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HelpTest Code LAB1892 Pompe DNA Sequencing
Clinical System Name
Pompe (GAA) Sequencing
Synonyms
Acid Alpha-Glucosidase Deficiency
Acid Maltase Deficiency
GAA Deficiency
GAA gene
GSD II
Glycogen Storage Disease type II
Glycogenosis Type II
Description
Pompe disease is caused by mutations in the GAA gene. Individuals with Pompe disease are unable to use the glycogen stored in the lysosomes for energy, resulting in the progressive storage of glycogen in the heart, liver, and skeletal muscle. Pompe disease can present in infancy with profound hypotonia, cardiomegaly and cardiomyopathy or later in childhood and adulthood with progressive muscle weakness and respiratory insufficiency.
Full gene sequencing - sequencing of all 20 exons and exon-intron boundaries of the GAA gene.
Also available: Targeted Gene Variant Sequencing (LAB1915) - For targeted analysis of variants previously identified through clinical testing of a family member or research testing of the individual. Please review requirements and restrictions for testing.
Sample Requirements
Note: For patients who have had a whole blood transfusion, wait 10 days post transfusion to draw for genetic testing. No wait time is necessary for blood or saliva collection if the patient received leuko-reduced red cells or plasma.
Specimen: Whole blood, cord blood
Container(s): Lavender/EDTA, Yellow/ACD A or B
Preferred Vol: 3 mL
Minimum Vol: 1 mL
Note: Heparin samples (Green tops) are unacceptable.
Specimen: Extracted DNA from EDTA blood
Minimum: 10µg
Note: Isolation of nucleic acids for clinical testing must be performed in a CLIA-certified
laboratory or a laboratory meeting equivalent requirements as determined by the CAP
and/or the CMS. DNA concentration minimum 50 µg/mL; 260/280 ratio 1.70-2.00.
Specimen: Cultured cells
Acceptable: Fibroblasts
Container(s): T-25 flasks
Preferred Vol: 2 flasks
Specimen: Saliva collected using Oragene Dx OGD-575/675 collection kit.
Container: Oragene Dx OGD-575/675 collection kit
IMPORTANT NOTE: Manufacturer instructions must be followed. The Oragene Dx OGD575/675 kit is not for children under 6 months. Contact Lab Client Services for more information or to obtain a kit 206-987-2617, labclientservices@seattlechildrens.org
Processing Instructions
Reject due to: Heparin
Spin: No
Aliquot: No
Temp: Refrigerate
Storage location: Molecular Genetics box in CPA refrigerator #2
Off-site collection: Refrigerate blood samples until ready to ship. Transport all sample types at room temperature via overnight shipping.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Cultured cells | Room temp | 3 days |
| Whole blood, extracted DNA | Room temp | 3-5 days |
| Whole blood, extracted DNA | Refrigerated | 7 days |
| Extracted DNA | Frozen | ok |
| Saliva, ORAgene Dx OGD-575/675 | Room Temp | 2 weeks |
Note: Whole blood samples > 7days may be submitted to be assessed by our lab for acceptability for testing.
Availability
| STAT | Performed | TAT |
|---|---|---|
| Contact lab | Monday - Friday | 2-3 weeks |
Performing Laboratory
Seattle Children's Laboratory
Department
Department: Molecular Genetics Laboratory
Phone: 206-987-3872
Lab Client Services: 206-987-2617
Lab Genetic Counselor: LabGC@seattlechildrens.org
CPT Codes
| GAA full gene seq | 81406 |
| GAA targeted variant analysis | 81403 |
Methodology
Method: Bi-directional sequencing of all exons and exon-intron boundaries. Full gene sequencing will identify two causative mutations in 83-93% of individuals with confirmed reduced or absent enzyme activity. Most mutations are point mutations but deletion of exon 18 accounts for 5-7% of alleles.
Limitations: Mutations in the promoter region, large deletions, large duplications, or rare recombinant mutations may not be detected by this method.
Reference Range
Interpretive report will be provided
Requisition
Special Instructions
Links to: Glycogen Storage Disease Type II (Pompe Disease) GeneReview
Clinical Utility
Pompe disease (glycogen storage disease type II) is an inherited disorder of glycogen metabolism, caused by mutations in the GAA gene and a deficiency of the enzyme alpha-glucosidase (also called acid-maltase). Pompe disease is a type of lysosomal storage disease. Individuals with Pompe disease are unable to use the glycogen stored in the lysosomes for energy, resulting in the progressive storage of glycogen in the heart, liver, and skeletal muscle. Pompe disease can present in infancy with profound hypotonia, cardiomegaly and cardiomyopathy or later in childhood and adulthood with progressive muscle weakness and respiratory insufficiency. Late onset Pompe disease presenting in the second to seventh decade of life can appear similar to a limb-girdle muscular dystrophy with lower limb proximal weakness.