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Pompe Disease Mutation Analysis (GAA) by Sequencing – Full Sequencing



Pompe disease is an inborn error of glycogen metabolism due to a deficiency of acid alpha-glucosidase. In the infantile form, clinical symptoms include hypotonia, failure to thrive and progressive hypertrophic cardiomyopathy. The late-onset form can present from childhood through adulthood with progressive muscle weakness and respiratory dysfunction. The physical disability is varied and does not directly correlate with chronological age.

Test Details


Indications for Pompe disease mutation analysis by sequencing include: Individuals with a family history or clinical characteristics of Pompe disease, or individuals who have tested positive for GAA deficiency by enzyme test or newborn screening assays.

Specimen Requirements


Whole blood, amniotic fluid culture, chorionic villi culture.  

Note: when ordering Pompe disease gene sequencing for prenatal samples, cultures will be needed.


10 mL whole blood or two T-25 flasks of confluent fetal cells


Lavender-top (EDTA) tube or yellow-top (ACD-A) tube

Special Instructions

Prenatal testing: Integrated Genetics clients should call 800-848-4436 to speak to a laboratory genetic coordinator before collecting any specimens.   In some circumstances, specimens from other family members may be required.  In cases in which there is a known mutation that can be documented, the physician may prefer to order Pompe disease partial gene sequencing.

All prenatal specimens (including cord blood) must be accompanied by a maternal blood or mouthwash specimen for analysis of possible maternal cell contamination. 

Discard first 2 mL; then 15 mL amniotic fluid in 15 ml orange-top polypropylene tube, 10-15 mg chorionic villi in laboratory-provided screw-top tubes with sterile transport medium or two T-25 flask of confluent cells.  Note: When ordering full Pompe disease gene sequencing for prenatal samples, cultures will be needed. 

Additional sample must be obtained for back-up culture at one of our cytogenetics laboratories or another facility.  If additional testing is desired, more amniotic fluid is needed. For example, chromosome analysis requires an additional 15-25 mL (see Cytogenetics – Amniotic Fluid Chromosome Analysis test page) and AFAFP requires an additional 2 mL (see Amniotic Fluid Alpha-Fetoprotein - AFAFP test page). 

Causes for Rejection

Frozen specimen; hemolysis; quantity not sufficient for analysis; improper container; unlabeled or mislabeled specimen

Storage Instructions

Maintain specimen at room temperature.

Additional Information

Treatment is available for symptomatic individuals with Pompe disease.


False positive or false negative results may occur for reasons that include: genetic variants, technical handling, blood transfusions, bone marrow transplantation, mislabeling of samples, or erroneous representation of family relationships. This method does not reliably detect mosaic variants; large deletions; large duplications, inversions, or other rearrangements; or deep intronic variants



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