Referrer's guide to NGS Testing in Haematological Malignancy

• All patients undergoing NGS testing for haematological malignancy should provide appropriate informed consent. This should include the possibility of detecting variants that require further investigation, including potential germline variants that may be relevant for both the patient and family members.

• Somatic testing for diagnostic purposes in cancer is typically considered a Level 1 test under the Australian Commission on Safety and Quality in Health Care (ACSQHC) ‘Requirements for medical testing for human genetic variation’ and does not require specific documentation of informed consent.

• When the risk of a clinically complex result is moderate, testing is considered Level 2 by ACSQHC and requires genetic counselling and written consent prior to testing. Examples of this type of testing include confirmatory germline, predictive, and pre-symptomatic testing.

For further information please see our full text version: Do I need to seek specific patient consent for NGS testing?

• For tumour testing using our AllHaem DNA and RNA panels, samples should be representative of the disease and ideally contain a minimum of 10% tumour burden. Suitable samples include:

• • Peripheral blood: for disease with a circulating component (e.g. chronic lymphocytic leukaemia, known or suspected myeloproliferative neoplasms, myelodysplastic syndromes, acute leukaemia with circulating disease, and lymphoma with circulating disease).
  • Bone marrow aspirate: for disease confined to, or predominantly present in, the bone marrow compartment (e.g. myeloma, AML).
  • Bone marrow trephine: may be tested in exceptional circumstances where there are no other suitable samples available.
  • Tissue: can be sent as fresh or FFPE (e.g. lymph node biopsy)
  • DNA or RNA extracted from the above sources

• Cell-free DNA (cfDNA) may be used for tumour profiling where a diagnostic sample cannot otherwise be obtained. The sample must be collected in a Streck Cell-Free DNA tube.
• For germline testing in the context of known or suspected haematological malignancy or bone marrow failure syndrome, suitable sources of germline DNA are hair follicles (typically eyebrows) or cultured skin fibroblasts.
• Peripheral blood is not a suitable sample for germline testing in haematological malignancies.

For further information please see our full text version: Which sample type should I send for NGS analysis?

• AllHaem DNA – Panel of 80 genes. Designed to provide diagnostic, prognostic, and therapeutic information across the spectrum of haematological malignancy.
• AllHaem RNA – Gene fusion panel of 71 genes. Designed to provide diagnostic, prognostic and therapeutic information primarily in the setting of ALL, AML, eosinophilia, and histiocytic disorders.
• Myeloproliferative Neoplasm (MPN) Gene Panel – Panel of 22 genes. Designed to provide diagnostic, prognostic, and therapeutic information primarily in the settings of MPN and MDS/MPN.
• Haematological Malignancy Predisposition Panel – Panel of 10 genes. A targeted panel designed to provide information on the presence of germline predisposition to haematological malignancy.

For information on available panels, please see our full text version: What NGS panel tests are available?

• Four pathology item numbers (73445, 73446, 73447, 73448) are listed on the MBS for NGS panel testing for variants associated with haematological malignancies of myeloid or lymphoid origin.
• These items relate to NGS panel testing of DNA/RNA for the determination of diagnosis, prognosis, and/or management of a patient presenting with a clinically suspected haematological malignancy of myeloid or lymphoid origin.
• Two MBS items (73398, 73399) are listed for NGS panel testing in patients with suspected myeloproliferative neoplasms (MPN).

For further information please see our full text version: How much does testing cost and is it reimbursed?

• Variants are initially classified according to their assumed origin in the patient: somatic, germline or uncertain (i.e. cannot distinguish between potential somatic or germline origin).
• Assumed somatic variants are classified according to their clinical relevance in the disease context being investigated into one of six categories: Diagnostic, Prognostic, Drug target, Drug resistance, MRD marker, and Clonal marker.
• Assumed germline variants are classified according to their association with a specific inherited phenotype/disease, as either: Pathogenic, Likely Pathogenic, Variant of Uncertain Significance, Likely Benign or Benign.
• Variants of uncertain origin are not classified further. Depending on the clinical context, testing of a non-haematological sample (e.g. hair) may be of value to determine the origin of these variants.
• Germline confirmation is recommended for all potentially clinically significant DDX41 variants.
• Assumed or confirmed germline variants classified as pathogenic or likely pathogenic may have diagnostic and management implications for the patient and their family. In these cases, referral to a genetics service is recommended for appropriate counselling and screening of at-risk family members.

For further information please see our full text version: How are variants classified and what do I do with the result?

• The AllHaem DNA panel and pipeline is designed to detect SNVs and small insertions/deletions across the range of specified genes or exons included on the panel. This panel does not currently provide information on copy number variants or structural variants.
• The AllHaem RNA panel and pipeline is designed to detect intergenic fusions. This panel does not currently provide information on abnormal isoforms of individual genes or expression data.
• Detection of internal tandem duplications (ITDs) is a recognised limitation of NGS panels. Whilst they may be detected with the AllHaem panel, if FLT3-ITD & UBTF-TD status is to be definitively determined, then capillary electrophoresis should be performed.

For further information please see our full text version: What are the limitations of NGS panel testing?

• NGS testing may be performed post-allogeneic haematopoietic stem cell transplantation (allo-HSCT), however, this testing scenario may be associated with more complex interpretation of results.
• Common reasons for NGS testing post allo-HSCT include investigation of cytopenias, detection/confirmation of relapse, and investigation of possible donor-derived malignancies.
• Testing of post allo-HSCT recipients may uncover genetic variants of potential donor origin (somatic or germline) that are of clinical relevance to the donor:
  
  
  • In Australia, any unrelated donor notifications should be directed through the Australian Bone Marrow Donor Registry (ABMDR).
  • Any related donor notifications (e.g. matched siblings, haploidentical donors) should be directed to the collection centre and/or donor physician in the first instance.

For further information please see our full text version: Can I request NGS testing on patients after allogeneic transplantation?

Genetic test reports from the Wilson Centre for Blood Cancer Genomics and Peter MacCallum Cancer Centre are uploaded to My Health Record. In some instances, there may be a delay of up to 4-6 weeks.

The Wilson Centre for Blood Cancer Genomics at Peter MacCallum Cancer Centre is happy to assist with questions relating to molecular haematology testing.

Please email This email address is being protected from spambots. You need JavaScript enabled to view it. with your enquiry and one of our team will contact you.