Lymphoid neoplasms arise from malignant transformation of lymphoid cells at various stages of differentiation. Genomic analysis that comprises of both molecular techniques (quantitative real-time PCR, microarray and somatic variant analysis) and cytogenetic methods (karyotyping and FISH) plays an important role for the diagnosis, prognostication and decision of treatment strategy in these disorders.  With the explosion in knowledge about the molecular landscape of lymphoid malignancies and the increasing availability of high throughput techniques, molecular diagnostics in haematopathology has moved from isolated marker studies to a more comprehensive approach, integrating results of multiple genes analysed with a variety of techniques on the DNA and RNA level.

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 Name BCR-ABL
Clinical Indication Used in the differential diagnosis, monitoring, and for treatment selection in patients with laboratory evidence of certain types of leukaemia.
Gene(s) BCR/ABL1 fusion
Method Real-time PCR
Turn around time 2 – 4 days
Medicare Eligibility 73314 – criteria apply
Sample Type/ Collection Type Blood 10mL EDTA tube or Bone Marrow 4mL EDTA tube
Special Instructions Bone marrow and diagnostic specimens must be received by the laboratory within 48 hours of collection. No collections Friday. Specimens for monitoring purposes must be received in the laboratory within 72hrs from collection. Collection can occur any day.

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)All chromosomes
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 in 1x lithium heparin tube and 6mL in 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)All chromosomes
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.Panel TestingIndividual Probes
Test Name FISH Haem-Oncology
Clinical Indication For diagnosis, classification, and prognosis in haem-oncology
Gene(s) See list of panels and individual targets below
Method FISH
Turn around time 2 – 14 days
Medicare Eligibility 73314 – Criteria applies
Sample Type Bone marrow Aspirate
Collection Type Lithium heparin tube
Special Instructions Doctor Collect. No additional sample required. Test is performed with Chromosome analysis.
AML Panel PML/RARA; CBFB; Del5q; MLL; Del7q; IGH/MYC; Del 20q
Myelodysplastic syndrome Del5q; del7q; IGH/MYC; MLL; ETV6; del 20q
ALL IGH/MYC; BCR/ABL1; MLL; ETV6; IGH/FGFR3; CEP9; CEP 10; TP53; E2A/PBX1
Chronic Lymphocytic Leukemia IGH/CCND1; ATM; CEP12; del 13q14; TP53; MYB; RB1
Multiple Myeloma 1pq; IGH/CCND1; IGH BA; del 13q14; TP53; IGH/FGFR3; IGH/MAF; IGH/MAFB; IGH/CCND3
Lymphoma BCL6; IGH/MYC; IGH/CCND1; BIRC3/MALT1; RB1; del 13q14
Syndrome/Indication Chromosome location
Acute myeloid leukemia AML/ETO t(8;21)(q22,q22)
Acute myeloid leukemia CBFB inv(16)(p12;q22)
Acute promyelocytic leukemia PML/RARA (15;17)(q22;q21.1)
B lymphocytic leukemia/lymphoma 1:19 rearrangements 1:19 rearrangements
B-cell disorders IGH 14q32
B-cell leukemias MLL 11q23
B-Cell lymphomas MYC 8q24
B-Cell lymphomas BIRC3/MALT t(11:18)(q21;q21)
B-Cell lymphomas IGK 2p11.2
B-Cell lymphomas IGL 22p11.2
Burkitt’s Lymphoma/ -like Leukemia IGH/MYC/CEP8 t(8;14)(q23;q32)
Chronic lymphocytic leukemia ATM 11q23
Chronic lymphocytic leukemia BCL3 19q13.32
Chronic lymphocytic leukemia Trisomy 12 centromere
Chronic lymphocytic leukemia MYB 6q23
Chronic lymphocytic leukemia/Myeloma 13q deletion 13q14.3
Chronic lymphocytic leukemia/Myeloma TP53 deletion 17p13
Chronic lymphocytic leukemia/Myeloma RB1 13q14.3
Chronic myelomonocytic leukemia PDGFRB BA 5q32
Follicular lymphoma IGH/BCL2 t(14;18)(q32;21)
Leukemia BCR/ABL t(9;22)(q34;q11.2)
Leukemias including treatment related Trisomy/monosomy 7 centromere
Mantle cell lymphoma/CLL IGH/CCND1-XT t(11;14)(q13;q32)
Multiple myeloma 1pq (CKS1B/CDKN2) amplification/deletion 1q21/1p32.3
Multiple myeloma IGH/CCND3 t(6;14)(p21;q32.2)
Multiple myeloma IGH/FGFR3 t(4;14)(p16.3;q32)
Multiple myeloma IGH/MAF translocation t(14;16)
Multiple myeloma IGH/MAFB translocation t(14;20)
Multiple myeloma IRF4 6p25.3
Myelodysplastic syndromes ETV6 12p13
Myeloid and lymphatic leukemias 1pq 1p36/1q25
Myeloid and lymphatic leukemias Trisomy 9 centromere
Myeloid and lymphoid neoplasms FIP1L1/PDGFRA: CHIC2- deletion 4q12
Myeloid leukemias EVI1 3q26.2
Myeloid neoplasms 5q deletion (5q- syndrome) 5q31.2
Myeloid neoplasms 7q deletion 7q22/7q31
Myeloproliferative disorders FGFR1 8p12
Myeloproliferative disorders/Myeloid neoplasms 20q deletion 20q12
Non-Hodgkin lymphomas BCL6 3q26
Non-Hodgkin lymphomas IGH/MALT1 t(14;18)(q32;q21)
Non-Hodgkin lymphomas PAX 5 9p12
T cell leukemias TCL1 breakapart 14q32.13

This panel offers comprehensive testing for genomic variants that can provide diagnostic and prognostic information for patients with lymphoid disorders including chronic lymphocytic leukaemia, mantle cell lymphoma, hairy cell leukaemia, lymphoplasmacytic lymphoma and follicular lymphoma. It is based on international guidelines and best practices. If required, customisation to suit individual patient needs can be offered.

Test NameLymphoid 66 gene panel
Clinical IndicationFor diagnostic/prognostic work up of lymphoid malignancies
Genes (66)ARID1A, ASXL1, ATM, B2M, BCL2, BIRC3, BRAF, BTK, CARD11, CCND1, CD79B, CREBBP, CRLF2, CXCR4, DNMT3A, EP300, ETV6, EZH2, FBXW7, FLT3, FOXO1, GNA13, ID3, IDH1, IDH2, IKZF1, IL7R, JAK1, JAK2, JAK3, KLF2, KMT2D, KRAS, MAP2K1, MEF2B, MYC, MYD88, NF1, NFKBIE, NOTCH1, NOTCH2, NRAS, PAX5, PHF6, PIM1, PLCG2, POT1, PRDM1, PTEN, PTPN11, RHOA, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT5B, STAT6, TCF3, TET2, TNFAIP3, TNFRSF14, TP53, U2AF1, WT1 and XPO1
MethodNext generation sequencing
Turn around time3 – 4 weeks
Medicare Eligibility73448
Sample Type/ Collection TypeBlood 4mL EDTA tube of Bone Marrow 4mL EDTA tube
Special InstructionsSpecialist/consultant physician request only

This panel combines genes from both Myeloid and Lymphoid Gene Panels, recognising that some haematological disorders require additional genes for their workup, classification and prognostication.

Test NamePAN Haem 96 gene panel
Clinical IndicationFor extended assessment of myeloid/lymphoid disorders.
Genes (96)ABL1, ANKRD26, ARID1A, ASXL1, ATM, B2M, BCL2, BCOR, BCORL1, BIRC3, BRAF, BTK, CALR, CARD11, CBL, CCND1, CD79B, CEBPA, CREBBP, CRLF2, CSF3R, CUX1, CXCR4, DDX41, DNMT3A, EP300, ETNK1, ETV6, EZH2, FBXW7, FLT3, FOXO1, GATA1, GATA2, GNA13, GNAS, HRAS, ID3, IDH1, IDH2, IKZF1, IL7R, JAK1, JAK2, JAK3, KDM6A, KIT, KLF2, KMT2A, KMT2D, KRAS, MAP2K1, MEF2B, MPL, MYC, MYD88, NF1, NFKBIE, NOTCH1, NOTCH2, NPM1, NRAS, PAX5, PDGFRA, PHF6, PIM1, PLCG2, POT1, PPM1D, PRDM1, PTEN, PTPN11, RAD21, RHOA, RUNX1, SETBP1, SETD2, SF3B1, SH2B3, SMC1A, SMC3, SOCS1, SRSF2, STAG2, STAT3, STAT5B, STAT6, TCF3, TET2, TNFAIP3, TNFRSF14, TP53, U2AF1, WT1, XPO1 and ZRSR2
MethodNext generation sequencing
Turn around time3 – 4 weeks
Medicare Eligibility73447 (Myeloid) or
73448 (Lymphoid)
Sample Type/ Collection TypeBlood 4mL EDTA tube of Bone Marrow 4mL EDTA tube
Special InstructionsSpecialist/consultant physician request only

All coding exons

ARID1A, ATM, B2M, BCL2, BCOR, BCORL1, CARD11, CEBPA, CREBBP, CSF3R, CUX1, CXCR4, DDX41, DNMT3A, EP300, ETV6, EZH2, FBXW7, FOXO1, GATA2, GNA13, ID3, IDH1, IDH2, IKZF1, IL7R, JAK1, JAK2, JAK3, KDM6A, KLF2, KMT2A, KMT2D, KRAS, MAP2K1, MPL, MYC, NF1, NFKBIE, NOTCH2, NRAS, PAX5, PDGFRA, PHF6, PIM1, POT1, PPM1D, PRDM1, PTEN, RAD21, RUNX1, SETD2, SH2B3, SMC1A, SOCS1, STAG2, STAT3, TCF3, TET2, TNFAIP3, TNFRSF14, TP53, ZRSR2

Targeted coverage

ABL1 (exons 4-10), ANKRD26 (exons 1-4), ASXL1 (exons 10,12-13), BIRC3 (exons 6-9), BRAF (exon 15), BTK (exons 10-19), CALR (exon 9), CBL (exons 8-9), CCDN1 (exon 1), CD79B (exons 5-6), CRLF2 (exon 6), ETNK1 (exon 3), FLT3 (exons 11,13-17,20), GATA1 (exons 2-4), GNAS (exons 8-9), HRAS (exons 2-3), KIT (exons 2,8-11,13,17-18), MEF2B (exons 2-3), MYD88 (exons 3-5), NOTCH1 (exons 26-28, 34), NPM1 (exons 10-11), PLCG2 (exons 18-33), PTPN11 (exons 3,7-13), RHOA (exon 2), SETBP1 (exon 4), SF3B1 (exons 10-16), SMC3 (exons 10,13,19,23,25,28), SRSF2 (exon 1), STAT5B (exons 14-17), STAT6 (exons 8-18), U2AF1 (exons 2,6), WT1 (exons 7,9), XPO1 (exons 15-16).

Exons described as per the MANE select reference transcript. 

All ROI include 5 bases into flanking introns.



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