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HelpTest Code LAB2943 Congenital Hyperinsulinism Sequencing Panel
Clinical System Name
Congenital Hyperinsulinism Sequencing Panel
Synonyms
CHI
Familial Hyperinsulinism
FHI
Description
The Congenital Hyperinsulinism Sequencing panel includes DNA sequencing of genes associated with this condition: ABCC8, FOXA2, GCK, GLUD1, HADH, HNF1A, HNF4A, INSR, KCNJ11, SLC16A1
Testing is appropriate for:
- Infants with hyperinsulinism
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
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 the lab directly for more information or to obtain a kit - 206-987-2617
Specimen: Extracted DNA (MUST specify source on requisition)
Preferred: 10µg
Minimum: 5µg
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.
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 |
|---|---|---|
| Whole blood, extracted DNA | Room temp | 3-5 days |
| Whole blood, extracted DNA | Refrigerated | 7 days |
|
Saliva, extracted from ORAgene Dx OGD-575/675 |
Room temp or refrigerated | up to 2 weeks |
| Extracted DNA | -20 C or -70 C | years |
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 | 4-6 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
Contact Client Services at 206-987-2617 or labclientservices@seattlechildrens.org for price and CPT information.
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.
Reported gene set: ABCC8, FOXA2, GCK, GLUD1, HADH, HNF1A, HNF4A, INSR, KCNJ11, SLC16A1
Limitations:
This testing is performed on an exome backbone with analysis restricted to the panel genes. 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.
Special Instructions
Links to: Familial Hyperinsulinism GeneReview; DiabetesGenes.org
Requisition
Clinical Utility
Testing is appropriate for:
- Infants with hyperinsulinism
ABCC8: Approximately 45% of CHI is attributed to pathogenic variants in ABCC8, the gene encoding the protein SUR-1, the second of the two components of the beta-cell plasma membrane ATP-dependent potassium channel.
KCNJ11: Approximately 5% of CHI is attributed to pathogenic variants in KCNJ11, the gene encoding the protein Kir6.2 which is one of the two components of the beta-cell plasma membrane ATP-dependent potassium channel.
HNF4A: Approximately 5% of CHI is attributed to pathogenic variants in HNF4A, the gene encoding the hepatocyte nuclear factor 4-alpha.
As of 5/30/18, the Congenital Hyperinsulinism Sequencing Panel will no longer include UCP2 gene sequencing This decision is based on recent knowledge that supports evidence that UCP2 variants are not a direct cause of congenital hyperinsulinism but instead are, at most, risk factors for CHI [Laver TW, Weedon MN, Caswell R, Hussain K, Ellard S, Flanagan SE. Analysis of large-scale sequencing cohorts does not support the role of variants in UCP2 as a cause of hyperinsulinaemic hypoglycaemia. Hum Mutat. 2017 Oct; 38(10):1442-1444. PMID: 28681398].