Lymphoid Neoplasms
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.
Test Name | BCR-ABL |
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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 |
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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 Name | Chromosomes Bone Marrow | Chromosomes Lymph Nodes | Chromosomes Unstimulated Blood |
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Clinical Indication | For diagnosis, classification, and prognosis in haem-oncology | ||
Gene(s) | All chromosomes | ||
Method | Conventional chromosome analysis | ||
Turn Around Time | Urgent 2 days; Routine 22 days | 10 – 12 days | 18 days |
Medicare Eligibility | 73290 | 73287 | 73290 |
Sample Type | Bone marrow aspirate | Lymph node | Blood |
Collection Type | 1mL in 1x lithium heparin tube | Sterile container of Antibiotic Transport Media. | 6mL in 1x lithium heparin tube and 6mL in 1x tube |
Special Instructions | Doctor 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 Name | Chromosomes Unstimulated Blood |
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Clinical Indication | For diagnosis, classification, and prognosis in haem-oncology |
Gene(s) | All chromosomes |
Method | Microarray analysis |
Turn around time | 18 days |
Medicare Eligibility | 73290 |
Sample Type | Blood |
Collection Type | 6mL 1x lithium heparin tube and 6mL 1x EDTA tube |
Special Instructions | None |
Test Name | FISH Haem-Oncology | |
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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 Name | Lymphoid 66 gene panel |
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Clinical Indication | For 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 |
Method | Next generation sequencing |
Turn around time | 3 – 4 weeks |
Medicare Eligibility | 73448 |
Sample Type/ Collection Type | Blood 4mL EDTA tube of Bone Marrow 4mL EDTA tube |
Special Instructions | Specialist/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 Name | PAN Haem 96 gene panel |
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Clinical Indication | For 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 |
Method | Next generation sequencing |
Turn around time | 3 – 4 weeks |
Medicare Eligibility | 73447 (Myeloid) or 73448 (Lymphoid) |
Sample Type/ Collection Type | Blood 4mL EDTA tube of Bone Marrow 4mL EDTA tube |
Special Instructions | Specialist/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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