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Test Code LAB3007 EpiXpanded Panel

Important Note

Note that this panel uses a trio approach that includes concurrent analysis of the patient (proband) and both parents.

Requires referral to Genetic Counseling Clinic for pre-test counseling and sample coordination.

Additional Codes

EpiXpand Pnl

Clinical System Name

EpiXpanded Panel



Sample Requirements

* Preferred sample is whole blood


Specimen: Whole Blood

Container(s): Lavender/EDTA

Preferred Vol: 5.0 mL

Minimum Vol: 2.0 mL (1.0 mL is acceptable for infants)



Specimen: DNA

Container(s): Sterile Plastic Tube

Preferred Vol: 5 µg of purified DNA at a concentration of ≥50 ng/µL AND a volume of ≥100 µL



Specimen: Buccal Swabs

Container(s): Oragene Dx OGD-100 collection kit

Information about alternate specimen collection kits can be found here on LabMan.



Dried blood spots are also accepted.


Processing Instructions

Reject due to:

Spin: N

Aliquot: N

Temp: 2 - 4 C

Storage location: Refrigerate in CPA refrigerator Sendouts rack. Samples drawn on a Friday can be refrigerated until Monday shipment. Samples drawn on a Friday before a Monday holiday must have DNA extraction.


Off-site collection: Send whole blood refrigerated.


Specimen Type Temperature Time
Whole Blood Room temp 3 d
Whole Blood Refrigerated 7 d
Whole Blood Frozen N
Extracted DNA Room temp 3-4 d
Extracted DNA Refrigerated 1 y
Extracted DNA Frozen Indefinitely



STAT Performed TAT
N   6 w


Performing Laboratory


207 Perry Parkway

Gaithersburg, MD 20877

Phone Number: (301) 519-2100


Department: Send Outs

Phone Number: (206) 987-2563


Method: Next-gen Sequencing


Using genomic DNA from the submitted specimen(s), the exonic regions and flanking splice junctions of the genome were captured using a proprietary system developed by GeneDx and sequenced by massively parallel (NextGen) sequencing on an Illumina sequencing system with 100bp or greater paired-end reads. Reads are aligned to human genome build GRCh37/UCSC hg19 and analyzed for sequence variants in targeted genes using a customdeveloped analysis tool (Xome Analyzer). Capillary sequencing or another appropriate method is used to confirm all potentially pathogenic variants identified in the proband and relative samples, if submitted. Sequence and copy number alterations are reported according to the Human Genome Variation Society (HGVS) and International System for Human Cytogenetic Nomenclature (ISCN) guidelines, respectively.


Please note that while the EpiXpanded panel captures and sequences the whole exome, analysis is targeted to the specific phenotype-driven gene list for the EpiXpanded panel. The EpiXpanded Panel gene list includes more than 1300 genes. The list was developed by searching for genes associated with the phenotypes “Seizures”, “Epilepsy”, and “Epileptic Encephalopathy” in multiple sources, including OMIM, HGMD, and Human Phenotype Ontology (HPO) terms categorized within the “Seizure” branch. Additionally, genes were added to the list using GeneDx data from clinical whole exome sequencing done on patients with epilepsy and from emerging literature about new genes causing epilepsy. The gene list is systematically updated at least quarterly.


The average coverage of all genes on the panel is greater than 98% at 10X (with a depth of 10 or more reads). Several genes with a high clinical sensitivity have an average coverage of less than 90% coverage at 10X, including ARX, FOXG1, EPM2A, and SLC6A8. The coverage of each gene on the panel for a specific patient may vary, and the actual coverage for each gene is included in the final report. Using a custom-developed analysis tool (XomeAnalyzer), data are filtered and analyzed to identify sequence variants and most deletions and duplications involving three or more coding exons (Retterer et al., 2015). Smaller deletions or duplications may not be reliably identified.


Some types of genetic disorders, such as those due to nucleotide repeat expansion/contraction, abnormal DNA methylation, and other mechanisms may not be detectable with this test. Additionally, small sections of a few individual genes have inherent sequence properties that yield suboptimal data and mutations in those regions may not be reliably detected. Specifically, the CGG repeat expansions in FMR1 causing fragile X syndrome, the polyalanine repeat expansions in ARX, the common dodecamer repeat expansion in CSTB associated with Unverricht-Lundborg disease, and abnormal methylation of UBE3A causing Angelman syndrome would not be detectable by this EpiXpanded Panel.


Variants of uncertain significance (VUS) are not routinely reported.

Reference Range

Interpretive report is provided

Send Out Instructions

Reference Test Name:

EpiXpanded Panel

Reference Lab Test Code: 921
Instructions: Ship via FedEx Priority Overnight. Saturday deliveries are accepted.


Special Instructions



Clinical Utility

Test information sheet


Epilepsy is a clinically and genetically heterogeneous group of genetic disorders. The EpiXpanded Panel uses a trio approach that includes concurrent analysis of the affected proband and both parents, which increases the likelihood of identifying a definitive genetic explanation for epilepsy.


The EpiXpanded Panel is based on whole exome capture (WEC), NextGeneration sequencing (NGS), and targeted analysis of a comprehensive list of genes currently associated with epilepsy. The design of the panel allows for a comprehensive, dynamic gene list that is updated regularly to ensure inclusion of genes recently associated with epilepsy.


In some cases, confirmation of the molecular genetic cause of epilepsy may have implications for treatment and management.