Home >> ALL ISSUES >> 2017 Issues >> Targeted NGS or exome? Consider the clinical context

Targeted NGS or exome? Consider the clinical context

image_pdfCreate PDF

William Check, PhD

December 2017—American writer Maile Meloy published a short story collection in 2009 titled Both Ways Is the Only Way I Want It. Molecular pathology laboratory directors faced with the variety of next-generation sequencing diagnostic panels might feel similarly. As the main character in Meloy’s title story asks, “What kind of fool wanted it only one way?”

However, the clinical laboratory is much different from Meloy’s fictional world. Depending on patient mix and the lab’s financial and technical resources and personnel expertise, selecting one NGS platform rather than another can be the wisest move. “There are benefits to both targeted NGS and more comprehensive exome and genome analyses. The decision to lean one way or the other is mainly dependent on the clinical context,” says Linnea M. Baudhuin, PhD, co-director of the Personalized Genomics Laboratory at Mayo Clinic, Rochester, Minn. Dr. Baudhuin gave a presentation at this year’s annual scientific meeting of the American Association for Clinical Chemistry, in the session, “Pros and Cons of Targeted vs. Comprehensive Genetic Testing,” and spoke with CAP TODAY recently.

Next-generation sequencing instruments interactive product guide

She presented two cases from her own laboratory to illustrate the benefits and shortcomings of targeted NGS testing versus the use of exomes. She focused on inherited (germline) disorders, such as cardiomyopathies and aortopathies, rather than somatic diseases. For tumor (somatic) sequencing, targeted NGS is generally the best approach at this time, she said, because of the need for a fast turnaround and greater depth of coverage.

In case No. 1, Dr. Baudhuin described a 35-year-old male commercial airline pilot who came in for a routine physical examination, during which an abnormal ECG with prolonged QTc (470 to 560 msec) was discovered. Neither the pilot’s physical history nor his family history was remarkable. He was healthy with no unexplained syncope. In 2011 an expert consensus group recommended genetic testing for LQTS in such patients.

In Dr. Baudhuin’s laboratory, an LQTS targeted panel for 13 genes involved in LQTS identified a likely pathogenic variant in KCNH2. In comparing this with an off-the-shelf exome reagent, she noted that exome analysis would not have detected this variant in this patient, due to poor coverage in this region of the gene. Exome sequencing is prone to incomplete coverage over the exome, particularly in regions with highly repetitive stretches of DNA. In fact, Dr. Baudhuin said, “There’s no such thing as ‘whole exome’ sequencing. Most exome sequencing platforms really cover only 85 to 90 percent of the exome.” Data have shown that 50 percent of exons have lower than 30× average coverage. “We are looking for at least 40× coverage for the most part,” she said. Thus, because of low-coverage regions, “exome sequencing can miss critically important regions or variants.”

CAP TODAY
X