Molecular Genetics Rett - Angelman Syndrome Panel

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Test Code:

2405
Department:

Molecular Genetics
Test Synonyms:

CDKL5 • CNTNAP2 • FOXG1 • IQSEC2 • MBD5 • MECP2 • MEF2C • MEIS2 • NRXN1 • SLC9A6 • TCF4 • UBE3A • WDR45 • ZEB2
CPT Code(s):

81406

Background:

Rett and Angelman syndromes and phenotypically related disorders are a class of neurodevelopmental conditions. Clinically these phenotypes may include intellectual delay/regression, seizures, and developmental delay. Typically Rett syndrome is seen in girls but Angelman syndrome has no gender bias. These conditions are typically inherited in an autosomal dominant, recessive or X-linked manner. Angelman syndrome is caused by mutations in the gene UBE3A, however due to genomic imprinting and only the maternal copy is active in the brain. Mutations in MECP2 are associated with Rett syndrome. Given this, methylation status of this genomic region should be considered for Angelman syndrome cases to assess paternal contribution or uniparental disomy.

Reasons for Referral:

Molecular confirmation for conditions related to Rett or Angelman syndrome
Carrier testing
Positive family history

Methodology:

Next generation sequencing will analyze the exons or coding regions of 14 Rett-Angelman-associated genes using Illumina NextSeq 500 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. Promoter, intronic, etc. regions are not assessed on our assay, 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.

Rett-Angelman Syndrome Panel (14 genes):
CDKL5, CNTNAP2, FOXG1, IQSEC2, MBD5, MECP2, MEF2C, MEIS2, NRXN1, SLC9A6, TCF4, UBE3A, WDR45, 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 Collection 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. ORAgene Saliva Kit(s) (OGR-500)

Assisted Saliva: 4 ORAgene™ Assisted Saliva Collection 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: 5-10µg 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).

Prenatal:

Direct Amniotic Fluid (10-20mL)
Direct CVS
Cultured Amniocytes (2 T-25 flasks)
Cultured CVS (2-T25 flasks)
Cultured Fetal Tissue: Product of Conception (2 T-25 flasks)
Cord Blood (1-2mL)

Notice Regarding Molecular Genetic Testing on CVS or Amniotic Fluid Specimens:

Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood in addition to the fetal specimen. Additional charges apply for the maternal cell rule-out test.

For routine testing of blood, saliva and buccal swabs, 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: