Label Name: GAA GSD II
Lab Discipline: Molecular Diagnostics
Institution:  Duke University Health System 
EAP ID:  LAB6356 
Last Review:  3/27/2017 10:05:19 PM
Specimen Type
Container & Volume
  Age Group   Container   Volume  
  0  - 18 Years LAVENDER TOP TUBE 3  ML
Label Reminders
  Be sure to include patient's name, history #, date and time of collection, and collector's initials.
Collection Notes
  • 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.
  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


No Reference Values
  This assay uses PCR amplification followed by Sanger DNA sequencing to detect mutations in the GAA gene that cause glycogen storage disease type II (Pompe Disease). The coding sequences and flanking intronic sequences (minimum of 20 base pairs) of the GAA 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
  • Additional Patient Information Required: 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

Pompe disease, also referred to as acid maltase deficiency or glycogen storage disease II, is an autosomal recessive disorder caused by mutations in the acid alpha glucosidase (GAA) gene. When the enzyme is deficient, lysosomal glycogen cannot be catabolized and accumulates in many tissues with skeletal, cardiac, and smooth muscle most prominently involved. Three clinically distinct subtypes are recognized. The infantile form is characterized by generalized hypotonia with muscle wasting, failure to thrive, and progressive hypertrophic cardiomyopathy. Massive storage of glycogen is seen in lysosomes of the heart, skeletal muscle, and liver. Patients with the juvenile form show skeletal muscle weakness in the first decade of life, but no cardiac involvement. The adult form is characterized by a much later onset (typically the third decade of life) with progressive muscle weakness. Both the juvenile and adult forms of the disease are associated with some residual enzyme activity. The combined incidence of all forms of Pompe disease is estimated to be 1:40,000. Over 100 different mutations in the GAA gene have been described in the literature, causing a spectrum of disease. Mutation analysis is important for disease diagnosis, management, and family studies including prenatal testing. In some cases in which the familial mutations are known, the analysis of one or two exons of the gene may be performed in lieu of full gene sequencing.


A definitive diagnosis of Pompe disease can made through full sequencing of the GAA gene. A definitive diagnosis can aid physicians in management and treatment (including enzyme replace therapy) of patients with Pompe disease.

Precise knowledge of the disease causing mutations in an individual can aid in the genetic counseling of parents and family members. Because Pompe disease is inherited as an autosomal recessive condition, the parents of children with Pompe disease are obligate carriers of the disorder and have a ¼ chance with each pregnancy of having another child with Pompe disease. Unaffected siblings of affected individuals have a 2/3 chance of being a carrier for Pompe disease.


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 Pompe 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).


Van Der Ploeg and Reuser (2008) Pompe’s disease. Lancet 11;372(9646):1342-1352.
    Patients with clinical symptoms consistent with Pompe disease or deficient GAA enzyme activity as well as individuals with a family history of Pompe disease should be tested. In cases of known familial mutations, amniocytes from an at-risk pregnancy may also be tested.
    The sensitivity of DNA sequencing is high for the detection of nucleotide base changes and small deletions and insertions in the regions analyzed. Only the coding regions of the GAA gene and immediate flanking intronic sequences are 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 GAA would not be identified. Large deletions, duplications, multiple exon insertions, sequence alterations adversely affected primer binding, and complete deletion of one allele may not be identified using these methods. Using a similar sequencing strategy, Hermans et al. identified 53 of the 58 mutant alleles in 29 unrelated patients with either infantile or adult-onset Pompe disease, indicating that 91% of disease-causing alleles can be detected by full gene sequencing. Hermans et al. (2004) Human Mutation 23:47-56.

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.

Test Synonyms
Synonym(s): glyocgen storage disease II
Synonym(s): Pompe
Molecular Diagnostics Laboratory

Medical Director:
 Michael Datto, M.D., Ph.D.
 Phone: 919-684-6965
Lab Director:
 Catherine Rehder Ph.D, FACMG
 Phone: 919-613-8434
Lab Director:
 Siby Sebastian Ph.D., DABMG
 Phone: 919-613-8432

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

Performing Times: