Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing

Abstract

BackgroundLate-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.MethodsWe 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.ResultsAt 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.ConclusionThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13023-016-0390-6) contains supplementary material, which is available to authorized users.

Targeted gene panel screening is an effective tool to identify undiagnosed late onset Pompe disease

“…On the other hand, currently NGS-based strategies are largely adopted to study genetically heterogeneous conditions, including muscle diseases (14). Recent NGS data prove that 20-30% of myopathic patients carry causative mutations in genes typically not associated with the observed phenotype (16,(32)(33)(34). Many studies (32)(33)(34)(35)(36)(37) identified mutations in genes responsible for LOPD and other metabolic myopathies in patients with a wide range of phenotypes (Table 2).…”

Sensitivity of whole exome sequencing in detecting infantile- and late-onset Pompe disease

“…However, it should be noted that some of these commercially available gene panels are not necessarily designed to detect all deletion variants [15] or intronic pathogenic variants in the GAA gene, and thus may fail to detect them.…”

“…Recently, next generation sequencing (NGS)-based panels have been shown to facilitate the diagnosis of LOPD [15,16]. Whole-exome sequencing (WES) is now routinely ordered in clinic for many conditions including undiagnosed causes of myopathy and neurological indications [16–18], and has successfully diagnosed patients with Pompe disease [19].…”

Особливості Клініко-Лабораторної Діагностики Хвороби Помпе У Дітей

“…Ген, який кодує фермент GAA, картований на хромосомі 17q25.2-q25. 3., складається з 20 екзо-нів. Описані 360 мутацій, які спричиняють часткове або цілковите блокування каталітичної активності ферменту, зниження його стабільності та скорочен-ня періоду напіврозпаду [3].…”