Molecular Neuropathology

Ò NEUROPATHOLOGY – Molecular Request Form (Version 5.0)  (updated 02/12/2022)

The Molecular Neuropathology Laboratory offers comprehensive NATA-accredited molecular testing for brain tumour specimens. We provide reliable, timely and appropriate services to patients.

Effective from 1 May 2020, some of the molecular diagnostic tests offered are included in the Medicare Benefit Scheme (MBS) for eligible patients.

Please refer to our request form or contact us for further details.

Next Generation Sequencing (NGS) Glioma Panel

The Next Generation Sequencing (NGS) glioma panel provides NATA accredited service for the assessment of relevant glioma-associated molecular alterations.

Detection of IDH1/2 pathological variant status (MBS item 73372) and chromosome 1p19q co-deletion (MBS item 73371) by NGS will be partially covered under MBS for eligible patients.

Additional genes are in the process of validation for NATA accreditation. Once accredited they will be added to our NATA accredited panel targets. At present, the results of the unaccredited component can only be released on request as “research use only” results, and cannot be used for clinical decision making.

Pyrosequencing

-             MGMT promoter methylation  
MGMT promoter methylation analysis has prognostic and predictive implications for high grade gliomas. The methylation status of four CpG sites within the first exon of the MGMT gene is assessed by bisulfite modification of tumour DNA from fresh or formalin fixed paraffin embedded brain tumour specimens and quantitative pyrosequencing.

MGMT promoter methylation test is one of the MBS rebatable test (MBS item 73373) for eligible patients. 

MGMT promoter methylation status assessed by Pyrosequencing

-              IDH1/2 pyrosequencing
The majority of low-grade diffuse gliomas and secondary glioblastomas have mutations in Isocitrate Dehydrogenase-1 or -2 (IDH-1/2). IDH mutations have been found to carry prognostic significance in both low and high-grade gliomas. We perform pyrosequencing to assess IDH1codon 132 and IDH2 codon 172 mutations on fresh or formalin fixed brain tumour samples.

IDH1/2 testing is one of the MBS rebatable test (MBS item 73372) for eligible patients. 

-             TERT promoter pyrosequencing
Two high frequency variants, chr5: g1295228 G>A and chr5: g1295250 G>A in TERT promoter positioned respectively 124 and 146 base pairs upstream of the ATG translational start site of TERT, examined by PCR and pyrosequencing. TERT promoter mutations are found in the vast majority of IDH-mutant and 1p/19q co-deleted oligodendrogliomas (present in > 95% of cases) and most IDH-wildtype glioblastomas (present in ~ 80% of cases). TERT promoter mutations are also found in some medulloblastomas (SHH-activated, TP53-wildtype), some meningiomas (usually higher grade meningiomas), some malignant peripheral nerve sheath tumours, and some metastatic melanomas (but not primary CNS melanocytic lesions).

-             H3F3A pyrosequencing
We perform PCR and pyrosequencing to assess codon 27 and codon 34 of H3F3A on fresh or formalin fixed brain tumour samples.H3F3A K27M variant is found in diffuse midline glioma including diffuse pontine gliomas ( e.g. Diffuse midline glioma, H3 K27M-mutant), whereas H3F3A G34R or (rarely) G34V variants are found exclusively in high grade gliomas of the cerebral hemispheres, which are more frequently seen in teenagers and young adults. In paediatrics high-grade gliomas, H3F3A variants grade gliomas, H3F3A variants are associated with variants in the chaperone ATRX and inversely related to IDH variants.

Methylation Profiling of Central Nervous System Tumours

 Ò NEUROPATHOLOGY – Methylation Profiling Request Form (Version 1.1)  (updated 28/10/2021)

As various tumours have shown distinctive patterns of CpG island methylation, Methylation Profiling of Central Nervous System Tumours service is based on the Illumina Infinium MethylationEPIC 850K array which interrogates 850,000 methylation sites across the genome. An algorithm for DNA methylation-based classification of central nervous system tumours has been developed by the German Cancer Research Center (DKFZ) / Heidelberg University Hospital (www.molecularneuropathology.org/mnp). The algorithm is based on a tumour reference cohort of over 2,800 cases. The algorithm version is periodically updated. (Please see reference: Capper D et al Nature (2018) PMID 29539639 for background information).

This is a non-NATA accredited test. The non-accredited results will be reported as “Research Use Only” results with the following disclaimer: “Classification using methylation profiling is a research tool under development, it is not verified and has not been clinically validated. Implementation of the results in the clinical setting is in the sole responsibility of the treating physician.”

The cost of the test is $1000. There is currently no Medicare rebate for this test. The turnaround time is 6-8 weeks from receipt of the specimen. Please note that this test requires a FFPE tissue block with at least 80% tumour cellularity to be sent for optimal test performance.

Please refer to our request form or contact us for further details.