Background:
Neurological disorders include a large group of conditions with genetic and phenotypic heterogeneity and often have overlapping clinical features, such as intellectual disability, seizures, microcephaly, motor disability, brain malformations (lissencephaly, molar tooth sign), vision loss, speech difficulties, and respiratory failure. Epilepsy is a common neurological disorder characterized by recurrent, unprovoked seizures. There are many different types of epilepsy and seizures including infantile epilepsy and childhood epilepsy. This next-generation sequencing test is designed to detect mutations in the coding region of 99 genes associated with Epilepsy.
Reasons for Referral:
- Electroencephalogram results suspicious for epilepsy.
- Occurrence of seizures.
- Positive family history for epilepsy (targeted testing is available if familial mutation is known).
- Carrier testing.
Methodology:
Next generation sequencing (NGS) will analyze the exons or coding regions of the genes using Illumina NextSeq 500/550 technology and preparing samples using hybridization probes to enrich exonic regions. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
Exon-level deletion/duplication analysis is performed by running the NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.
Epilepsy/Seizure panel (99 genes): ABAT, ADSL, ALDH5A1, ALDH7A1, AMT, ARHGEF9, ARX, ASPM, ATP1A2, BTD, CACNA1A, CACNB4, CASK, CASR, CDKL5, CHRNA2, CHRNA4, CHRNB2, CLN3, CLN5, CLN6, CLN8, CNTNAP2, CPA6, CSTB, CTSD, DCX, DNAJC5, EFHC1, EPM2A, FLNA, FOLR1, FOXG1, GABRA1, GABRG2, GAMT, GATM, GCH1, GLDC, GOSR2, GPR56, GPR98, GRIN2A, KCNJ10, KCNMA1, KCNQ2, KCNQ3, KCTD7, LGI1, LIAS, MAGI2, MBD5, MCPH1, MECP2, MEF2C, MFSD8, MMACHC, MTHFR, NHLRC1, NRXN1, OPHN1, PAFAH1B1, PCBD1, PHGDH, PLCB1, PNKP, PNPO, POLG, PPT1, PRICKLE1, PRICKLE2, PRRT2, PSPH, PTS, QDPR, SCARB2, SCN1A, SCN1B, SCN2A, SCN8A, SCN9A, SLC19A3, SLC25A22, SLC2A1, SLC6A8, SLC9A6, SPTAN1, STXBP1, SYN1, TBC1D24, TCF4, TPP1, TSC1, TSC2, TSEN54, UBE3A, WDR45, WDR62, ZEB2
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5 mL
- Child: 5 mL
- Infant: 2-3 mL
Saliva: 2 ORAgene Saliva Kits (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene Assisted Saliva Kits (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for an Assisted Saliva Collection Kit for patients that cannot provide a blood sample.
Skin Fibroblast: Punch Biopsy (cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks
DNA: 3-4µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)
For routine testing of blood and saliva (or DNA extracted from them), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.
Test Performed (Days):
Weekly
Turn Around Time:
8 weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
- http://www.epilepsy.com/
Additional Info: