NeuroSURESM: Epilepsy Gene Panel

CPT: 81403(x2); 81404(x6); 81405(x3); 81406(x11); 81407(x2); 81479
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Test Details

Synonyms

  • Epilepsy Comprehensive NGS Genetic Test Panel Del/Dup

Test Includes

Sequencing and copy number analysis of 69 genes: ALDH7A1, AMT, ARX, ASAH1, ATP1A2, ATP1A3, CDKL5, CERS1, CHD2, CHRNA7, CNTNAP2, CSTB, DNM1, DOCK7, EPM2A, FOLR1, FOXG1, GAMT, GATM, GLDC, GOSR2, GRIN2A, GRIN2B, HCN1, KCNC1, KCNJ10, KCNJ11, KCNQ2, KCNQ3, KCNT1, KCTD7, LMNB2, MBD5, MECP2, MEF2C, MOCS1, NECAP1, NEU1, NHLRC1, NRXN1, PCDH19, PHGDH, PLCB1, PNKP, PNPO, POLG, PRICKLE2, PRRT2, PSAT1, PSPH, SCARB2, SCN1A, SCN1B, SCN2A, SCN8A, SCN9A, SLC2A1, SLC6A8, SLC9A6, SPTAN1, STXBP1, SUOX, SYNGAP1, TBC1D24, TCF4, TSC1, TSC2, UBE3A, ZEB2

Use

Individuals with epilepsy who may benefit from genetic testing include those with infantile onset, epilepsy refractory to treatment, epilepsy plus developmental delay, or families that may choose to have prenatal testing in future pregnancy. Epilepsy is a group of phenotypically and genetically heterogeneous diseases that are characterized by recurrent and unprovoked seizures. It can develop at any age, but most commonly in early childhood, particularly in the first year of life. About two thirds of epilepsies have a genetic component, displaying two important features: one gene can be associated with multiple epilepsy disorders, and multiple genes can be associated with one epilepsy disorder.

Limitations

This assay does not detect low level germline mosaicism and does not rule out the presence of large chromosomal aberrations including deletions, insertions, and rearrangements, or pathogenic variants in regions or genes not included in this test, and possible inter/intragenic interactions between sequence variants. False-positive or false-negative results may occur for reasons that include genetic variants, blood transfusions, bone marrow transplantation, mislabeling of samples, or erroneous representation of family relationships. Testing is highly accurate, however, rare diagnostic errors can arise from specimen mishandling or misinterpretation; and it has been reported that as much as 0.5% error rate may occur in any of the pre-analytical/analytical or post analytical phases of the test.

This test was developed, and its performance characteristics determined by, Impact Genetics, LabCorp. It has not been cleared or approved by the US Food and Drug Administration (FDA).

Methodology

All coding exons and 20 bp of flanking intronic sequence are enriched using a custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All exons have >1000x mean read depth coverage, with a minimum 200x coverage at a single nucleotide resolution. This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis. All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request. This assay has been validated at a level of sensitivity equivalent to the Sanger sequencing and standard copy number analysis (>99%).

Specimen Requirements

Specimen

Whole blood

Volume

8.5 mL

Minimum Volume

4 mL

Container

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

Collection

Whole blood samples must be received at Impact Genetics within five days of collection.

Storage Instructions

Room temperature. Stable at room temperature for five days.

Causes for Rejection

Frozen specimen; hemolysis; quantity not sufficient for analysis; improper container

Clinical Information

Special Instructions

Testing referred to Impact Genetics, Ontario, Canada. Please direct any questions regarding this test to 877-624-9769.

References

Kerkhof J, Schenkel LC, Reilly J, et al. Clinical validation of copy number variant detection from targeted next-generation sequencing panels. JMol Diagn. 2017 Nov;19(6):905-920. doi: 10.1016/j.jmoldx. 2017.07.004. Epub 2017 Aug 15.28818680
Schenkel LC, Kerkhof J, Stuart A, et al. Clinical next-generation sequencing pipeline outperforms a combined approach using sanger sequencing and multiplex ligation-dependent probe amplification in targeted gene panel analysis. J Mol Diagn. 2016 Sep;18(5):657-67. doi: 10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 2.27376475

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