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Test Code LAB1862 Hyperoxaluria Type 1 (AGXT) Sequencing

Clinical System Name

Hyperoxaluria Type 1 (AGXT) Sequencing

Synonyms

Oxalosis

Description

Primary hyperoxaluria type I (PH1) is an autosomal recessive disorder of glyoxylate metabolism resulting from a deficiency of the liver peroxisomal enzyme alanine-glyoxylate transaminase, encoded by the AGXT gene. This leads to calcium salts forming in the kidneys and other organs causing progressive decline in renal function and end stage renal disease (ESRD).

 

 

AGXT gene sequencing: testing is appropriate for

  • Frequent recurrent nephrolithiasis
  • End-stage renal disease with a history of renal stones or calcinosis
  • Stone composition of pure calcium oxalate monohydrate (whewellite)

 

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

AGXT full gene seq 81479
AGXT targeted variant analysis 81403

Methodology

Method:

Full gene sequencing - bi-directional sequencing of all 11 exons and flanking regions of the AGXT gene.

Targeted variant analysis - bi-directional sequencing of targeted variants

 

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

Clinical Utility

Primary hyperoxaluria type I (PH1) is an autosomal recessive disorder of glyoxylate metabolism resulting from a deficiency of the liver peroxisomal enzyme alanine-glyoxylate transaminase, encoded by the AGXT gene. This leads to calcium salts forming in the kidneys and other organs causing progressive decline in renal function and end stage renal disease (ESRD).

 

The age of onset of symptoms ranges from childhood to adulthood, but 80-90% of affected individuals present in late childhood or early adolescence. Presumptive diagnosis is made measuring urine oxalate:creatinine ratio and plasma oxalate concentration. Diagnostic confirmation can be made by AGT enzyme activity from liver biopsy, or by gene sequencing, which is less invasive. 

Requisition

Molecular Genetics

Special Instructions

Links to: Primary Hyperoxaluria Type I GeneReviews