Targeted Sequencing Panel May Aid Diagnosis of Movement Disorders

A high-coverage sequencing panel is a useful and efficient means to identify genes associated with movement disorders, according to a study published online June 18 in JAMA Neurology. The authors say the panel was a cost-effective diagnostic alternative to whole-exome and whole-genome sequencing (WES and WGS).

Movement disorders, including Parkinson’s disease, are known for their marked heterogeneity in genotype and phenotype, which complicate diagnosis. The authors say that molecular diagnosis by standard Sanger sequencing is “tedious, time consuming, and inefficient,” plus analyses of the known implicated genes are not yet always routinely available. Further, they say that that variants of unknown significance (VUS) uncovered using WES and WGS can complicate return of results.

So, the French researchers developed a targeted sequencing approach using a panel of 127 genes involved in movement disorders and evaluated its performance in a cohort of 378 patients seen at tertiary movement disorder clinics (September 2014 to July 2016). Patients had at least one chronic movement disorder and had an age at onset younger than 40 years and/or a family history of movement disorders (37 percent). Patients were classified as parkinsonism, dystonia, chorea, paroxysmal movement disorder, and myoclonus. Twenty-three patients suspected of having inherited cerebellar ataxia underwent WES. Using a Hiseq 4000 Sequencing System (Illumina) the researchers achieved a mean depth of coverage of 1266 × with a mean of 99.7% of targeted regions well covered in each patient (× >30).

The diagnostic yield was 22 percent and uncovered 49 novel pathogenic variants.

Patients diagnosed with pathogenic variants were significantly younger versus patients without diagnosis (median age, 27 versus 35 years). Diagnostic yield was also significantly lower in patients with dystonia versus the overall cohort and the parkinsonism group.

The 49 novel probable pathogenic variants were identified most commonly in PARKIN, GBA, and LRRK2 genes. A total of 74 VUS were identified in 60 other patients. WES analysis of the cohort of 23 patients with cerebellar ataxia had an overall diagnostic yield of 26 percent, similar to panel analysis; however, the cost was much greater.

“The high depth of coverage and the smaller portion of poorly covered regions achieved with our strategy ensure a high sensitivity and specificity of detecting pathogenic events in the regions of interest and enable the identification of single-nucleotide variants, indels, but also copy number variants, which remain a challenge in next-generation sequencing,” write the authors led by Solveig Montaut, M.D., from Hôpitaux Universitaires de Strasbourg in France.

The estimated cost of the gene panel strategy without labor costs was $156 per patient ($70 for reagents cost, $68 for run cost, and $18 for consumable items). For the WES cohort, the cost was between $850 and $1,113 per patient without labor costs. To complete the gene panel strategy for a series of 24 patients turnaround time varied between 2 to 3 full days, while data analysis of a series of six exomes required 7 to 10 days.

Takeaway: Targeted sequencing strategies may be more effective for diagnosis of movement disorders.