title: Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing.
abstract: BACKGROUND
  Late-onset Pompe disease (LOPD) is a rare treatable lysosomal storage disorder characterized by progressive lysosomal glycogen accumulation and muscle weakness, with often a limb-girdle pattern. Despite published guidelines, testing for LOPD is often overlooked or delayed in adults, owing to its low frequency compared to other muscle disorders with similar muscle patterns. Next-generation sequencing has the capability to test concurrently for several muscle disorders. This could potentially lead to increased diagnosis of LOPD, disorders with non-specific muscle weakness or atypical patients.
  
  
  METHODS
  We developed a gene panel to further study its clinical utility in a cohort of patients with suspected muscle disorders. We designed a gene panel to analyze the coding sequences and splice site junctions of GAA causing LOPD, along with 77 other genes causing muscle disorders with overlapping phenotypes.
  
  
  RESULTS
  At a median coverage of ~200X (sequences per base), all GAA exons were successfully covered with >20X and only 0.3 % of exons across all genes were <20X. The panel showed an excellent sensitivity (100 %) and specificity (98 %) across all selected genes, using known variations in Pompe patients and controls. We determined its clinical utility by analyzing 34 patients with suspected muscle disorders of undetermined etiology and various muscle patterns, who were referred or followed in neuromuscular and genetics clinics. A putative diagnosis was found in up to 32 % of patients. The gene panel was instrumental in reaching a diagnosis in atypical patients, including one LOPD case. Acid alpha-glucosidase activity was used to confirm the molecular results in all patients.
  
  
  CONCLUSIONS
  This work highlights the high clinical utility of gene panels in patients with suspected muscle disorders and its potential to facilitate the diagnosis of patients showing non-specific muscle weakness or atypical phenotypes. We propose that gene panels should be used as a first-tier test in patients with suspected muscle disorders of undetermined etiology, which could further increase overall diagnosis of muscle conditions, and potentially reduce diagnostic delay. Further studies are necessary to determine the impact of first-tier gene panels on diagnostic delay and on treatment outcome for LOPD.
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada. Sebastien.A.Levesque@USherbrooke.ca.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lévesque
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Christiane
authors.initials: C
authors.lastname: Auray-Blais
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Elaine
authors.initials: E
authors.lastname: Gravel
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Michel
authors.initials: M
authors.lastname: Boutin
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Laura
authors.initials: L
authors.lastname: Dempsey-Nunez
authors.affiliation: Departments of Biology and Computer Science, Faculty of Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
authors.forename: Pierre-Etienne
authors.initials: PE
authors.lastname: Jacques
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Chenier
authors.affiliation: Department of Neurology, Notre-Dame Hospital, Université de Montréal, Montreal, QC, Canada.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Larue
authors.affiliation: Department of Neurology, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Rioux
authors.affiliation: Department of Pediatrics, Cumming School of Medicine, University of Calgary, and Alberta Children's Hospital, Calgary, AB, Canada.
authors.forename: Walla
authors.initials: W
authors.lastname: Al-Hertani
authors.affiliation: Department of Pediatrics, Division of Pediatric Neurology, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.
authors.forename: Amelie
authors.initials: A
authors.lastname: Nadeau
authors.affiliation: Neuromuscular Clinic, Centre de réadaptation en déficience physique de Jonquière, Saguenay, QC, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Mathieu
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Bruno
authors.initials: B
authors.lastname: Maranda
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Valérie
authors.initials: V
authors.lastname: Désilets
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, and Centre Hospitalier Universitaire de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, J1H 5N4, Canada.
authors.forename: Paula J
authors.initials: PJ
authors.lastname: Waters
authors.affiliation: Genzyme Corporation, a Sanofi Company, Cambridge, MA, USA.
authors.forename: Joan
authors.initials: J
authors.lastname: Keutzer
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Austin
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA.
authors.forename: Priya
authors.initials: P
authors.lastname: Kishnani
mesh_terms: D000293:Adolescent; D000328:Adult; D017668:Age of Onset; D002648:Child; D002675:Child, Preschool; D005260:Female; D006009:Glycogen Storage Disease Type II / Q000175:diagnosis*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007223:Infant; D008297:Male; D009135:Muscular Diseases / Q000175:diagnosis*; D055815:Young Adult
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