Targeted next generation sequencing (NGS) — a powerful genetics method that can identify mutations in several genes simultaneously — may help diagnose people with spinal muscular atrophy (SMA)-like symptoms who do not carry SMA-causative mutations, a Japanese study shows.
This low-cost, non-invasive, fast, and efficient approach might be useful for both research and clinical diagnosis of undiagnosed patients with symptoms associated with damage in lower motor neurons, which are nerve cells that connect the spinal cord with skeletal muscles, regulating voluntary movement.
The study, “Analysis of spinal muscular atrophy-like patients by targeted resequencing,” was published in the journal Brain and Development.
Damage in lower motor neurons is associated with several diseases, including SMA. Different diseases “with clinical symptoms similar to those of [lower motor neurons] disorders, including peripheral neuropathies, such as Charcot-Marie-Tooth disease (CMT), may mimic the clinical manifestations of SMA,” the researchers wrote.
Over the years, simple and effective genetic tests have been developed to confirm the diagnosis of SMA and other such diseases.
Conventional Sanger sequencing is useful for the diagnosis of people whose symptoms suggest the presence of diseases associated with mutations in only one or a few genes. However, “for patients with atypical [symptoms], with the possibility of several candidate genes or one large candidate gene, NGS assays offer better options,” the researchers wrote.
NGS is a more advanced technique that enables the rapid identification of mutations in multiple genes (including larger ones) simultaneously.
Japanese researchers set out to evaluate the usefulness of targeted NGS — focused on a pre-selected panel of disease-associated genes — in diagnosing people with SMA-like symptoms, but who did not carry SMA-causative mutations.
The study involved 157 people (from 147 families) with symptoms suggestive of SMA, and who were followed at Tokyo Women’s Medical University (TWMU).
SMA-specific genetic testing confirmed a SMA diagnosis in 86 of those people. Among the remaining 71 patients, the team conducted targeted-NGS in 12 of them (from eight families), who had no symptoms of damage in upper motor neurons and whose diagnosis remained unknown through other neuroimaging or conventional genetic tests.
Upper motor neurons originate in the brain and travel downward to connect with lower motor neurons in the spinal cord.
Targeted-NGS analyzed the presence of mutations in 4,813 genes linked to diseases associated with the patients’ symptoms. Sanger sequencing then was used to confirm the identified candidate mutations and to analyze their presence in the patients’ relatives to assess their inheritance pattern.
These analyses confirmed the diagnosis of diseases other than SMA in three boys from two families.
After exclusion of mutations found in genes not related to muscular diseases, two potentially disease-causative mutations in the TTN gene (c.6621delG, p. W2207Cfs*28 and c.23718T>A, p.F7906L) were both identified in twin brothers (age 6) while two new disease-causative mutations in the KIF1A gene (c.3871C>T, p. R1291C and c.3898G>A, p.V1300M) were detected in the third boy (age 10).
TTN protein is involved in muscle contraction, and TTN mutations are associated with several muscular diseases. Mutations in the KIF1A gene are associated with hereditary sensory neuropathy type 2C, spastic paraplegia 30, and mental retardation 9.
The team concluded that the boys’ clinical and genetic data suggested both twins had a mild type of congenital centronuclear myopathy, while the third boy had hereditary sensory neuropathy type 2C.
“We conclude that targeted NGS panels … can be used to detect mutations in undiagnosed patients with LMN [lower motor neurons] symptoms quickly, efficiently, at a low cost, and in a minimally invasive manner,” the researchers wrote.
They added that “[clinicians] can arrive at the causative gene mutation by examining the influence of each mutation of candidate genes and finally make an accurate diagnosis.”
While these broader methods are still very expensive, the researchers believe that future cost reductions in equipment and reagents, “WGS or WES may be more widely used to obtain diagnostic clues for undiagnosed diseases in clinical genetic practice.”