Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing

Abstract

Purpose: Glycogen storage disease (GSD) is an umbrella term for a group of genetic disorders that involve the abnormal metabolism of glycogen; to date, 23 types of GSD have been identified. The nonspecific clinical presentation of GSD and the lack of specific biomarkers mean that Sanger sequencing is now widely relied on for making a diagnosis. However, this gene-by-gene sequencing technique is both laborious and costly, which is a consequence of the number of genes to be sequenced and the large size of some genes. Methods:This work reports the use of massive parallel sequencing to diagnose patients at our laboratory in Spain using either a customized gene panel (targeted exome sequencing) or the Illumina Clinical-Exome TruSight One Gene Panel (clinical exome sequencing (CES)). Sequence variants were matched against biochemical and clinical hallmarks.Results: Pathogenic mutations were detected in 23 patients. Twenty-two mutations were recognized (mostly loss-of-function mutations), including 11 that were novel in GSD-associated genes. In addition, CES detected five patients with mutations in ALDOB, LIPA, NKX2-5, CPT2, or ANO5. Although these genes are not involved in GSD, they are associated with overlapping phenotypic characteristics such as hepatic, muscular, and cardiac dysfunction. Conclusions:These results show that next-generation sequencing, in combination with the detection of biochemical and clinical hallmarks, provides an accurate, high-throughput means of making genetic diagnoses of GSD and related diseases. Genet Med advance online publication 25 February 2016

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

“…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). At the same time, a well-known homozygous mutation in ANO5, responsible for a wide spectrum of disorders described under the umbrella term "anoctaminopathy" (38,39), was identified in a patient suspected of having glycogen storage disease because of the presence of glycogen containing vacuoles on muscle biopsy (40).…”

Large gene panel sequencing in clinical diagnostics—results from 501 consecutive cases

“…Recently, a large cohort from Saudi‐Arabia sequenced by custom large gene panels was reported to yield 43% of clinical diagnostic findings in a consanguineous population . In addition, large gene panels have been used in disease‐specific study groups . To our knowledge, however, there have been no published reports on the clinical utility of large gene panel sequencing in a large unselected diagnostic cohort from an outbred population.…”

“…11 In addition, large gene panels have been used in disease-specific study groups. 12,13 To our knowledge, however, there have been no published reports on the clinical utility of large gene panel sequencing in a large unselected diagnostic cohort from an outbred population. In this report, we aim to share our experience from the first 1.5 years of large gene panel sequencing in a clinical setting, which involved 501 cases.…”

Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants

“…With both panels, the libraries generated were sequenced using 150 bp paired-end reads employing the Illumina MiSeq or Nextseq500 NGS platforms. SNVs was annotated and subsequently filtered as previously described [ 26 ]. Variants were always confirmed by conventional Sanger sequencing employing both patient genomic DNA and that of their parents if available.…”