GLA SEQUENCING FOR FABRY DISEASE - FULL GENE
Label Name: GLA FABRY
Lab Discipline: Molecular Diagnostics
Institution:  Duke University Health System 
EAP ID:  LAB6372 
Last Review:  3/27/2017 10:13:55 PM
Specimen Type
  Whole Blood (EDTA)
Container & Volume
  Age Group   Container   Volume  
  0  - 18 Years LAVENDER TOP TUBE 3  ML
Patient Preparation
  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
  Deliver peripheral blood specimens to lab at ambient temperature. If there is a delay of more than 24 hours in delivery, refrigerate the sample. DO NOT FREEZE.
Turn Around Time -  Routine: 14 - 28 days   Stat: STAT is Unavailable
Reference Values


GLA FABRY



No Reference Values
Methodology
  This assay uses PCR amplification followed by Sanger DNA sequencing to detect mutations in the GLA gene that cause Fabry disease. The coding exons 1-7 and flanking intronic sequences (minimum of 20 base pairs) of the GLA gene are amplified from purified genomic DNA by PCR. The primers used in these 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 (ExoSAP-IT) 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 (ABI). These products are purified with the Big Dye XTerminator Purification Kit (ABI) and resolved using the ABI 3130xl Genetic Analyzer. Data is analyzed using the ABI Data Collection software v3.0, Sequencing Analysis software 5.2 and SeqScape software v2.6. Sequences are compared to the reference DNA sequence (GenBank Accession: NM_000169.2).

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

Fabry disease is an X-linked lysosomal storage disease characterized by the accumulation of glycosphingolipids due to alpha-galactosidase A deficiency. Disease prevalence is estimated at 1:40,000 - 50,000 males. Hemizygous males (classic form with <1% enzyme activity) begin showing symptoms in childhood or adolescence with periodic pain in the extremities, vascular cutaneous lesions (angiokeratomas), hypohydriosis, corneal and lenticular opacities, and proteinuria. Renal function diminishes with age, typically resulting in end-stage renal disease (ESRD). Symptoms may progress to cardiovascular and cerebrovascular disease, which can be fatal. Males with >1% activity are less severely affected and may present either with a cardiac variant (left ventricular hypertrophy and proteinuria presenting in the sixth to eighth decade) or a renal variant associated with ESRD. Heterozygous females range in disease severity from very mild manifestations with late-onset to disease symptoms comparable to hemizygous males.

Patients with clinical symptoms consistent with Fabry disease or deficient GLA enzyme activity as well as individuals with a family history of Fabry disease should be tested. In cases of known familial mutations, amniocytes from an at-risk pregnancy may also be tested.

Testing is performed by sequencing the -galactosidase (GLA) gene. The gene encoding GLA is found on Xq22, and spans 13kb of genomic DNA (7 exons, cDNA of 1290 bases). The GLA gene encodes a 429 amino acid protein, of which the first 31 residues form a lysosomal signal peptide. Classical phenotypes are typically caused by misssense, nonsense, severe splicing mutations and large gene defects. Variant phenotypes are typically caused by splicing defects that express residual enzyme activity. The coding sequences and flanking intronic sequences (minimum of 20 base pairs) of exons 1-7 of the GLA gene are amplified from purified genomic DNA and sequenced in the forward and reverse directions. Sequencing of a single exon is available for targeted mutation analysis. Patient sequences are compared to the reference DNA sequence (GenBank Accession: X14448, NM_000169.1).

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 Fabry disease; 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).

REFERENCES:

Zarate YA and Hopkin RJ (2008) Fabry's disease. The Lancet 372; 1427-1435
   
Indications
    Patients with clinical symptoms consistent with Fabry disease or deficient GLA enzyme activity as well as individuals with a family history of Fabry disease 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 GLA 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 GLA 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.

These results are not intended to be used as the 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.
   
Test Synonyms
  Synonym(s): alpha galactosidase
Synonym(s): Fabry
Synonym(s): galactosidase
Synonym(s): galactosidase A deficiency
Synonym(s): GLA
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

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