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Test Code LAB1892 Pompe DNA Sequencing

Clinical System Name

Pompe (GAA) Sequencing

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.


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

Container(s): Lavender/EDTA

Preferred Vol: 3 mL

Minimum Vol: 1 mL

Note: Heparin samples (Green tops) are unacceptable.

 

Specimen: Extracted DNA (MUST specify source on requisition)

Preferred: 5µg

Minimum: 2µg

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: 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

Specimen Type Description

Temperature

 Storage instructions
Whole blood EDTA or ACD tube Refrigerate Molecular Genetics box in CPA refrigerator #2
Extracted DNA DNA aliquot tube Refrigerate Molecular Genetics box in CPA refrigerator #2
Saliva OGD-575/675 kit Room temp Place in CPA Cytogenetics room temp box 

Off-site collection: Refrigerate blood samples until ready to ship.  Transport blood or DNA at room temperature via overnight shipping.  

Stability

Specimen Type Temperature Time
Whole blood Room temp 3-5 days
Whole blood Refrigerated 7 days
Extracted DNA RT, refrig or frozen stable
Saliva, ORAgene Dx OGD-575/675 Refrig or room temp up to 2 weeks

 

Note: Whole blood samples > 7days may be submitted to be assessed by our lab for acceptability for testing.

Performing Laboratory

Seattle Children's Laboratory

Department

Department:  Molecular Genetics Laboratory

Phone: 206-987-3872

Lab Client Services: 206-987-2617, labclientservices@seattlechildrens.org

Lab Genetic Counselor: LabGC@seattlechildrens.org

Synonyms

Acid Alpha-Glucosidase Deficiency

Acid Maltase Deficiency

GAA Deficiency

GSD II

Glycogen Storage Disease type II

Glycogenosis Type II

Availability

STAT Performed TAT
Contact lab Monday - Friday 4-6 weeks

Follow-up testing requested based on Washington State Lab Newborn Screening Program referrals will be expedited.

Methodology

Method: Next Generation Sequencing technology using an Illumina NextSeq instrument. Target region includes coding exons and a minimum of 10 bp of flanking intron boundaries of the genes tested. Target enrichment performed using a custom Integrated DNA Technologies (IDT) Exome Hyb Panel v2. 

 

Average coverage ~150x, depth of coverage for all target regions is at least 20x.

 

Limitations:

This testing is performed on an exome backbone with analysis restricted to the target gene. This method can detect single nucleotide variants (SNVs), small deletions, small insertions, and copy number variants in the regions targeted. Some regions cannot be efficiently captured due to sequence homology or sequence properties. This method will not detect large insertions and deletions, complex indels, structural variants (e.g. inversions, translocations), short tandem repeats, or other complex variants. Variants located outside of targeted regions will not be detected.

 

Based on validation studies, the bioinformatics pipeline showed precision and detection >99% for SNVs in regions with coverage greater than 20x and high mapping quality. Sensitivity for CNVs involving multiple genes is >99% and sensitivity for intragenic CNVs is >90%. Mosaic sequence variants present at <25% allele frequency may not be reliably detected, and detection sensitivity is dependent on the nature of the variant. The sensitivity of detection of mosaic copy number variants has not been evaluated.

Reference Range

Interpretive report will be provided. Variants are not reported if they are considered benign.

CPT Codes

81406

Requisition

Molecular Genetics

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.