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JAX OncoMethyl Array
Clinical Genetic Test
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offered by
The Jackson Laboratory for Genomic Medicine
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GTR Test Accession: Help GTR000613388.2
CANCERNERVOUS SYSTEMENDOCRINOLOGY ... View more
Last updated in GTR: 2024-10-24
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Last annual review date for the lab: 2024-09-30 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Prognostic; Therapeutic management
Conditions (15): Help
Glioma; Astrocytoma; Brain glioma more...
Chromosomal regions/ Mitochondria (1): Help
classification prediction score indicating the resemblance to a CNS tumor subtype based on methylation profile.
Methods (1): Help
Molecular Genetics - Methylation analysis: Microarray
Target population: Help
Not provided
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
The Jackson Laboratory for Genomic Medicine
View lab's website
View lab's test page
Manufacturer's name: Help
Infinium MethylationEPIC v2.0
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
JAX OncoMethyl Array
View other test codes
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Lab contact: Help
Melissa Kelly, PhD, CC(ABB), HCLD(ABB), Lab Director
[email protected]
Contact Policy: Help
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: Help
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 …
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Order URL
Test development: Help
Manufactured (research use only; not FDA-reviewed)
Informed consent required: Help
No
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Recommended fields not provided:
Test strategy
Conditions Help
Total conditions: 15
Condition/Phenotype Identifier
Test Targets
Chromosomal regions/Mitochondria Help
Total chromosomal regions/mitochondria: 1
Chromosomal region/Mitochondrion Associated condition
Methodology
Total methods: 1
Method Category Help
Test method Help
Instrument
Methylation analysis
Microarray
Illumina iScan
Clinical Information
Test purpose: Help
Diagnosis; Prognostic; Therapeutic management
Variant Interpretation:
Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
No.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
No. The lab does not re-contact the ordering physicians as routine practice.
Sample reports:
Sample Positive Report Help
Sample Positive Report
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: Help
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 … View more
Test Platform:
Infinium MethylationEPIC v2.0
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
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: Help
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 … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
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: Help
Category: FDA exercises enforcement discretion
Additional Information

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