GTR Test Accession:
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GTR000613388.2
Last updated in GTR:
2024-10-24
View version history
GTR000613388.2,
last updated:
2024-10-24
GTR000613388.1,
registered in GTR:
2024-09-30
Last annual review date for the lab: 2024-09-30
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At a Glance
Test purpose:
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Diagnosis;
Prognostic;
Therapeutic management
Conditions (15):
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classification prediction score indicating the resemblance to a CNS tumor subtype based on methylation profile.
Methods (1):
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Molecular Genetics - Methylation analysis: Microarray
Target population: Help
Not provided
Clinical validity:
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Not provided
Clinical utility:
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Not provided
Ordering Information
Offered by:
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Manufacturer's name:
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Infinium MethylationEPIC v2.0
Specimen Source:
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- Formalin-fixed, paraffin-embedded (FFPE) blocks or slides
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
Test Order Code:
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JAX OncoMethyl Array
View other test codes
View other test codes
CPT codes:
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Lab contact:
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Melissa Kelly, PhD, CC(ABB), HCLD(ABB), Lab Director
melissa.kelly@jax.org
melissa.kelly@jax.org
Contact Policy:
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Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order:
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For JAX OncoMethyl Array, we accept formalin-fixed, paraffin-embedded (FFPE) material only, including tumor blocks.
We require one representative hematoxylin and eosin (H&E) stained slide if possible. We require a minimum of 11 adjacent unstained 5 um sections on uncoated, unbaked slides if you are not submitting a tumor block.
The …
We require one representative hematoxylin and eosin (H&E) stained slide if possible. We require a minimum of 11 adjacent unstained 5 um sections on uncoated, unbaked slides if you are not submitting a tumor block.
The …
Order URL
Test development:
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Manufactured (research use only; not FDA-reviewed)
Informed consent required:
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No
Pre-test genetic counseling required:
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No
Post-test genetic counseling required:
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No
Recommended fields not provided:
Test strategy
Conditions
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Total conditions: 15
| Condition/Phenotype | Identifier |
|---|
Test Targets
Chromosomal regions/Mitochondria
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Total chromosomal regions/mitochondria: 1
| Chromosomal region/Mitochondrion | Associated condition |
|---|
Methodology
Total methods: 1
Method Category
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Test method
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Instrument
Methylation analysis
Microarray
Illumina iScan
Clinical Information
Test purpose:
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Diagnosis;
Prognostic;
Therapeutic management
Variant Interpretation:
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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No.
No.
Will the lab re-contact the ordering physician if variant interpretation changes?
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No. The lab does not re-contact the ordering physicians as routine practice.
No. The lab does not re-contact the ordering physicians as routine practice.
Sample reports:
Recommended fields not provided:
Clinical validity,
Clinical utility,
Target population,
What is the protocol for interpreting a variation as a VUS?,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report
Technical Information
Test Procedure:
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The JAX OncoMethyl™ Array utilizes a machine learning algorithm for the classification of central nervous system (CNS) tumors based on genomic methylation profiling data. As necessary (for FFPE blocks or unstained slides), specimens are sectioned and stained using Fisher Chemical Eosin Y and Richard-Allan Scientific™ Hematoxylin Stain (Modified Mayer). Slides …
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Test Platform:
Infinium MethylationEPIC v2.0
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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During validation, 98% of samples with Methylation Class calibrated scores ≥0.84 were considered “classifiable” and resulted in either confirmation, refinement, or reassignment of diagnosis.
Assay limitations:
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The JAX OncoMethyl™ Array uses a machine learning algorithm to classify central nervous system cancers based on genomic methylation profiling. As per the WHO 2021 classification of central nervous system tumors, careful attention must be paid to the common calibrated score threshold and pathologists should be wary about endorsing suggested …
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Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Alternative Assessment
Yes
Method used for proficiency testing: Help
Alternative Assessment
Recommended fields not provided:
Test Confirmation,
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Reviews:
Clinical resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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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.