Targeted re-sequencing emulsion PCR panel for myopathies: Results in 94 cases | DuchenneXchange

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Scientific Articles

Targeted re-sequencing emulsion PCR panel for myopathies: Results in 94 cases

key information

source: Journal of Neuromuscular Diseases

year: 2016

authors: Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP

summary/abstract:

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.

organisation: Children's National Medical Center, USA; The George Washington University School of Medicine and Health Sciences, USA; University of Sydney, Australia; University of Melbourne, Australia; Porter Neuroscience Research Center, USA; National Institutes of Health, USA; Duke University Medical Center, USA; The University of Tennessee Health Science Center, USA; McMaster University, Neuromuscular Disease Clinic, Health Sciences Centre, Canada; Johannes Gutenberg University, Germany; Mossakowski Medical Research Centre, Polish Academy of Sciences, Poland

DOI: 10.3233/JND-160151

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