Key result
Targeted 45-gene panel sequencing detects pathogenic mutations in ~35% of undiagnosed myopathies, matching exome sequencing.
Why the study?
Molecular diagnostics for genetic myopathies require efficient sequencing of large complex genes, and the comparative efficiency of targeted re-sequencing versus exome sequencing needed evaluation.
Does a targeted re-sequencing emulsion PCR panel provide efficient molecular diagnostics compared to exome sequencing in patients with previously undiagnosed myopathies?
Observational (n=94)
Does a targeted re-sequencing emulsion PCR panel provide efficient molecular diagnostics compared to exome sequencing in patients with previously undiagnosed myopathies?
Exome sequencing is recommended as the standard approach for molecular diagnostics of myopathies due to similar costs, less laboratory processing time, and better read distribution compared to targeted re-sequencing.
May favor exome sequencing for technical reasons in myopathies; leaves open diagnostic yield gains versus targeted panels in larger studies.
BACKGROUND: Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. OBJECTIVE: To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. METHODS: We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. RESULTS: We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. CONCLUSIONS: Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.
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Punetha et al. (2016) conducted an observational in undiagnosed myopathies (n=94). Targeted re-sequencing (45 gene emulsion PCR myopathy panel) vs. Exome sequencing was evaluated on Detection of likely pathogenic mutations (molecular diagnostic rate). Targeted re-sequencing using a 45-gene panel detected likely pathogenic mutations in approximately 35% of patients with undiagnosed myopathies, a rate similar to exome sequencing.
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