Next-generation sequencing (NGS) is becoming more prominent in the clinical laboratory. However, a difference is 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, NGS 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.
D. 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 Matthew Ferber, Ph.D., and Eric Klee, Ph.D. “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 just not real happy with 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.”
Limitations of the chemistry are preventing them from moving to whole exome or whole genome platforms. “What ends up happening,” he 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 for more information on targeted panel testing and whole exome sequencing in next generation sequencing.