GBE1 SEQUENCING FOR GSD IV - FULL GENE
Label Name: GBE1 GSDIV
Lab Discipline: Molecular Diagnostics
Institution:  Duke University Health System 
EAP ID:  LAB6369 
Last Review:  3/27/2017 10:10:18 PM
Specimen Type
  Whole Blood (EDTA)
Container & Volume
  Age Group   Container   Volume  
  0  - 18 Years LAVENDER TOP TUBE 2  ML
Patient Preparation
  Be sure to include patient's name, history #, date and time of collection, and collector's initials.

 
Collection Notes
  Adult:
  • Peripheral Blood: One lavender-top EDTA tube (minimum of 3 mls) is required for testing. Forward unprocessed peripheral blood promptly to the laboratory at ambient temperatures. THE SPECIMEN CANNOT BE FROZEN. GREEN-TOP (HEPARIN) TUBES ARE NOT ACCEPTABLE FOR TESTING.

    Amniocytes: 2-4ml of amniotic fluid is required. Forward promptly at ambient temperature only. Contact the Laboratory for additional information and instructions on sample requirements and shipping instructions. SPECIMEN CANNOT BE FROZEN.

    Cultured amniocytes / fibroblasts: Please contact the Laboratory for sample requirements and shipping instructions.
 
Transport
  Please deliver to lab at ambient temperature. If there is a delay of more than 24 hours in delivery, please refrigerate the sample. DO NOT FREEZE!

Turn Around Time -  Routine: 14-28 days   Stat: N/A
Reference Values


GBE1 GSDIV



No Reference Values
Methodology
  This assay uses PCR amplification followed by Sanger DNA sequencing to detect mutations in the GBE1 gene that cause glycogen storage disease type IV. The coding sequences and flanking intronic sequences (minimum of 20 base pairs) of the GBE1 gene are amplified from purified genomic DNA by PCR. The primers used for PCR contain M13 universal primer "tails" at their 5' ends, and have 3' ends that are homologous to their genomic target sequence. PCR products are treated with an exonuclease/phosphatase mixture (ExoSAP-IT) and sequenced using universal M13 forward and reverse primers (M13 Forward/-20 and M13 Reverse/-27) with the Big Dye Terminator v3.1 Cycle Sequencing Kit. These products are purified with the Big Dye XTerminator Purification Kit and resolved using the ABI 3130xl Genetic Analyzer. Data is analyzed by the ABI Data Collection software v3.0, Sequencing Analysis software 5.2 and SeqScape software v2.6.

This test was developed and its performance characteristics determined by the DUHS Clinical Molecular Diagnostics Laboratory. It has not been cleared or approved by the U.S. Food and Drug Administration. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 ("CLIA") as qualified to perform high complexity clinical testing.
   
Special Information
  All:
  • Additional Patient Information Required: Due to the unique nature of genetic testing, patients offered this test should receive pre-test and post-test genetic counseling. Counseling should help the patient understand the strengths and limitations of DNA testing and the medical implications for the patient as well as for other family members. Patients are also required to give consent for testing.
 
   
Clinical Significance and Interpretive Data
    BACKGROUND

Glycogen storage disease type IV, also known as Andersen disease, is an autosomal recessive disease with many different clinical manifestations. The typical clinical presentation is liver dysfunction which manifests in early childhood and often progresses to lethal cirrhosis. Neuromuscular dysfunction is also seen in GSD IV and is classified by age of onset into the perinatal, congenital, childhood, and adult forms. The perinatal neuromuscular form manifests as fetal hydrops, multiple limb contractures, alterations in muscle tone, and eventual perinatal death. The congenital neuromuscular form presents with severe hypotonia, neuronal involvement, and occasionally cardiomyopathy with eventual death in early infancy. With the childhood neuromuscular form, myopathy, neuropathy, and cardiomyopathy are the most common symptoms. These symptoms usually manifest in late childhood. The adult neuromuscular form manifests as diffuse central and peripheral nervous system dysfunction accompanied by the accumulation of polyglucosan bodies in the nervous system (so-called adult polyglucosan body disease).

Glycogen storage disease type IV is caused by a deficiency in the activity of the glycogen branching enzyme, GBE1. This enzyme is involved in glycogen synthesis. It catalyzes the hydrolysis of alpha-1,4 glycogen bonds and the formation of alpha-1,6 glycogen bonds, thus creating branches in the glycogen chain. Branching of the glycogen chain increases its solubility. Deficient activity of this enzyme results in tissue accumulation of abnormal glycogen with fewer branching points which in turn causes dysfunction of the affected tissues. The precise molecular basis for the tissue dysfunction is not well understood.

Deficient glycogen branching enzyme activity is caused by mutations in the glycogen branching enzyme gene (GBE1) located on chromosome 3p12. At least 20 different mutations causing glycogen storage disease type IV have been identified so far in GBE1. Missense mutations, nonsense mutations, frameshift mutations, and insertions have all been implicated in this disease. These mutations are located throughout the length of the gene. Some studies suggest that some missense mutations may lead to preservation of some enzyme activity and a milder phenotype. Thus, DNA sequencing of the GBE1 gene will provide a comprehensive molecular genetic analysis rendering accurate disease diagnosis and/or information for genetic counseling to the family members of individuals affected with glycogen storage disease type IV.

INTERPRETATION:

Coding and flanking intronic sequences are compared to a reference sequence. Sequence changes found in these regions will be reported as (1) known disease-causing mutations, (2) a mutation previously unreported, but of the type expected to cause GSD IV; i.e. frameshift mutations, nonsense mutations, etc. (3) sequence variation of uncertain clinical significance, or (4) benign polymorphisms. Variants of uncertain clinical significance may require additional studies including gene sequencing of other family members or other functional studies. All sequence changes, with the exception of benign polymorphisms, are confirmed by reamplification and resequencing of the relevant exon(s).
   
Indications
    Patients with clinical symptoms consistent with Pompe disease or deficient GBE enzyme activity as well as individuals with a family history of GSD IV should be tested. In cases of known familial mutations, amniocytes from an at-risk pregnancy may also be tested.
   
Limitations
    The sensitivity and specificity of DNA sequencing is high for the detection of nucleotide base changes, small deletions and insertions in the regions analyzed. Only the coding regions of the GBE1 gene and immediate flanking intronic sequences were examined. Changes in the promoter region, farther into the introns, or in other non-coding regions of the gene, would not be detected. Mutations in genes other than GBE1 would not be identified. Large deletions, duplications, multiple exon insertions, sequence alterations adversely affecting primer binding, and complete deletion of one allele may not be identified using these methods. Mutations or polymorphisms in the DNA oligonucleotide primer binding regions, poor DNA quality, insufficient DNA quantity or the presence of PCR inhibitors can result in uninterpretable or (rarely) inaccurate results.

Due to the rarity of GSD IV, and the lack of comprehensive published sequencing and deletion mutation analysis, the exact percentage of cases that would not be detected by DNA sequencing alone is not known. For this reason, parallel biochemical enzyme testing is highly recommended.
   
Test Synonyms
  Synonym(s): Adult Polyglucosan Body Disease
Synonym(s): Andersen Disease
Synonym(s): Glycogen storage disease
Synonym(s): GSD
Synonym(s): GSDIV
Molecular Diagnostics Laboratory
(MDX)

Medical Director:
 Michael Datto, M.D., Ph.D.
 Phone: 919-684-6965
 Email: michael.datto@duke.edu
Lab Director:
 Catherine Rehder Ph.D, FACMG
 Phone: 919-613-8434
 Email: catherine.rehder@duke.edu
Lab Director:
 Siby Sebastian Ph.D., DABMG
 Phone: 919-613-8432
 Email: siby.s@duke.edu

Address: 
 Wadsworth Bldg, Cytogenetics, Rm 0220
 2351 Erwin Rd
 Durham,  NC  27705
 Phone: 919-684-2698
 FAX: 919-668-5424

Performing Times: