The Latin American experience with a next generation sequencing genetic panel for recessive limb-girdle muscular weakness and Pompe disease

Abstract

Background: Limb-girdle muscular dystrophy (LGMD) is a group of neuromuscular disorders of heterogeneous genetic etiology with more than 30 directly related genes. LGMD is characterized by progressive muscle weakness involving the shoulder and pelvic girdles. An important differential diagnosis among patients presenting with proximal muscle weakness (PMW) is late-onset Pompe disease (LOPD), a rare neuromuscular glycogen storage disorder, which often presents with early respiratory insufficiency in addition to PMW. Patients with PMW, with or without respiratory symptoms, were included in this study of Latin American patients to evaluate the profile of variants for the included genes related to LGMD recessive (R) and LOPD and the frequency of variants in each gene among this patient population. Results: Over 20 institutions across Latin America (Brazil, Argentina, Peru, Ecuador, Mexico, and Chile) enrolled 2103 individuals during 2016 and 2017. Nine autosomal recessive LGMDs and Pompe disease were investigated in a 10gene panel (ANO5, CAPN3, DYSF, FKRP, GAA, SGCA, SGCB, SGCD, SGCG, TCAP) based on reported disease frequency in Latin America. Sequencing was performed with Illumina's NextSeq500 and variants were classified according to ACMG guidelines; pathogenic and likely pathogenic were treated as one category (P) and variants of unknown significance (VUS) are described. Genetic variants were identified in 55.8% of patients, with 16% receiving a definitive molecular diagnosis; 39.8% had VUS. Nine patients were identified with Pompe disease. Conclusions: The results demonstrate the effectiveness of this targeted genetic panel and the importance of including Pompe disease in the differential diagnosis for patients presenting with PMW.

Sequential targeted exome sequencing of 1001 patients affected by unexplained limb-girdle weakness

“…No SNVs and only one CNV were identified in the SGCD gene, in keeping with other sequencing projects from China (n = 756), 24 Italy (n = 504), 6 and the United States (n = 4656) 7 where no SGCD variants were found. Interestingly, LGMD R6 δ-sarcoglycan-related patients accounted for >1% of the diagnosed cases in a South American cohort (n = 2103), 25 highlighting that the geography-specific prevalence of some diseases should be considered during clinical work-ups. Per sex bias, we corroborated previous findings that ANO5 diagnosis is more frequent in males.…”

Highlights on Genomics Applications for Lysosomal Storage Diseases

“…This is particularly useful when applied to specific diagnostic contexts, including carrier screening studies in high-risk populations (e.g., the Ashkenazi Jewish population) [ 60 , 61 ], prenatal diagnosis [ 62 ], unsolved cases where traditional molecular diagnostic approaches have failed [ 63 ], unclear or suspected LSD cases [ 64 , 65 ], as well as in defining genotype–phenotype correlations [ 66 ] or to find out genetic disease modifiers [ 67 ]. More interesting is the use of NGS to differentiate genetically heterogeneous diseases with overlapping clinical phenotypes, such as Pompe disease, limb-girdle muscular dystrophies [ 68 , 69 ], and Gangliosidosis [ 70 ], or to investigate mosaic conditions [ 71 , 72 ]. Many companies developed commercial panels and offer direct-to-consumer sequencing services for suspected LSD cases, utilizing custom panels that target few or many genes (causative genes, lysosomal pathway-related genes, or peroxisome disorder-related genes) and are based on arbitrary research ( Supplementary Table S2 ).…”

Cardiomyopathy in limb girdle muscular dystrophy R9, FKRP related

“…The gene most commonly associated with disease is fukutin‐related protein ( FKRP ) . FKRP mutations rarely cause congenital muscular dystrophy (MDC1C), and more typically cause limb girdle muscular dystrophy type R9 (LGMDR9), which is one of the more common types of LGMD 4‐10 . There is a common founder FKRP mutation, c.826C>A (p. L276I), which is present in at least one copy in most patients with LGMDR9 8,11 …”

“…FKRP mutations rarely cause congenital muscular dystrophy (MDC1C), and more typically cause limb girdle muscular dystrophy type R9 (LGMDR9), which is one of the more common types of LGMD. [4][5][6][7][8][9][10] There is a common founder FKRP mutation, c.826C>A (p. L276I), which is present in at least one copy in most patients with LGMDR9. 8,11 Glycosylated α-dystroglycan is present in cardiac as well as skeletal muscle.…”