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OUR SERVICES
Molecular Genetics
Molecular Diagnostics (Haematology and Solid Tumour)
Austin Pathology Molecular Diagnostics laboratory offers services including massively parallel sequencing, fragment analysis, droplet digital PCR and quantitative RT-PCR for haematology and solid tumour testing in a NATA accredited setting.
Knowledge about the human genome and opportunities to use medical genetics and genomics in medical practice has expanded over the last couple of decades. Diagnosis, classification, therapeutics and disease monitoring of haematological and solid organ diseases rely on integration of morphological, immunophenotypic and genomic information.
Austin Pathology provides patient focused service with a high-level of clinical and scientific guidance that is supported by Haematologists, Anatomical Pathologists and Molecular Scientists.
Contact Details
- Lead Molecular Genetics Scientist: Dr Wasanthi De Silva
- Email: wasanthi.desilva@austin.org.au
- Supervising Molecular Haematologist: Dr Rishu Agarwal
- Email: rishu.agarwal@austin.org.au
- Supervising Solid Tumour Molecular Pathologist: Dr Jonathan Clark
- Email: jonathan.clark@austin.org.au
General Enquiries
- Email: molecular@austin.org.au
- Phone: 03 9496 5657
Click here to download the Molecular Haematology Request Form
Please check government eligibility criteria on the MBS Online Website for Medicare funded tests with the relevant MBS item numbers.
The Myeloid, MPN (Myeloproliferative Neoplasm) and MF (Myelofibrosis) Panels utilise massively parallel sequencing technology to assess genetic variants (also referred to as mutations) that are important in different myeloid disorders. Genes assessed in these panels are currently known to have important diagnostic, prognostic and therapeutic implications.
Myeloid NGS Panel
Clinical Indication: Suspected myeloid malignancy
Gene List: ASXL1, BRAF, CALR, CBL, CEBPA, CSF3R, CXCR4, DNMT3A, DDX41, ETNK1, EZH2, FBXW7, FLT3*, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PPM1D, PTEN, RHOA, RUNX1, SETBP1, SF3B1, SRSF2, STAT3, STAT5B, STAT6, TET2, TP53, U2AF1, WT1.
*FLT3-ITD is reported using fragment analysis.
MBS Item No. 73447
Please contact us for pricing for Non-Medicare eligible patients.
Myeloproliferative Neoplasm (MPN) NGS Panel
Clinical Indication: Myeloproliferative neoplasm (PV / ET)
Gene List: ASXL1, CALR, CSF3R, JAK2, KIT, MPL, IDH1, IDH2
MBS Item No: 73398
Please contact us for pricing for Non-Medicare eligible patients.
Primary Myelofibrosis (MF), Transplant Eligible
Clinical Indication: Primary Myelofibrosis, transplant eligible
Gene List: ASXL1, BRAF, CALR, CBL, CEBPA, CSF3R, CXCR4, DNMT3A, DDX41, ETNK1, EZH2, FBXW7, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, MYD88, NOTCH1, NPM1, NRAS, PPM1D, PTEN, RHOA, RUNX1, SETBP1, SF3B1, SRSF2, STAT3, STAT5B, STAT6, TET2, TP53, U2AF1, WT1.
MBS Item No. 73399
Please contact us for pricing for Non-Medicare eligible patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 3-4 Weeks
Test Information and Sample Requirements:
Myeloid NGS Panel: Blood, Bone Marrow
Myeloproliferative Neoplasm (MPN) NGS Panel: Blood, Bone Marrow
Primary Myelofibrosis (MF): Blood, Bone Marrow
The Lymphoid Panel utilises massively parallel sequencing technology to assess genetic variants (also referred to as mutations) that are important in different lymphoid disorders including both low-grade lymphomas and acute lymphoblastic leukaemias. Genes assessed in these panels are currently known to have important diagnostic, prognostic and therapeutic implications.
Clinical Indication: Suspected lymphoid malignancy
Gene List: BCL2, BCL2L1, BIRC3, BRAF, BTK, CARD11, CD274, CD79B, CXCR4, DNMT3A, EZH2, FYN, ID3, IDH1, IDH2, IRF8, JAK3, KRAS, MAP2K1, MCL1, MYD88, NOTCH1, NOTCH2, NRAS, PDCD1LG2, PHF6, PLCG1, PLCG2, RHOA, RUNX1, SF3B1, STAT3, STAT5B, STAT6, TCF3, TP53, XPO1.
Due to its recent introduction, NATA/RCPA accreditation does not cover the performance of this test. Austin Pathology is currently in the process of seeking accreditation.
Please contact us for pricing.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 3-4 Weeks
Test Information and Sample Requirements:
Lymphoid NGS Panel: Blood, Bone Marrow, Tissue
IGH (Immunoglobulin heavy chain) and TCRɣ (T-cell receptor gamma) gene rearrangement tests utilise massively parallel sequencing to assess the IGH or TCRɣ sequences in the sample. The presence of a dominant IGH or TCRɣ sequence is suggestive of a monoclonal B- or T-cell lymphocyte population. This test is helpful in diagnosing B- or T-cell malignancies.
In acute lymphoblastic leukaemia (ALL), the IGH rearrangement identified at diagnosis can be used to assess response to therapy. Detection of the diagnostic IGH rearrangement at later timepoints of treatment is called measurable residual disease (MRD) and is more sensitive than routine morphological assessment. Monitoring MRD allows for prognostication and treatment decisions in ALL.
IGH Minimal Residual Disease (MRD) NGS Monitoring
Acute Lymphoblastic Leukaemia (ALL): MBS Item No. 73310
Please refer to the link in the Test Information and Sample Requirements for further information for non ALL patients.
IGH Gene Rearrangement NGS for Clonality Assessment
Acute Lymphoblastic Leukaemia (ALL): MBS Item No. 73310
Please refer to the link in the Test Information and Sample Requirements for further information for non ALL patients.
TCRɣ Gene Rearrangement NGS for Clonality Assessment
Non-Medicare Rebatable
Acute Lymphoblastic Leukaemia (ALL): MBS Item No. 73310
Please refer to the link in the Test Information and Sample Requirements for further information for non ALL patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 3-4 Weeks
Test Information and Sample Requirements:
IGH Gene Rearrangement NGS for Clonality Assessment: Blood, Bone Marrow, Tissue
T-cell Receptor Gamma (TCRG) Gene Rearrangement NGS for Clonality Assessment: Blood, Bone Marrow, Tissue
IGH Minimal Residual Disease (MRD) NGS Monitoring: Blood, Bone Marrow, Tissue
Chronic Lymphocytic Leukaemia (CLL) Somatic Hypermutation Analysis utilises massively parallel sequencing to assess the presence or absence of abnormal VH gene sequences in the CLL population. The assay is part of the initial work-up for CLL and used for assessing disease prognosis and treatment decisions.
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 3-4 Weeks
Test Information and Sample Requirements:
IGHV Somatic Hypermutation Analysis: Blood, Bone Marrow
This test utilises the Cepheid GeneXpert Instrument Systems Xpert® BCR-ABL Ultra test to detect the presence of BCR::ABL1 p190 and p210. It is part of the diagnostic workup for new cases of chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL). It can also be used during treatment and on follow-up to assess for response to therapy and detect early disease relapse.
MBS Item No. 73314
Please contact us for pricing for Non-Medicare eligible patients.
Method: GeneXpert Reverse transcription quantitative PCR (RT-qPCR)
Expected Turnaround Time: 2-5 Days
Test Information and Sample Requirements:
BCR::ABL1 Translocation: Blood, Bone Marrow
This test utilises the Cepheid GeneXpert Instrument Systems to detect the presence of NPM1 Type A, Type B and Type D mutations (in NM_002520.6 exon 11). This test is used to assess the response to therapy in AMLs with NPM1 mutations and is more sensitive than morphological assessment to detect measurable residual disease (MRD). Monitoring MRD in AML allows for prognostication and treatment decisions.
Please note that the Xpert NPM1 Mutation assay does not distinguish among the different NPM1 Type A, B, or D mutations and is not designed to detect or monitor other rare types of mutant NPM1. Full assessment of NPM1 exon 11 is available with the Myeloid NGS Panel assay.
MBS Item No. 73314
Please contact us for pricing for Non-Medicare eligible patients.
Method: GeneXpert Reverse transcription quantitative PCR (RT-qPCR)
Expected Turnaround Time: 2-5 Days
Test Information and Sample Requirements:
NPM1 MRD (Type A, B or D): Blood, Bone Marrow
This test utilises PCR amplification and capillary electrophoresis to detect FLT3 and NPM1 mutations for the workup of new cases of acute myeloid leukaemia (AML). It is specific for FLT3 internal tandem duplications (ITD) and FLT3 mutations in the tyrosine kinase domain (TKD) at codon position 835 and 836. Also detects possible exon 11 clustered multiple insertional or insertion/deletions of NPM1 gene. It has a rapid turnaround time to assess in diagnosing and risk assessment of new cases of AML. Full sequencing assessment of FLT3 and NPM1 is available with the Myeloid NGS Panel assay.
MBS Item No. 73314
Please contact us for pricing for Non-Medicare eligible patients.
Method: Fragment Analysis
Expected Turnaround Time: 7 Days
Test Information and Sample Requirements:
Initial Diagnosis: Blood, Bone Marrow
Mutation Analysis: Blood, Bone Marrow
This test utilises droplet digital PCR (ddPCR) to assess for the presence of the JAK2 V617F mutation. Detection of JAK2 mutations is essential for the diagnosis of myeloproliferative neoplasms (MPN). Utilising ddPCR also allows for accurate quantification of the JAK2 V617F mutation, providing valuable information on prognosis and treatment response.
MBS Item No. 73325
Please contact us for pricing for Non-Medicare eligible patients.
Method: Droplet Digital PCR
Expected Turnaround Time: 1-2 Weeks
Test Information and Sample Requirements:
JAK2 (V617F): Blood
This test utilises droplet digital PCR (ddPCR) to assess for the presence of the MYD88 L265P mutation. Detection of the MYD88 mutation assists in the diagnosis of Waldenstrom’s macroglobulinaemia and other B-cell lymphoproliferative disorders.
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: Droplet Digital PCR
Expected Turnaround Time: 1-2 Weeks
Test Information and Sample Requirements:
MYD88 (L265P): Blood, Bone Marrow
This test utilises the Cepheid GeneXpert Instrument System to detect the presence Prothrombin (also known as FII) G20210A and Factor V Leiden G1691A mutations. Testing for these 2 mutations is commonly performed to assess the cause and risk for thromboembolism (blood clots).
Please contact us for pricing for Non-Medicare eligible patients.
Method: GeneXpert RT-PCR
Expected Turnaround Time: 7 Days
Test Information and Sample Requirements:
Factor II & V Leiden: Blood
Click here to download the Molecular Solid Tumour Request Form
Please check government eligibility criteria on the MBS Online Website for Medicare funded tests with the relevant MBS item numbers.
The mutation status of KRAS/NRAS and BRAF is indicative of the sensitivity of anti-EGFR and targeted BRAF therapies. A small proportion of colorectal carcinomas have amplification of ERBB2 (HER2), and may respond to anti-Her2 therapy.
Gene List: KRAS, NRAS, BRAF, PIK3CA, ERBB2, POLE.
MBS Item No. 73338
Please contact us for pricing for Non-Medicare eligible patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Colorectal NGS Panel: Tissue
The mutation status of this panel holds significant therapeutic implications, particularly with regard to the BRAF gene, which is linked to therapeutic responses in metastatic melanoma, specifically in relation to BRAF and MEK-inhibitor therapies. Additionally, mutations in the NRAS and KIT genes are gaining attention for their potential roles in targeted therapies. Melanomas with KIT mutations may exhibit responsiveness to KIT tyrosine kinase inhibitors, while those with NRAS mutations could demonstrate enhanced sensitivity to MEK inhibitors.
Gene List: NRAS, BRAF, KIT, GNA11, GNAQ, TERT promoter.
MBS Item No. 73336
Please contact us for pricing for Non-Medicare eligible patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Melanoma NGS Panel: Tissue
BRAF mutations have been associated with clinical responses to Tyrosine Kinase Inhibitors (TKIs) in individuals diagnosed with metastatic melanoma. Furthermore, clinical trials indicate that patients with BRAF mutations exhibit enhanced responses when treated with combined therapies.
MBS Item No. 73336
Please contact us for pricing for Non-Medicare eligible patients.
Method: Automated real-time PCR (Idylla) – List of targeted mutations
|
BRAF V600E |
(c.1799T>A) |
|
BRAF V600E2 |
(c.1799_1800delinsAA) |
|
BRAF V600D |
(c.1799_1800delinsAT & c.1799_1800delinsAC) |
|
BRAF V600K |
(c.1798_1799delinsAA) |
|
BRAF V600R |
(c.1798_1799delinsAG) |
|
BRAF V600M |
(c.1798G>A) |
|
BRAF Wild Type |
(c.1799T) |
Expected Turnaround Time: 1-2 Business Days
Test Information and Sample Requirements:
Melanoma Idylla (BRAF) Test: Tissue
The identification of particular EGFR mutations in non-small cell lung cancer (NSCLC) serves as a marker for either sensitivity or resistance to specific tyrosine kinase inhibitors available through the Pharmaceutical Benefits Scheme. The descriptions of MBS Items are provided below for reference. Furthermore, mutations in BRAF, ERBB2 (HER2), and MET can guide targeted therapeutic strategies. In the context of previous targeted therapy for NSCLC with fusion genes involving ALK and ROS1 this NGS assay can identify acquired resistance mutations (single nucleotide substitutions) in ALK or ROS1 which may influence the selection of therapeutic options.
Gene List: EGFR, KRAS, BRAF, PIK3CA, ERBB2, MET, ALK, ROS1.
MBS Item No. 73438 - New Diagnosis (EGFR, BRAF, KRAS and MET exon 14)
MBS Item No. 73337 - EGFR gene status for access to an EGFR TKI or Pembrolizumab
MBS Item No. 73351 - NSCLC (Stage IIIB or IV), new sample following progression after treatment with an EGFR tyrosine kinase inhibitor. To determine EGFR T790M status for access to Osimertinib.
MBS Item No. 73436 - Locally advanced, to determine requirements relating to MET exon 14 skipping status for access to Tepotinib.
Please contact us for pricing for Non-Medicare eligible patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Non-Small Cell Lung Carcinoma (NSCLC) NGS Panel: Tissue
The identification of particular EGFR mutations in non-small cell lung cancer (NSCLC) serves as a marker for either sensitivity or resistance to specific treatments available through the Pharmaceutical Benefits Scheme. The descriptions of MBS Items are provided below for reference.
MBS Item No. 73337 - EGFR gene status for access to an EGFR TKI or Pembrolizumab
MBS Item No. 73351 - NSCLC (Stage IIIB or IV), new sample following progression after treatment with an EGFR tyrosine kinase inhibitor. To determine EGFR T790M status for access to Osimertinib.
Please contact us for pricing for Non-Medicare eligible patients.
Method: Automated real-time PCR (Idylla)
|
Exon 18 |
G179A |
c.2156G>C |
|
G179C |
c.2155G>T; c.2154_2155delinsTT |
|
|
G179S |
c.2155G>A |
|
|
Del9 |
c.2238_2248delinsGC c.2239_2248delinsC |
|
|
|
c.2240_2248del c.2239_2247del |
|
|
Del12 |
c.2239_2251delinsC c.2240_2251del |
|
|
Exon 19 |
Del15 |
c.2235_2249del c.2236_2250del c.2239_2253del c.2240_2254del c.2238_2252del c.2237_2251del c.2235_2252delinsAAT c.2237_2252delinsT c.2234_2248del c.2236_2253delinsCTA c.2237_2253delinsTA c.2235_2251delinsAG c.2236_2253delinsCAA c.2230_2249delinsGTCAA |
|
Del18 |
c.2240_2257del c.2237_2255delinsT c.2239_2256del c.2236_2253del c.2239_2258delinsCA c.2237_2254del c.2238_2255del c.2237_2257delinsTCT c.2236_2256delinsAT c.2236_2256delinsATC c.2237_2256delinsTT c.2237_2256delinsTC c.2235_2255delinsGGT |
|
|
Del21 |
c.2238_2258del c.2236_2256del |
|
|
Del24 |
c.2253_2276del |
|
|
Exon 20 |
T790M |
c.2369C>T |
|
S768I |
c.2303G>T |
|
|
insG |
c.2310_2311insGGT |
|
|
insASV9 |
c.2308_2309insGCCAGCGTG |
|
|
insASV11 |
c.2308_2311delinsCCAGCGTGGAT |
|
|
insSVD |
c.2311_2312insGCGTGGACA |
|
|
insH |
c.2319_2320insCAC |
|
|
Exon 21 |
L858R |
c.2573T>G |
|
c.2573_2574delinsGT |
||
|
c.2573_2574delinsGA |
||
|
L861Q |
c.2582T>A |
Expected Turnaround Time: 1-2 Business Days
Test Information and Sample Requirements:
Non-Small Cell Lung Carcinoma (NSCLC) EGFR Idylla Test: Tissue
Granulosa Cell Tumour represents a specific category of ovarian neoplasm. FOXL2 belongs to the Forkhead box (FKHD) family of transcription factors. Mutations in FOXL2 are found in a significant proportion of both primary and metastatic adult granulosa cell tumours and assists in confirming this diagnosis.
Gene List: FOXL2
MBS Item No. 73377
Please contact us for pricing for Non-Medicare eligible patients.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Ovarian Granulosa Cell Tumour NGS: Tissue
The next-generation sequencing (NGS) panel for endometrial carcinoma assesses the mutation status of POLE, PIK3CA, ERBB2 and TP53, which could influence the prognosis and management strategies for patients.
Gene List: POLE, PIK3CA and TP53.
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Endometrial Carcinoma NGS Panel: Tissue
The gastrointestinal stromal tumor (GIST) NGS panel is characterised by the presence of activating mutations in genes such as KIT, PDGFRA, or BRAF. The nature of these mutations can influence both prognosis and the effectiveness of tyrosine kinase inhibitor (TKI) therapy.
Gene List: KIT, PDGFRA, BRAF
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Gastrointestinal Stromal Tumour (GIST) NGS Panel: Tissue
The methylation of the MLH1 promoter is associated with loss of MLH1 protein expression. Tumours that display elevated microsatellite instability (MSI-H) and/or demonstrate absent MLH1/PMS2 staining through immunohistochemical analysis will undergo assessment for MLH1 promoter methylation. Absence of MLH1 promoter methylation is associated with an increased likelihood of germline mutation in a DNA mismatch repair gene.
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: MS-MLPA
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
MLH1 Promoter Methylation Analysis: Tissue
The coverage of genes listed in all the sub panels (colorectal, melanoma, NSCLC, ovarian granulosa cell tumour, endometrial carcinoma, GIST) and the full solid tumour NGS panel are listed below.
AKT1 (NM_005163.2: Exons 3,6)
ALK (NM_004304.4: Exons 21, 22, 23, 24, 25)
BRAF (NM_004333.4: Exons 8, 11, 12, 13, 14, 15)
EGFR (NM_005228.4: Exons 2, 3, 6, 7, 8, 9, 15, 18, 19, 20, 21)
ERBB2 (NM_004448.3: Exons 10, 19, 20, 21, 24)
FOXL2 (NM_023067.3: Exon 1)
GNA11 (NM_002067.4: Exon 5)
GNAQ (NM_002072.4: Exons 4, 5)
GNAS (NM_000516.5: Exons 6, 7, 8, 9)
H3F3A (NM_002107.4: Exon 2)
HRAS (NM_002107.4: Exons 2, 3)
IDH1 (NM_005896.3: Exons 3, 4)
IDH2 (NM_002168.3: Exon 4)
KIT (NM_000222.2: Exons 2, 8, 9, 10, 11, 13, 14, 15, 17, 18)
KRAS (NM_033360.3: Exons 2, 3, 4, 6)
MAP2K1 (NM_002755.3: Exons 2, 3, 5, 6, 7)
MET (NM_000245.3: Exons 2, 11, 14, 16, 19, 21)
NRAS (NM_002524.4: Exons 2, 3, 4, 5)
PDGFRA (NM_006206.5: Exons 12, 14, 15, 18, 23)
PIK3CA (NM_006218.3: Exons 2, 5, 7, 8, 10, 12, 14, 19, 20, 21)
POLD1 (NM_002691.3: Exons 8, 9, 10, 11, 12)
POLE (NM_006231.4: Exons 9, 10, 11, 12, 13, 14)
RET (NM_020975.4: Exons 10, 11, 13, 14, 15, 16)
ROS1 (NM_002944.2: Exons 36, 37, 38, 39, 40, 41, 42)
TERT (NM_198253.2: Promoter)
TP53 (NM_000546.5: Exons 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
Non-Medicare Rebatable
Please refer to the link in the Test Information and Sample Requirements.
Method: Next Generation Sequencing (NGS)
Expected Turnaround Time: 2-3 Weeks
Test Information and Sample Requirements:
Solid Tumour NGS Full Panel: Tissue
