SLC37A4 SEQUENCING FOR GSD IB - FULL GENE
Label Name: SLC37A4GSD1b
Lab Discipline: Molecular Diagnostics
Institution:  Duke University Health System 
EAP ID:  LAB6826 
Last Review:  3/27/2017 10:57:55 PM
Specimen Type
  Whole Blood (EDTA)
Container & Volume
  Age Group   Container   Volume  
  0  - 18 Years LAVENDER TOP TUBE 2  ML
Label Reminders
  Be sure to include patient's name, history #, date and time of collection, and collector's initials.

Collection Notes
  All:
  • 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


SLC37A4GSD1b



No Reference Values
Methodology
  This assay uses PCR amplification followed by Sanger DNA sequencing to detect mutations in the SLC37A4 gene that cause glycogen storage disease type 1b (GSD Ib). This assay targets exons 1-6 and 8-9 of the SLC37A4 gene. These specific coding sequences and flanking intronic sequences (minimum of 20 base pairs) of the SLC37A4 gene are amplified from purified genomic DNA by PCR. The primers used in the PCR reactions contain M13 universal primer “tails” at their 5’ends, and have 3’ ends that are homologous to their genomic target sequence. The resulting PCR products are treated with an exonuclease/ phosphatase mixture to remove excess PCR primers and nucleotides. These purified DNA amplicons are then sequenced using universal M13 forward and reverse primers and the Big Dye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems). These products are then purified with the Big Dye XTerminator Purification Kit (Applied Biosystems) and resolved using the ABI 3130xl Genetic Analyzer. Data is analyzed using the ABI Data Collection software v3.0, Sequencing Analysis software v5.2 and SeqScape software v2.5. Sequences are compared to the reference DNA sequence (GenBank Accession: NT_33899.8; NM_001164277.1).

This test was developed and its performance characteristics determined by Duke Clinical Molecular Diagnostic 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
    Mutations within the SLC37A4 gene are associated with glycogen storage disease type Ib (GSD1b), an autosomal recessive disease characterized by a deficiency in glucose-6-phosphate translocase activity and a resulting accumulation of glycogen in the liver and kidneys, neutropenia, hypoglycemia, lactic acidosis, hyperuricemia and hyperlipidemia.

References:

Melis D, et al. Genotype/phenotype correlation in glycogen storage disease type 1b: a multicentre study and review of the literature. Eur J Pediatr. 2005; 164: 501–508.

   
Limitations
    Mutations in the SLC37A4 gene account for approximately 20% of all cases of GSDI cases (including GSD1a and GSD1b). Sequence analysis of the SLC37A4 gene detects approximately 94% of all SLC37A4 mutations that cause GSD1b. Therefore, the probability that no mutations in SLC37A4 are detected an individual with GSD1b is less than 1%.

These results are not intended to be used as sole criteria for clinical diagnosis or patient management decisions and are not a substitute for a physician's judgment and clinical experience. Correlation with other laboratory testing or clinical findings is required.

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 SLC37A4 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 SLC37A4 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. Poor genomic DNA quality or quantity, the presence of PCR inhibitors, and mutations or polymorphisms in the PCR primer binding sequences can result in un-interpretable or (rarely) inaccurate results.
   
Test Synonyms
  Synonym(s): glycogen storage disease 1b
Synonym(s): GSD 1b
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: