Whole Exome Sequencing Reveals Ultra-Rare Neuromuscular Disorders

Kevin M. Flanigan, MD
Kevin Flanigan, MD, director of the Neuromuscular Disorders program at Nationwide Children’s and senior author on this paper.

Traditionally, diagnosis of neuromuscular disorders follows a pattern: review the clinical phenotype and narrow down the likely options; run a targeted test for the suspected disorder; diagnose. In cases with challenging phenotypes or unresolved diagnoses after these initial assessments, many neuromuscular clinics resort to a range of additional tests, including microarray, electromyography, a muscle or nerve biopsy and next generation gene panel testing — a broader genetic screen capturing more of the possible single-gene neuromuscular diseases.

For patient families with inconclusive results throughout this battery of tests, it used to be the end of the road. Over the past several years, however, whole exome sequencing (WES) has become a clinically available test, offering physicians the chance to cast a much broader net in the search for genetic alterations at the root of a child’s symptoms. To find out whether the test offers clinically meaningful diagnostic utility, physician-scientists at Nationwide Children’s Hospital reviewed the results of four years of WES testing among patients in their Neuromuscular Disorders Clinic.

“There is a large subset of patients we can successfully diagnose by observing their phenotypes and matching them to a targeted gene test,” says Megan Waldrop, MD, a member of the Division of Neurology at Nationwide Children’s and first author on the Neuropediatrics paper detailing the study’s results. “But WES is a great tool for a select subset of patients with more complicated, complex phenotypes. Rather than having several tests and a very expensive diagnostic odyssey, WES allows us to get answers quickly.”

Dr. Waldrop and her colleagues obtained WES on 31 previously undiagnosed children with symptoms suggestive of a neuromuscular condition (hypotonia, weakness or gait disturbance) between 2013 and 2017. They used external commercial labs for the study but have since brought this testing in house, via the Nationwide Children’s Institute for Genomic Medicine, a program that enables shorter turnaround time for WES and other genetic screens, plus a bevy of resources for test interpretation. In all cases, patients had already undergone numerous other diagnostic tests with no success.

Twelve of the patients (39%) received a confirmed diagnosis based on WES findings, most commonly for genetic syndromes associated with myopathy or congenital myopathy (n=8), including three children (including two siblings) with the ultra-rare Vici syndrome. Two patients were diagnosed with central nervous system disorders. WES led to changes in the clinical management of numerous patients, including one who had had a long-standing presumptive diagnosis of mitochondrial disease.

“These were patients in whom our standard genetic testing algorithm did not show a result,” says Kevin Flanigan, MD, director of the Neuromuscular Disorders program at Nationwide Children’s and senior author on the paper. “WES is now a mature technology, and we think that, when it’s properly applied, WES can rapidly and economically shorten the diagnostic odyssey for parents and add to our understanding of the range of clinical phenotypes associated with mutations in given genes.”

Drs. Flanigan and Waldrop also suspect that using WES after initial failed gene panel tests, rather than moving on to invasive tests in between, is likely more cost-effective and beneficial for families. It should be noted, however, that WES is only useful in cases of single-gene disorders, rather than for broad syndromes that result in similar phenotypes. This may account for the substantial proportion of children who remain undiagnosed even after WES.

For some of these patients, Drs. Flanigan and Waldrop request whole genome sequencing — an expanded genomic screen analyzing billions of pieces of genetic code instead of the thousands studied by WES. The test is extremely resource intensive both in manpower and computational technology. While not yet available clinically due to its expense and experimental nature, it is offered through the Institute for Genomic Medicine as part of a research program for children who remain undiagnosed after exhausting all other options.

“We believe that additional gene therapies will be coming down the road in the coming years, so it’s important to identify as many patients as possible by their genetic disease traits,” says Dr. Flanigan, who is also director of the Center for Gene Therapy at Nationwide Children’s. “We want to give them the opportunity for participation in trials and treatments that will require a complete understanding of the genetic disorder a patient has. And similarly, as we identify syndromes associated with mutations in certain genes via WES, we can determine whether those genes are candidates to develop new gene therapies.”

Drs. Flanigan and Waldrop are not the only ones to use WES tests for clinical practice at Nationwide Children’s. The tests are often used by other neurologists to better classify epilepsy syndromes, and by hospital geneticists to probe for other rare diagnoses. The clinician-researchers believe their patients benefit from constant access to the expertise of the molecular geneticists and counselors in the Institute for Genomic Medicine, who help them rapidly gauge the significance of genetic abnormalities and pursue further testing if panels or WES find something interesting but nondefinitive.

“We have very comprehensive approach to help patients who remain without a clear diagnosis for neuromuscular disease symptoms,” says Dr. Flanigan, who welcomes referrals to assist with the diagnosis and management of patients with challenging phenotypes. “What is extraordinary for us is to have WES done internally, which makes a huge difference in coordination of care, cost and time.”

Drs. Flanigan and Waldrop also investigate genetic variants in neuromuscular conditions that result in dramatically different phenotypes, and they have plans to use WES to expand the catalog of known genotype-phenotype correlates for rare neuromuscular diseases.

Reference:

Waldrop MA, Pastore M, Schrader R, Sites E, Bartholomew D, Tsao CY, Flanigan KM. Diagnostic utility of whole exome sequencing in the neuromuscular clinic. Neuropediatrics, 21 Jan 2019. [E-pub ahead of print.]