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Test Code LAB1898 Rett/Angelman Syndrome Sequencing

Clinical System Name

Rett/Angelman Syndrome Sequencing

Description

The Rett/Angelman Syndrome Sequencing Panel targets genes known to cause neurodevelopmental disorders with overlapping clinical features that include developmental delay and/or regression, epilepsy, intellectual disability, movement disorders, microcephaly, and stereotypical behaviors.

  • Rett/Angelman Syndrome Sequencing Panel 

CDKL5, CLCN4, CNTNAP2, DYRK1A, EHMT1, FOXG1, MBD5, MECP2, MEF2C, NRXN1, SATB2, SLC9A6, TCF4, UBE3A, WDR45, ZEB2

 

  • Additional testing options - we offer the following additional options for custom Rett/AS testing:
    • Single-gene sequencing When there is strong clinical suspicion, any gene listed on our Rett/AS Sequencing Panel is available as a single-gene sequencing test.
    • Reflex to Rett/AS Sequencing Panel The option to reflex to the full Rett/AS panel when the single-gene test  is non-diagnostic.

 

Please contact LabGC@seattlechildrens.org if you would like to order reflexive testing after the original testing report has been issued.

 

Sample Requirements

Note: For patients who have had a whole blood transfusion, wait 10 days post transfusion to draw for genetic testing. No wait time is necessary for blood or saliva collection if the patient received leuko-reduced red cells or plasma.

 

Specimen: Whole blood

Container(s): Lavender/EDTA

Preferred Vol: 3 mL

Minimum Vol: 1 mL

Note: Heparin samples (Green tops) are unacceptable.

 

Specimen: Saliva collected using Oragene Dx OGD-575/675 collection kit.

Container: Oragene Dx OGD-575/675 collection kit

IMPORTANT NOTE: Manufacturer instructions must be followed. The Oragene Dx OGD575/675 kit is not for children under 6 months. Contact the lab directly for more information or to obtain a kit - 206-987-2617

 

Specimen: Extracted DNA (MUST specify source on requisition)

Preferred: 5 mcg

Minimum: 2 mcg

Note: Isolation of nucleic acids for clinical testing must be performed in a CLIA-certified
laboratory or a laboratory meeting equivalent requirements as determined by the CAP
and/or the CMS. DNA concentration minimum 50 µg/mL; 260/280 ratio 1.70-2.00.

Processing Instructions

Reject due to: Heparin

Spin: No

Aliquot: No

Temp: 2 - 8 C

Storage location: Molecular Genetics box in CPA refrigerator #2

Off-site collection: Refrigerate blood samples until ready to ship.  Transport all sample types at room temperature via overnight shipping.

Stability

Specimen Type Temperature Time
Whole blood, extracted DNA RT 3-5 d
Whole blood, extracted DNA 2 - 8 C

7 d

Saliva, extracted from ORAgene Dx OGD-575/675

 room temperature or refrigerated up to 2 weeks
Extracted DNA -20 C or -70 C  years

Note: Whole blood samples > 7days may be submitted to be assessed by our lab for acceptability for testing.

Availability

STAT Performed TAT
Contact lab Monday - Friday 4-6 weeks

Performing Laboratory

Seattle Children's Laboratory

Department

Department:  Molecular Genetics Laboratory

Phone: 206-987-3872

Lab Client Services: 206-987-2617

Lab Genetic Counselor: LabGC@seattlechildrens.org

CPT Codes

81479

 

Methodology

Method: Next Generation Sequencing technology using an Illumina NextSeq instrument. Target region includes coding exons and a minimum of 10 bp of flanking intron boundaries of the genes tested. Target enrichment performed using a custom Integrated DNA Technologies (IDT) Exome Hyb Panel v2. 

 

Average coverage ~150x, depth of coverage for all target regions is at least 20x.

 

Reported gene set: CDKL5, CLCN4, CNTNAP2, DYRK1A, EHMT1, FOXG1, MBD5, MECP2, MEF2C, NRXN1, SATB2, SLC9A6, TCF4, UBE3A, WDR45, ZEB2

 

Limitations:

This testing is performed on an exome backbone with analysis restricted to the panel genes. This method can detect single nucleotide variants (SNVs), small deletions, small insertions, and copy number variants in the regions targeted. Some regions cannot be efficiently captured due to sequence homology or sequence properties. This method will not detect large insertions and deletions, complex indels, structural variants (e.g. inversions, translocations), short tandem repeats, or other complex variants. Variants located outside of targeted regions will not be detected.

 

Based on validation studies, the bioinformatics pipeline showed precision and detection >99% for SNVs in regions with coverage greater than 20x and high mapping quality. Sensitivity for CNVs involving multiple genes is >99% and sensitivity for intragenic CNVs is >90%. Mosaic sequence variants present at <25% allele frequency may not be reliably detected, and detection sensitivity is dependent on the nature of the variant. The sensitivity of detection of mosaic copy number variants has not been evaluated.

Reference Range

Interpretive report will be provided. Variants are not reported if they are considered benign.

Clinical Utility

This panel can provide a molecular diagnosis when the clinical differential diagnosis may include Rett syndrome, atypical Rett syndrome, Angelman syndrome, Angelman-like syndrome, Pitt-Hopkins syndrome, Mowat-Wilson syndrome, Glass syndrome, Christianson syndrome, and/or Kleefstra syndrome. Timely identification of the genetic cause of a neurodevelopmental disorder can direct clinical management and assist with decisions about treatment.

 

When there is strong clinical suspicion of Angelman syndrome, DNA methylation analysis is the preferred first test for molecular confirmation of Angelman syndrome (PWS/AS MS-MLPA is available). Approximately 10% of individuals with Angelman syndrome have normal methylation analysis and a pathogenic sequencing variant in UBE3A.

Requisition

Molecular Genetics

Special Instructions

Links to: MECP2-Related Disorders GeneReviews