medical, surgical, and diagnostic procedures and services to entities such as physicians, health insurance companies, and accreditation organizations. CPT codes are used in conjunction with numerical diagnostic coding during the electronic medical billing process.

Limitations of the chemistry are preventing the lab from moving to whole exome or whole genome platforms. “What ends up happening,” Dr. Dawson says, “is that the more sequences you do, the more the depth of coverage decreases. For a targeted panel, you can have much higher depth of coverage for specific genes of interest. And depth of coverage impacts our ability to detect genetic alterations.”

On the optimistic side, Dr. Dawson adds, “We are getting pretty close to reliably detecting copy number variants with some algorithms.” The methods that have been optimized for coverage, however, may not be the best for determining copy number variants. “Better algorithms plus enhanced sequencing should allow us to start calling copy number variants soon.”

Read the full article from CAP TODAY for more information on targeted panel testing and whole exome sequencing in next generation sequencing.

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Much of this article came via Mayo Medical Laboratories. To stay abreast of the latest developments at Mayo Medical Laboratories, follow all the news on its excellent blog.

 

Tags: center for individualized medicine, DNA, DNA Sequencing, Dr. Brian Dawson, Dr. Eric Klee, Dr. Matthew Ferber, gene sequencing, mayo medical laboratories, MML, next generation sequencing, Uncategorized, whole exome sequencing

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