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HelpTest Code LAB1894 Prader-Willi/Angelman Methylation & Copy Number Analysis
Clinical System Name
Prader Willi + Angelman Methylation & Del/Dup
Synonyms
Prader-Willi/Angelman Methylation and Deletion/Duplication by MS-MLPA
Prader-Willi + Angelman Methylation & Del/Dup
PWS+AS
PWS DNA
AS DNA
Angelman Methylation Analysis and CNV Analysis
Prader Willi Methylation Analysis and CNV Analysis
15q11-q13 Duplication Syndrome
Description
DNA methylation and deletion/duplication study of the Prader-Willi syndrome (PWS)/Angelman syndrome (AS) Critical Region of chromosome 15. If the methylation pattern is characteristic of only maternal inheritance (absence of the paternally-inherited critical region), this is diagnostic for PWS. If the methylation pattern is characteristic of only paternal inheritance (absence of the maternally-inherited critical region), this is diagnostic for AS. This combined assay will provide information regarding the genetic mechanism by which an abnormal methylation result arises, e.g. by deletion vs. another mechanism such as uniparental disomy (UPD) or an imprinting defect. This assay does not distinguish between UPD and an imprinting defect. Knowledge of the molecular class can inform risk for relatives. There is emerging evidence for genotype-phenotype correlations. Broadly, all genetic mechanisms that give rise to either PWS or AS are associated with a similar clinical presentation for that syndrome.
Copy number variants that include the 15q11.2 BP1 to BP3 or 4 regions are reported.
In addition, this assay can detect the PWS/AS critical region duplication that causes 15q11-q13 duplication syndrome (BP1 to BP3 or BP1 to BP4). Duplication of the maternal chromosome 15 is characterized by developmental delay, intellectual disability, hypotonia, and seizures. Copy number variants that are limited to the 15q11.2 BP1 to BP2 region are not reported.
| Indications for Prader-Willi testing: | Indications for Angelman testing: |
| Neonatal hypotonia & feeding difficulties | Developmental delay, intellectual disability |
| Persistent hypotonia | Seizures |
| History of poor suck | Expressive speech impairment |
| Developmental delay | Ataxia |
| History of above, plus excessive eating | Inappropriate happy demeanor, hand flapping |
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 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: Extracted DNA from EDTA blood may be accepted at the discretion of the laboratory director. Please contact the laboratory genetic counselors at LabGC@seattlechildrens.org prior to sending extracted DNA.
Minimum: 5µg
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 100 µg/mL; 260/280 ratio 1.70-2.00
Processing Instructions
Reject due to: Heparin
Spin: No
Aliquot: No
Temp: Refrigerate
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 |
|---|---|---|
| Extracted DNA | RT, refrig, frozen | stable |
| Whole blood | Room temp | 3-5 days |
| Whole blood | Refrigerated | 7 days |
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 | 2-3 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
81331 (updated 5/1/19 by cmyers)
Methodology
Method: Methylation-specific assay of the SNRPN and MAGEL2 alleles and deletion/duplication analysis of the 15q11.2-q13.1 loci, which contains the Prader-Willi/Angelman critical region (SALSA MLPA probemix ME028; MRC-Holland).
Limitations: 99% of cases of Prader-Willi detect and ~78% of cases of Angelman syndrome syndrome will be diagnosed by this method. 11% of individuals with a clinical diagnosis of Angelman syndrome will have a pathogenic variant in the UBE3A gene. UBE3A gene sequencing may be considered for individuals with a clinical diagnosis of Angelman syndrome but normal methylation studies.
This assay cannot provide detailed information regarding the size of a copy number change, but it can distinguish between type I (larger class, BP1-BP3) and type II (smaller class, BP2-BP3) copy number changes. Copy number variants that are limited to the BP1 to BP2 region of 15q11.2 are not reported.
Reference Range
Interpretive report will be provided.
Special Instructions
If the methylation test is positive and a deletion is not detected by this assay, subsequent UPD 15 testing can distinguish between uniparental disomy and an imprinting defect.
11% of individuals with a clinical diagnosis of Angelman syndrome will have a pathogenic variant in the UBE3A gene. DNA sequencing of the UBE3A gene should be considered in individuals with a clinical diagnosis of Angelman syndrome but normal methylation studies. Sequencing of UBE3A is available from the Seattle Children’s Hospital Laboratory as a single gene assay or as part of a larger panel for Angelman syndrome and related disorders.
Links to: Prader-Willi Syndrome GeneReview; Angelman Syndrome GeneReview; 15q Duplication Syndrome and Related Disorders GeneReview
Requisition
Clinical Utility
Prader-Willi syndrome is associated with neonatal hypotonia and feeding difficulties, changing to excessive eating later in infancy and childhood. Motor, cognitive, and language development are typically delayed. Prader-Willi syndrome is caused by the absence of the paternally-inherited critical region of chromosome 15.
Angelman syndrome is associated with ataxia, seizures, absence of speech, hyperactivity, hypopigmentation, and severe intellectual disability, and is caused by absence of the maternally-inherited critical region of chromosome 15.
For diagnosis, DNA methylation study of the PWS/AS Critical Region is the recommended method. If the methylation pattern is characteristic of only maternal inheritance, this is diagnostic for Prader-Willi syndrome. Maternal inheritance of the PWS/AS critical region can be caused by deletions of the paternal allele, receiving two copies of chromosome 15 from the mother (uniparental disomy) or defects in the imprinting process. If the methylation pattern is characteristic of only paternal inheritance, this is diagnostic for Angelman syndrome. Paternal inheritance of the PWS/AS critical region can be caused by deletions of the maternal allele, receiving two copies of chromosome 15 from the father (uniparental disomy) or defects in the imprinting process. This assay, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), will distinguish a deletion from disomy (UPD or imprinting defect). It will not distinguish between uniparental disomy (UPD) and an imprinting defect. In the case of a deletion, this assay can distinguish between a type I (larger class, BP1-BP3) and type II (smaller class, BP2-BP3) deletion. Knowledge of the molecular class can inform risk for siblings and there is emerging evidence for genotype-phenotype correlations. Broadly, all genetic mechanisms that give rise to either PWS or AS lead to a similar clinical presentation.
In addition, this same assay can detect duplication of the Prader-Willi/Angelman critical region that causes the 15q11-q13 duplication syndrome. Duplication of the maternal chromosome 15 is characterized by developmental delay, intellectual disability, hypotonia, and seizures.