Epileptic Encephalopathy and Intellectual Disability via the CHD2 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 4123 | CHD2 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Epileptic encephalopathy with childhood onset (EEOC; OMIM:615369) is a neurocognitive disorder characterized by seizure onset within the first 3 years of life and moderate to severe intellectual disability. Seizure types observed in EEOC include myoclonic, absence, tonic, tonic-clonic and febrile. Developmental delay, language impairment and cognitive regression are features commonly seen in EEOC cases (Carvill et al. 2013; Capelli et al. 2012).
Genetics
EEOC can be caused by heterozygous variations in the CHD2 gene. Reported cases of EEOC are sporadic and may result from de novo mutations in the CHD2 gene. Missense, nonsense, splice site and frameshift variants in CHD2 as well as large deletions encompassing the CHD2 locus have been reported in patients with epilepsy and intellectually disability (Carvill et al. 2013; Capelli et al. 2012; Rauch et al. 2012). CHD2 encodes a chromodomain helicase DNA-binding protein (CHD). CHD family members have been implicated in chromatin remodeling, transcriptional regulation and DNA damage repair (Marfella and Imbalzano 2007; Rajagopalan et al. 2012).
Clinical Sensitivity - Sequencing with CNV PG-Select
Targeted sequencing of 500 patients with epileptic encephalopathies identified causative de novo missense and nonsense CHD2 variants in ~1% (6/500) of cases (Carvill et al. 2013). Another study of patients with non-syndromic sporadic intellectual disability identified ~2% (1/51) of patients with causative CHD2 variants (Rauch et al. 2012).
Testing Strategy
This test provides full coverage of all coding exons of the CHD2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for CHD2 testing include patients with sporadic epilepsy or intellectual disability of unknown cause.
Candidates for CHD2 testing include patients with sporadic epilepsy or intellectual disability of unknown cause.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| CHD2 | 602119 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Epileptic encephalopathy, childhood-onset | AD | 615369 |
Citations
- Capelli LP, Krepischi ACV, Gurgel-Giannetti J, Mendes MFS, Rodrigues T, Varela MC, Koiffmann CP, Rosenberg C. 2012. Deletion of the RMGA and CHD2 genes in a child with epilepsy and mental deficiency. European Journal of Medical Genetics 55: 132–134. PubMed ID: 22178256
- Carvill GL, Heavin SB, Yendle SC, McMahon JM, O’Roak BJ, Cook J, Khan A, Dorschner MO, Weaver M, Calvert S, Malone S, Wallace G, Stanley T, Bye AM, Bleasel A, Howell KB, Kivity S, Mackay MT, Rodriguez-Casero V, Webster R, Korczyn A, Afawi Z, Zelnick N, Lerman-Sagie T, Lev D, Møller RS, Gill D, Andrade DM, Freeman JL, Sadleir LG, Shendure J, Berkovic SF, Scheffer IE, Mefford HC. 2013. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nature Genetics 45: 825–830. PubMed ID: 23708187
- Marfella CG, Imbalzano AN. 2007. The Chd family of chromatin remodelers. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 618: 30–40. PubMed ID: 17350655
- Rajagopalan S, Nepa J, Venkatachalam S. 2012. Chromodomain helicase DNA-binding protein 2 affects the repair of X-ray and UV-Induced DNA damage. Environmental and Molecular Mutagenesis 53: 44–50. PubMed ID: 22223433
- Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Donato N Di. 2012. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. The Lancet. PubMed ID: 23020937
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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ORDER OPTIONS
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