Module - Genomics of Sporadic Cancers (SLS423)

STP

Aim of this module

This module will provide the trainee with knowledge and understanding of the role and application of genetic and genomic testing in the diagnosis and management of patients with sporadic cancers.

 

The content for this module will focus on (as exemplars) patients who present with acquired cancers including Chronic Myeloid Leukaemia (CML), Acute Lymphoblastic Leukaemia (ALL), Acute Myeloid Leukaemia (AML), sporadic colorectal cancer and lung cancer.

Work-based learning outcomes


  1. Apply appropriate sample selection criteria, taking into account the implications of acquired sporadic cancer with respect to sampling mixed cell populations, limits of detection, sensitivity of assay and patient management.
  2. Apply an appropriate testing strategy for the commonly referred acquired sporadic cancers at all stages of the patient pathway.
  3. Perform targeted testing for patients referred with sporadic cancer.
  4. Perform whole genome testing for patients referred with sporadic cancer.
  5. Analyse the results from genetic and genomic testing in  acquired sporadic cancers.
  6. Interpret and report a range of genetic and genomic testing relevant to acquired sporadic cancer.

Work-based Competencies


Learning outcome Title Knowledge
1 1,2

Select the correct genetics test for patients referred with acquired cancer.

  • As examples: sporadic colorectal cancer, lung cancer and leukaemia (CML, ALL and AML).
  • The principal referral reasons and guidelines in the cancer patient care pathway.
  • Role of genetics testing in the diagnosis and treatment (clinical utility) of acquired solid tumours (e.g. sporadic colorectal cancer and lung cancer).
  • Role of genetics testing in the diagnosis of leukaemia.
  • The concept of minimal residual disease (MRD) and the utility of genetic testing in disease treatment and monitoring.
  • The use of genetic testing in transplantation and chimerism monitoring.
  • Concept of Precision Medicine and the applicability of genetic testing in guiding the treatment including the principles of cost effectiveness.
  • The requirement for adherence to Turnaround Times including, but not limited to, those in national guidance such as Improving Outcomes guidance.
  • The use and limitations of a range of sample types including formalin fixed paraffin embedded material, fresh frozen tissue, cell free circulating tumour DNA, bone marrow and peripheral blood.
  • Wide but high level knowledge of different technologies and their application to enable appropriate decisions regarding processing and testing.
2 1,2,3

Perform gene fusion analysis using appropriate current technology on oncology samples.

  • As examples: sporadic colorectal cancer, lung cancer and leukaemia (CML, ALL and AML).
  • Rearrangements and translocations commonly associated with solid tissue cancer and named leukaemic types, as well as their clinical significance.
  • Principles of main technologies (apart from chromosome analysis) utilised in the identification of rearrangements associated with cancer.
  • Use of appropriate nomenclature for reporting gene fusions according to the technology utilised.
  • Best practice guidelines for gene fusion analysis technologies in cancer patients (internal and external QA).
3 1,2,4

Perform whole genome analysis on samples from patients with leukaemia at diagnosis.

  • Examples CML, ALL and AML.
  • Use of ISCN for malignancy analysis
  • The local guidance for whole genome analysis from patients with Leukaemia.
  • Best practice guidelines, national/international guidance and QA (external and internal).
  • Selection and analysis in mixed cell populuations
  • Validation and verification of findings
  • Prognostic and diagnostic genetic markers.
4 1,2,3

Perform appropriate molecular testing on various cancer samples.

  • Principles underpinning current methods of mutation detection and genetic changes.
  • The use and limitations of a range of sample types to analyse tumour DNA.
  • Hot-spot mutation and multiple gene panel analysis associated with a number of cancer types.
  • Utility and limitations of whole genome sequencing.
  • Appropriate use of controls.
  • Sensitivity of different testing methodologies and the relevance to mixed cell populations.
  • The use of HGVS guidance for reporting of sequence variation in acquired disease.
5 1,2,3

Perform appropriate genetic testing for monitoring and measurement of disease in relation to both treatment and prognosis.

  • The principles of technologies used to monitor patients for response to treatment and recurrence of disease.
  • The sensitivity and specificity of different technologies in the different diseases and associated limitations in use.
  • The importance of genetic testing in monitoring disease and the importance of factors such as TAT.
6 5,6

Interpret and report on a range of genetic testing in haematological malignancy, including both diagnostic and follow-up (monitoring) analysis.

  • Interpretation of results including diagnostic and treatment recommendations, taking into account the relationships between chromosome abnormalities/genetic markers, other testing modalities and clinical diagnosis
  • Use and critical appraisal of relevant literature and online databases.
  • Role of multidisciplinary team (MDT) meetings and guidelines such as Improving Outcomes Guidance and NICE Guidelines
  • The role of large scale national and international projects focussed on acquired disease. 
  • Recognising that all tests have been completed to a satisfactory standard for the referral reason.  
  • All information has been validated as correct. 
  • Selection of correct report template for referral reason. 
  • Recommendations for further referral (e.g. clinical genetics). Identify the requirements for any follow up testing, the testing methods available and the appropriate choice of test. Describe any limitations.
  • Use of correct scientific and clinical terminology
  • Use of relevant databases and literature in the interpretation of results.
  • Communication of complex scientific information to clinicians and patients.
  • Best practice guidelines compared with laboratory practice and any differences between the two
  • How to identify pertinent EQA schemes; their role and practice, how these are incorporated into laboratory practice and ISO standards for lab participation in EQA schemes.

Work-based assessment


Complete 2 Case-Based Discussion(s)
Complete 2 of the following DOPS and/or OCEs
Type Title
DOPS Perform duty scientist checking of samples referred for acquired cancer
DOPS Analyse chromosomes from a routine haematological malignancy
DOPS Interpret the results of analysis to monitor Minimal Residual Disease
DOPS Analyse the results of RQ PCR analysis
DOPS Analyse the results of gene fusion testing by FISH
DOPS Analyse the results of microsatellite analysis for monitoring bone marrrow transplantation
DOPS Analyse results generated by Next Generation Sequencing
DOPS Use bioinformatic tools to interpret the clinical significance of a sequence variant
DOPS Prepare a clinical report for a patient referred with an aquired cancer
DOPS Assess microsatellite results from a colorectal cancer sample for a mismatch repair defect
OCE Participate in an MDT meeting with other healthcare professionals
OCE Take a patient history can be undertaken in virtual patient environment
OCE Discuss patient results with a healthcare professional telephone or in person