PTEN Sequencing and Deletion/Duplication on Blood
GTR Test Accession: Help GTR000551654.4
DYSMORPHOLOGYINHERITED DISEASESYNDROMIC DISEASE ... View more
Last updated in GTR: 2023-06-07
Last annual review date for the lab: 2023-06-07 LinkOut
At a Glance
Diagnosis; Screening
PTEN hamartoma tumor syndrome; Bannayan-Riley-Ruvalcaba syndrome; Macrocephaly-autism syndrome; ...
Genes (1): Help
PTEN (10q23.31)
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Individuals suspected to have PTEN-related disorders, individuals who seek confirmation …
Not provided
Not provided
Ordering Information
Offered by: Help
Test short name: Help
PTEN1
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
CPT codes: Help
**AMA CPT codes notice
Lab contact: Help
Brandon Shaw, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
brandonshaw@uabmc.edu
205-934-1520
Bryce Brown, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
ebfincher@uabmc.edu
205-934-5525
Contact Policy: Help
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
How to Order: Help
Additional information regarding the specific details needed for test submission can be found on our website
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
From a fresh EDTA blood sample, DNA is extracted and used as the starting material for direct sequencing of the entire coding region .MLPA analysis to detect copy number changes is performed. Mutations screened for include truncating mutations (nonsense, frameshift, splicing mutations), missense mutations, multi-exon deletions and total gene deletions. … View more
View citations (1)
  • PTEN: one gene, many syndromes. Eng C, et al. Hum Mutat. 2003;22(3):183-98. doi:10.1002/humu.10257. PMID: 12938083.
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Conditions Help
Total conditions: 5
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose: Help
Diagnosis; Screening
Target population: Help
Individuals suspected to have PTEN-related disorders, individuals who seek confirmation of a clinical diagnosis, and individuals who want to prepare for prenatal/pre-implantation diagnosis.
View citations (1)
  • PTEN: one gene, many syndromes. Eng C, et al. Hum Mutat. 2003;22(3):183-98. doi:10.1002/humu.10257. PMID: 12938083.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
In order to further investigate a VUS, the laboratory will: 1. Review software predictions (SIFT, PolyPhen, etc) 2. Review internal database to compare against alterations seen in alleles previously tested in laboratory 3. Offer free of charge family studies for any individuals that would provide useful information for interpretation

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Yes.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Research:
Is research allowed on the sample after clinical testing is complete? Help
Further studies may be performed for other disorders that may also help to explain the patient's phenotype.
Recommended fields not provided:
Technical Information
Test Procedure: Help
From a fresh EDTA blood sample, DNA is extracted directly. The complete PTEN coding region is analyzed by a cascade of complementary mutation detection techniques, including RT-PCR, direct sequencing, microsatellite marker analysis, and copy number analysis by MLPA.
Test Confirmation: Help
Mutations found are confirmed on a second extraction from the original sample.
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Analytical validity is phenotype-dependent. Sequence analysis is able to identify a mutation in ~80% of persons with Cowden syndrome, 60% with Bannayan–Riley–Ruvalcaba syndrome, 50% with Proteus-like syndrome, and 20% with Proteus syndrome. In addition, deletion/duplication analysis can identify a mutation in ~11% of those with Bannayan–Riley–Ruvalcaba syndrome.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Alternative Assessment

PT Provider: Help
Intra-laboratory with samples reanalyzed blindly
VUS:
Software used to interpret novel variations Help
Alamut, Google search, PolyPhen, SIFT, evolutionary consevation, grantham score, splicing prediction software, disorder specific databases as necessary

Laboratory's policy on reporting novel variations Help
The laboratory will issue an interim report summarizing what is currently known about the variant and familial studies will be offered. Upon completion of the familial studies, a final report will be provided with a conclusion of what is suspected for the alteration.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.