METHYLATION SPECIFIC PCR ANAL OF SNRPN FOR PRADER WILLI
Label Name: METHYL SNRPN
Lab Discipline: Molecular Diagnostics
Institution:  Duke University Health System 
EAP ID:  LAB6656 
Last Review:  3/17/2017 10:12:52 AM
Specimen Type
  Blood
Container & Volume
  Age Group   Container   Volume  
  0  - 18 Years LAVENDER TOP TUBE 3  ML
Patient Preparation
  Be sure to include patient's name, history #, date and time of collection, and collector's initials.
 
Collection Notes
  All:
  • Peripheral Blood: One lavender-top EDTA tube (minimum of 3 mls) is required for testing. Forward unprocessed peripheral blood promptly to the laboratory at ambient temperatures. The specimen cannot be frozen. Green-Top (Heparin) tubes are not acceptable for testing.

    Buccal swab: (Using the Clinical Molecular Diagnostics Laboratory specimen collection kit): Scrape the inside of the mouth using 10 strokes with a sterile nylon bristle cytology brush. Dip the brush up and down 10 times in the provided solution (Cell Lysis Solution) contained in the 1.5mL microfuge tube. Forward to the lab at ambient temperature.
 
Transport
  Please deliver to lab at ambient temperature. If there is a delay of more than 24 hours in delivery, please refrigerate the sample. No not freeze.
Turn Around Time -  Routine: 10 days   Stat: N/A
Reference Values
METHYL SNRPN
METHYLATED (MATERNAL) AND UNMETHYLATED (PATERNAL) SNRPN ALLELE WERE DETECTED.
PATTERN CONSISTENT WITH BIPARENTAL INHERITANCE OF SNRPN ALLELES
Methodology
  This assay uses methylation-specific PCR to determine the maternal or paternal origin of the Small Nuclear Ribonucleoprotein Polypeptide N (SNRPN) gene within the Prader Willi / Angelmann critical region. Genomic DNA is extracted from peripheral blood, and treated with sodium bisulfate to convert unmethylated cytosines to uracil. Bisulfite modified DNA is added to a multiplex PCR amplification reaction with fluorescently (FAM) tagged primers that specifically amplify either the uracil-containing SRNPN locus (originally unmethylated, paternal DNA producing a 101 bp amplification product) or the methylated cytosine-containing SRNPN locus (originally methylated maternal DNA producing an 177 bp amplification product). Amplification products are resolved and analyzed on an ABI 3130xl genetic analyzer and reviewed for the presence or absence of the maternal and paternal SNRPN alleles.

This test was developed and its performance characteristics determined by the Duke Molecular Diagnostics Laboratory. It has not been cleared or approved by the U.S. Food and Drug Administration. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 as qualified to perform high complexity clinical testing.

   
Special Information
  All:
  • Additional Patient Information Required: Due to the unique nature of genetic testing, patients offered this test should receive pre-test and post-test genetic counseling. Counseling should help the patient understand the strengths and limitations of DNA testing and the medical implications for the patient as well as for other family members. Patients are also required to give consent for testing.
 
   
Clinical Significance and Interpretive Data
    Angelman syndrome (AS) is a genetic disease characterized by severe developmental delay, gait ataxia, microcephaly, seizures and a unique happy and excitable demeanor. Prader-Willi syndrome (PWS) is a genetic disease characterized by severe hypotonia and feeding difficulty in the new born, followed by excessive eating, delay of motor milestones, a variable degree of cognitive impairment and hypogonadism. PWS and AS are both caused by abnormalities in imprinted genes located on chromosome 15q11-q13 and are often referred to as reciprocal imprinting disorders. The specific region involved in PWS/AS within 15q11-q13 is called the PWS/AS critical region and includes the Small Nuclear Ribonucleoprotein Polypeptide N (SNRPN) gene. The genes within this region are differentially methylated depending on whether they are inherited from the mother or father. Methylation differences lead to expression differences; methylation of a gene is associated with a lack of expression.

PWS results from the absence (or lack of expression) of genes normally expressed from the paternal allele. AS results from the absence (or lack of expression) of genes normally expressed from the maternal allele. Lack of expression of genes in this region may be the result of a large deletion, uniparental disomy (inheritance of both copies of the PW/AS critical region from one parent) or an imprinting error such that both chromosome 15 homologues (maternal and paternal) have the same imprinting or methylation pattern. Within the PWS/AS critical region, the maternal SNRPN gene is methylated (not expressed) and the paternal SNRPN allele is not methylated (expressed). By determining the methylation status of the SNRPN gene, a laboratory based diagnosis of PWS or AS syndrome can be made (PWS; loss of paternal allele, only the methylated maternal allele is present, AS; loss of maternal allele, only that unmethylated paternal allele is present)

References:

Buiting K, Gross S, Lich C, Gillessen-Kaesbach G, el-Maarri O, Horsthemke B. Epimutations in Prader-Willi and Angelman syndromes: a molecular study of 136 patients with an imprinting defect. Am J Hum Genet. 2003;72:5717.

Cassidy and Schwartz S. Prader-Willi Syndrome. Editors In: Pagon RA, Bird TD, Dolan CR, Stephens K, editors. Source GeneReviews (www.genetests.org) Seattle (WA): University of Washington, Seattle; 1993- [updated 2009 Sep 03].

Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994 Aug 11;22(15):2990-7.

Dagli and Williams CA. Angelman Syndrome. Editors In: Pagon RA, Bird TD, Dolan CR, Stephens K, editors. Source GeneReviews[http://www.genetests.org]. Seattle (WA): University of Washington, Seattle; 1993-[updated 2011 Jun 16].

Gunay-Aygun M, Schwartz S, Heeger S, O'Riordan MA, Cassidy SB. The changing purpose of Prader-Willi syndrome clinical diagnostic criteria and proposed revised criteria. Pediatrics. 2001;108:E92

Kubota T, Das S, Christian SL, Baylin SB, Herman JG, Ledbetter DH. Methylation-specific PCR simplifies imprinting analysis. Nat Genet. 1997 May;16(1):16-7.

   
Indications
    Testing should be considered in a child with a clinical diagnosis or suspicion of PWS or AS
   
Contraindications
    None
   
Limitations
    This test will identify large disease-causing deletions, uniparental disomy or methylation patterning defects in the Prader-Willi / Angelman critical region. Other cause of PWS or AS, including small deletions within the disease critical region, point mutations within the UBE3A gene or mechanisms other than those cited above, will not be detected by this assay. This assay detects 99% of PWS cases and about 80% of AS cases. Somatic mosaicism in a PWS or AS patient may cause a false negative result. This result does not rule out a diagnosis of PWS or AS due to small deletions or other mechanisms not detected by this assay. Poor genomic DNA quality or quantity, the presence of PCR inhibitors, and mutations or polymorphisms in the PCR primer binding sequences can result in un-interpretable or (rarely) inaccurate results.
   
Test Synonyms
  Synonym(s): angelman
Synonym(s): AS
Synonym(s): prader-willi
Synonym(s): PWS
Synonym(s): SNRPN
Molecular Diagnostics Laboratory
(MDX)

Medical Director:
 Michael Datto, M.D., Ph.D.
 Phone: 919-684-6965
 Email: michael.datto@duke.edu
Lab Director:
 Catherine Rehder Ph.D, FACMG
 Phone: 919-613-8434
 Email: catherine.rehder@duke.edu
Lab Director:
 Siby Sebastian Ph.D., DABMG
 Phone: 919-613-8432
 Email: siby.s@duke.edu

Address: 
 Wadsworth Bldg, Cytogenetics, Rm 0220
 2351 Erwin Rd
 Durham,  NC  27705
 Phone: 919-684-2698
 FAX: 919-668-5424

Performing Times: