Cortical Malformations and Epilepsy Panel | NGS

Genes SequencedN39 genes sequenced: ACTB, AKT1, AKT3, ARFGEF2, BRAF, CCM2, CCND2, CDKL5, DCX, DEPDC5, DYNC1H1, FLNA, GABRA1, GABRG2, GRIN2B, KCNQ2, KIF5C, MECP2, MTOR, NACC1, NPRL2, NPRL3, PAFAH1B1, PCDH19, PIK3CA, PIK3R2, PRKACA, PRKACB, PTEN, RHEB, RPS6, SCN1A, SCN2A, SLC35A2, SMO, TSC1, TSC2, TUBA1A and TUBB2B. Also targets a small intronic region of FLNA.
Test DetailsThis targeted hybrid capture-based test is designed to detect somatic single nucleotide variants, insertions and deletions (indels). At a mean depth of coverage of at least 4000x across the captured region, this test has 89.84% sensitivity for variants at a variant allelic fraction (VAF) of 1.25% and 99.48% for variants at a VAF of at least 2.5%. Identified variants classified using ACMG/AMP, ClinGen and internally developed guidelines.
MethodologyNext Generation Sequencing
PerformedMonday – Friday
Turnaround3 weeks
Specimen RequirementsFresh or Formalin fixed paraffin embedded tissue from the affected area.
Sample CollectionFresh tissue placed in media (4 mm skin punch or tissue 4 mm in size).

Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block or 15 unstained slides with matched H&E slide.
Minimum Sample Volume 3 millimeters
Storage/Transport ConditionsFresh tissue: Refrigerated temperature (cold packs). Please ship in media for overnight delivery.
FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope for overnight delivery. In seasonal warmer weather, include cold pack
Unacceptable ConditionsFFPE specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
CPT Code(s)81479