Haematological Oncology was one of the first specialties to routinely incorporate genetic testing for diagnostic, prognostic, and therapeutic purposes.

Genetic testing plays a pivotal role in most haematologic neoplasms. The utilisation of genetic tests can clarify or make the diagnosis of a specific haematological malignancy, provide information about eligibility for specific treatments or prognosis, as well as help to monitor and evaluate depth of treatment response. There are many actionable and clinically significant genetic variations in haematological malignancies, with testing performed on blood or bone marrow. Genetic testing in haematological malignancies spans the full range of genetic techniques, from karyotyping to advanced molecular methods such as massively parallel sequencing.

The BCR-ABL1 gene fusion is commonly seen in chronic myeloid leukaemia and acute lymphoblastic leukaemia. The detection and quantitation of transcript levels is important in the diagnosis, treatment, and monitoring of the patients with these disorders.

Test NameBCR-ABL
Clinical IndicationUsed in the differential diagnosis, monitoring, and for treatment selection in patients with laboratory evidence of certain types of leukaemia.
Gene(s)BCR/ABL1 fusion
MethodReal-time PCR
Turn around time7 days
Medicare Eligibility73314 – criteria apply
Sample Type/ Collection TypeBlood 10mL EDTA tube or Bone Marrow 4mL EDTA tube
Special InstructionsMust be received in the laboratory within 48hrs from collection time. No collections Fridays.

Mutations in the FLT3 and NPM1 genes are seen in acute myeloid leukaemia (particularly in cases with a normal cytogenetic karyotype) and are of prognostic significance.

Test NameNucleophosmin & FLT3
Clinical IndicationFor diagnosis, prognosis, and classification in acute myeloid leukaemia
Gene(s)NPM1; FLT3
MethodReal-time PCR analysis; Conventional PCR and capillary electrophoresis
Turn around time14 days
Medicare Eligibility73314
Sample Type/ Collection Type6mL Blood EDTA tube or 1 mL bone marrow EDTA tube
Special InstructionsTest is performed on either Peripheral Blood or Bone Marrow Aspirate. Peripheral blood can be collected by collector, Bone marrow aspirate (Doctor collect only) must be placed into EDTA.

The V617F mutation is seen in a number of myeloproliferative disorders such as polycythaemia vera, essential thrombocytosis and idiopathic myelofibrosis.

Test NameJAK2 V617F
Clinical IndicationTo aid in the differential diagnosis and prognostic risk classification for myeloproliferative neoplasms, e.g. polycythaemia vera, essential thrombocythaemia and primary myelofibrosis
Gene(s)JAK2
MethodPCR genotyping
Turn around time2 weeks
Medicare Eligibility73325 – criteria apply
Sample Type/ Collection TypeBlood 10mL EDTA tube or Bone Marrow 4mL EDTA tube
Special InstructionsNone

Calreticulin (CALR) exon 9 mutations are seen in a number of myeloproliferative neoplasms. Consider CALR mutations in conjunction with or following other molecular tests for these disorders.

Test Name CALR (Calreticulin)
Clinical Indication In the diagnostic workup of myeloproliferative neoplasms
Gene(s) CALR
Method PCR fragment size analysis
Turn around time 14 days
Medicare Eligibility No
Sample Type Blood EDTA 10mL or Bone Marrow EDTA 4mL
Special Instructions None

The MPL mutations W515L and W515K are seen in a number of myeloproliferative disorders such as polycythaemia vera, essential thrombocytosis and idiopathic myelofibrosis. Consider testing in conjunction with or following other molecular tests for these disorders.

Test NameMPL (W515 mutations)
Clinical IndicationTo aid in the differential diagnosis and prognostic risk classification for myeloproliferative neoplasms, e.g. polycythaemia vera, essential thrombocythaemia and primary myelofibrosis
Gene(s)MPL (Thrombopoietin)
MethodPCR Genotyping
Turn around time4 weeks
Medicare Eligibility73325– criteria apply
Sample Type / Collection TypeBlood 10mL EDTA tube or Bone Marrow 4mL EDTA tube
Special InstructionsNone

B-cell immunoglobulin heavy chain (IgH) gene rearrangements

This test is for the IgH gene rearrangements (FR1, FR2 and FR3) and will detect greater than 80% of B-cell lymphoproliferative disorders.

T-cell Receptor (beta and gamma) gene rearrangements:

This test is for detecting monoclonality of T lymphocytes using primers targeted at both beta and gamma gene rearrangements, and will detect at least 90% of T-cell lymphoproliferative disorders.

Bcl-2

This test is specific for the major breakpoint region (mbr) of the bcl-2 associated translocation [t(14;18)]. This translocation is associated with up to 85% of lymphomas with a follicular morphology, and with approximately one third of diffuse large cell lymphomas.

Bcl-1

This test is specific for the translocation involving the Cyclin D1 gene [t(11;14)]. It is commonly associated with Mantle Cell Lymphoma (MCL).

Test Name T &/or B cell rearrangement
Clinical Indication To determine clonality in lymphoproliferative disorders
Gene(s) IGH
Method Conventional PCR and fragment analysis
Turn around time 2 weeks
Medicare Eligibility No
Sample Type Blood or bone marrow or Lymph node or Tumour
Special Instructions None

Non-random chromosomal rearrangements are associated with different types of haematology-oncology neoplasms. Cytogenetic investigation using a combination of technologies may assist in the diagnosis, prognosis and staging of the haematological malignancy.

Conventional cytogenetic analysis

Conventional chromosome analysis and targeted FISH are the premier tests for the investigation of haematological malignancies. The conventional chromosome study involves microscopic examination and screening of the whole genome at the cellular level to detect large genomic changes and chromosomal rearrangements that may be prognostic or diagnostic indicators in malignant disease.

Test NameChromosomes Bone MarrowChromosomes Lymph NodesChromosomes Unstimulated Blood
Clinical IndicationFor diagnosis, classification, and prognosis in haem-oncology
Gene(s)Chromosome Analysis
MethodConventional chromosome analysis
Turn Around TimeUrgent 2 days; Routine 22 days10 – 12 days18 days
Medicare Eligibility732907328773290
Sample TypeBone marrow aspirateLymph nodeBlood
Collection Type1mL in 1x lithium heparin tubeSterile container of Antibiotic Transport Media.6ml 1x lithium heparin tube and 6mL 1x tube
Special InstructionsDoctor collect only. Add aspirate to a 2mL lithium heparin tube and mix gently. Transport cooled or at room temperature.See important notes below*.None

*Doctor collect. Sample must be kept sterile and moist. DO NOT USE FORMALIN. USE ANTIBIOTIC TRANSPORT MEDIA available from the Histology Department of your local laboratory. For overnight transport cover large specimens with ANTIBIOTIC TRANSPORT MEDIA OR STERILE NORMAL SALINE and sent to your local laboratory IMMEDIATELY. Please indicate if specimen is to be shared with Histology.

Chromosome microarray (also known as molecular karyotyping) is an advanced genome-wide investigation used to detect sub-microscopic DNA changes that are not detectable by conventional karyotype and/or fluorescence in-situ hybridisation (FISH). This technique can be used in the diagnostic investigation of haematological malignancies such as chronic lymphocytic leukemia, to detect regions of loss and/or gain of DNA and copy neutral loss of heterozygosity (CNLOH). This test will provide information about the genes involved in regions of copy number alteration. The information provided will assist in diagnosis, prognosis and staging of the malignancy and patient management.

Microarray and targeted FISH analysis has recently been established as the gold standard cytogenomic investigation of CLL.

Test NameChromosomes Unstimulated Blood
Clinical IndicationFor diagnosis, classification, and prognosis in haem-oncology
Gene(s)Genome Wide Chromosomal Analysis
MethodMicroarray analysis
Turn around time18 days
Medicare Eligibility73290
Sample TypeBlood
Collection Type6ml 1x lithium heparin tube and 6mL 1x EDTA tube
Special InstructionsNone

Fluorescence in-situ hybridisation (FISH) is a targeted molecular cytogenetic technique used for the investigation of precise chromosome regions, particularly relevant when a specific condition is suspected. The technique binds a colour labelled DNA probe to a specific region on the patient chromosomes. As this is a targeted test it is important when requesting a FISH test to indicate the clinical condition that is being tested for.

A broad range of FISH is available for the detection of non-random rearrangements, deletions and chromosome aneuploidy that are associated with a haematological malignancy. FISH is a targeted investigation and has the benefit of screening large numbers of cells to detect clonal abnormalities.

Test NameFISH Haem-Oncology
Clinical IndicationFor diagnosis, classification, and prognosis in haem-oncology
Gene(s)See list of panels and individual targets below
MethodFISH
Turn around time2 – 14 days
Medicare Eligibility73314 – Criteria applies
Sample TypeBone marrow Aspirate
Collection TypeLithium heparin tube
Special InstructionsDoctor Collect. No additional sample required. Test is performed with Chromosome analysis.

Panel Testing

AML PanelPML/RARA; CBFB; Del5q; MLL; Del7q; IGH/MYC; Del 20q
Myelodysplastic syndromeDel5q; del7q; IGH/MYC; MLL; ETV6; del 20q
ALLIGH/MYC; BCR/ABL1; MLL; ETV6; IGH/FGFR3; CEP9; CEP 10; TP53; E2A/PBX1
Chronic Lymphocytic LeukemiaIGH/CCND1; ATM; CEP12; del 13q14; TP53; MYB; RB1
Multiple Myeloma1pq; IGH/CCND1; IGH BA; del 13q14; TP53; IGH/FGFR3; IGH/MAF; IGH/MAFB; IGH/CCND3
LymphomaBCL6; IGH/MYC; IGH/CCND1; BIRC3/MALT1; RB1; del 13q14

Individual Probes

Syndrome/Indication Chromosome location
Acute myeloid leukemiaAML/ETOt(8;21)(q22,q22)
Acute myeloid leukemiaCBFBinv(16)(p12;q22)
Acute promyelocytic leukemiaPML/RARA(15;17)(q22;q21.1)
B lymphocytic leukemia/lymphoma1:19 rearrangements1:19 rearrangements
B-cell disordersIGH14q32
B-cell leukemiasMLL11q23
B-Cell lymphomasMYC8q24
B-Cell lymphomasBIRC3/MALTt(11:18)(q21;q21)
B-Cell lymphomasIGK2p11.2
B-Cell lymphomasIGL22p11.2
Burkitt’s Lymphoma/ -like LeukemiaIGH/MYC/CEP8t(8;14)(q23;q32)
Chronic lymphocytic leukemiaATM11q23
Chronic lymphocytic leukemiaBCL319q13.32
Chronic lymphocytic leukemiaTrisomy 12centromere
Chronic lymphocytic leukemiaMYB6q23
Chronic lymphocytic leukemia/Myeloma13q deletion13q14.3
Chronic lymphocytic leukemia/MyelomaTP53 deletion17p13
Chronic lymphocytic leukemia/MyelomaRB113q14.3
Chronic myelomonocytic leukemiaPDGFRB BA5q32
Follicular lymphomaIGH/BCL2t(14;18)(q32;21)
LeukemiaBCR/ABLt(9;22)(q34;q11.2)
Leukemias including treatment relatedTrisomy/monosomy 7centromere
Mantle cell lymphoma/CLLIGH/CCND1-XTt(11;14)(q13;q32)
Multiple myeloma1pq (CKS1B/CDKN2)
amplification/deletion
1q21/1p32.3
Multiple myelomaIGH/CCND3t(6;14)(p21;q32.2)
Multiple myelomaIGH/FGFR3t(4;14)(p16.3;q32)
Multiple myelomaIGH/MAF translocationt(14;16)
Multiple myelomaIGH/MAFB translocationt(14;20)
Multiple myelomaIRF46p25.3
Myelodysplastic syndromesETV612p13
Myeloid and lymphatic leukemias1pq1p36/1q25
Myeloid and lymphatic leukemiasTrisomy 9centromere
Myeloid and lymphoid neoplasmsFIP1L1/PDGFRA: CHIC2- deletion4q12
Myeloid leukemiasEVI13q26.2
Myeloid neoplasms5q deletion (5q- syndrome)5q31.2
Myeloid neoplasms7q deletion7q22/7q31
Myeloproliferative disordersFGFR18p12
Myeloproliferative disorders/Myeloid neoplasms20q deletion20q12
Non-Hodgkin lymphomasBCL63q26
Non-Hodgkin lymphomasIGH/MALT1t(14;18)(q32;q21)
Non-Hodgkin lymphomasPAX 59p12
T cell leukemiasTCL1 breakapart14q32.13

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