Molecular Anatomical Pathology

The Molecular Anatomic Division was established in the early 1990s and provides a unified NATA accredited Molecular Diagnostic Service for all public and regional hospitals and several private laboratories in Perth.  

The Molecular Pathology section provides patients and clinicians specialised DNA and RNA-based testing of tumours for purposes of accurate diagnosis, prognostication and prediction of response to tumour-specific therapies. Diagnostic modalities include the use of PCR, RT-PCR, digital PCR, capillary electrophoresis, pyrosequencing, multiplex-ligation dependent probe amplification (MLPA) including methylation specific MLPA, microsatellite instability (MSI), T- and B-cell gene rearrangements, Array Comparative Genomic Hybridisation, massively parallel sequencing and comprehensive genomic profiling.

In lymphomas the tests are used to establish cell lineage and B-cell or T-cell clonality, essential for accurate classification and treatment. Somatic mutation testing for a number of non-inherited cancers, such as EGFR testing for non-small cell lung cancer, are performed to determine response to tyrosine kinase inhibitor therapy. Similar testing for other genes is performed in the setting of metastatic malignant melanoma (BRAF and C-KIT mutations), gastrointestinal stromal tumours (C-KIT, PDGFRα) and colorectal cancers (KRAS and BRAF mutations), results of which impact on the choice of therapy. Testing for microsatellite instability in colorectal carcinomas is also performed to identify patients who may have hereditary non-polyposis colorectal carcinoma (Lynch Syndrome), which has implications for further genetic testing in families. In addition, methylation specific MLPA is used to further exclude Lynch Syndrome in colorectal and endometrial carcinomas.

The laboratory performs PCR-based chromosome translocation assays for accurate subtyping of lymphomas and diagnosis of sarcomas as deemed necessary by the lymphoma pathologist.  Array Comparative Genomic Hybridisation is used as an ancillary test for refining the diagnosis of morphologically ambiguous metastatic lesions.   MLPA is used for the prognostic stratification of uveal melanomas. Latest technology is in digital PCR, a highly sensitive and specific assay that can be used to detect variants that are present at very low levels, including in low amounts of DNA, for example circulating cell-free DNA extracted from blood samples are utilised. This assay is used to detect the EGFR T790M variant that confers resistance  to tyrosine kinase inhibitors in lung cancers; the MYD88 p.L265P variant for diagnosis of Lymphoplasmacytic Lymphoma and the C-KIT p.D816V variant which is used for diagnosis of mastocytosis.

The laboratory runs a number of massively parallel sequencing (MPS, Next Generation Sequencing (NGS)) panels, including a customised 33 gene cancer panel that covers clinically important biomarkers for diagnosis, prognostication and treatment selection for a broad range of common cancer types. This panel is highly suited to the analysis of colorectal, lung, melanoma, ovarian, GIST, glioma and breast cancers as it covers the most common variants in these cancer types. The panel also covers the MYD88 and KIT genes and TERT promoter which is part of the WHO guidelines for diagnostic and prognostic stratification of glioma.

In addition, the laboratory performs comprehensive genomic profiling using large MPS cancer panels which are able to analyse both DNA and RNA, thereby analysing single nucleotide and insertion/deletions variants, copy number variants, gene rearrangements, gene fusions and structural variants. This panel is particularly suitable for patients who have progressive disease, exhausted conventional treatment options, have rare cancer types or for alignment with clinical trials. The TST170 and TSO500 gene panels also analyse microsatellite instability (MSI) status and Tumour Mutation Burden which is predictive for immunotherapies. The Molecular Pathology laboratory has links with Genetic Services of WA, PathWest Discipline of Diagnostic Genomics and the Cytogenetics Laboratory.

Molecular Anatomical Pathology (AP) Community Health and Hospital Program (CHHP)

• The Community Health and Hospital Program (CHHP) has now ended.
• The TSO500 Comprehensive Genomic Profiling assay can still be ordered for patients with advanced or metastatic disease using the request form below. 
• A fee of $2600 will be charged to private patients and confirmation that the patient agrees to this is required before proceeding.
• Consent forms will no longer be required for these test requests; however, we will still require the Clinical Information Form to be completed. 

TSO500 Request Form

Medicare Approved Tests

Non-Medicare Tests