Diagnostic Test Directory

Molecular Genetics Laboratory

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Early Infantile Epileptic Encephalopathy Next Generation Sequencing Panel (15 genes)

  • Synonyms: ARHGEF9, ARX, CDKL5, GABRD, GABRG2, KCNQ2, MEF2C, PCDH19, PLCB1, PNKP, SCN1A, SCN2A, SLC25A22, SPTAN1, STXBP1,

    Collect

    Collect whole blood in a purple top (EDTA) tube (preferred). Extracted DNA is also acceptable.

    Volume Required

    5 ml whole blood or 8 ug extracted DNA

    Minimum Required

    3 ml whole blood

    Transport

    Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday within 24 hours of collection.

    Stability

    Whole blood can be refrigerated until shipment.

    Unacceptable conditions

    Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.

    Specimen Handling

    Do not heat, freeze or centrifuge blood before shipment. Refrigerate sample until shipment.

Days Performed

Mon - Fri 9:00am to 4:00pm

Reported

6-8 weeks

CPT

81404, 81405(x2), 81406(x3), 81407, 81479(x8)

Disease Information

Clinical Features:

Early Infantile Epileptic Encephalopathy (EIEE) is a severe age-related epileptic encephalopathy. Major characteristics of EIEE include onset in early infancy (neonatal period through the first few months of life), impaired motor development, cognitive development, and sensory development. Genetic etiology of EIEE is heterogeneous and the EIEE panel includes 15 genes (see Table 1 for additional details). Mutations in these genes have been described in individuals with an EIEE phenotype.

Molecular Genetics:

The genes involved in the EIEE panel include ARX, CDKL5, SLC25A22, STXBP1, SPTAN1, SCN1A, GABRG2, KCNQ2, ARHGEF2, PCDH19, PNKP, SCN2A, PLCB1, GABRD, and MEF2C. Mutations in these disorders can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern.

Test Methods:

Genomic DNA is extracted from blood or other patient tissues following standard DNA extraction protocols. This test is performed by next generation sequencing using the SureSelectXT Target Enrichment System (Agilent Inc) followed by Illumina MiSeq sequencing (2x 150bp paired end) of the coding regions and splice sites of the targeted genes. FASTQ data is de-multiplexed based on sample-specific index sequence using the MiSeq Reporter software and aligned to human reference genome hg19 using Novoalign. Variants are then called using the GATK pipeline and annotated using ANNOVAR and SnpEff. Sanger sequencing is performed to confirm clinically significant variants and to fill in regions with insufficient coverage (bases with less than 30X coverage). Variants that are classified as benign or likely benign will not be confirmed.

Results:

Test results with interpretation will be mailed and/or faxed to the referring physician or send out lab following completion of the test. Additional reports will be provided as requested.

Utility:

The clinical utility of the assay is to support a clinical diagnosis of the disease, facilitate genetic counseling, and assess the risk to other first degree relatives and to facilitate testing of at - risk family members.

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