Module information
Module details
- Title
- Solid Cancers 2
- Type
- Specialist
- Module code
- S-CG-S3
- Credits
- 15
- Phase
- 3
- Requirement
- Compulsory
Aim of this module
This module will build on the trainees knowledge of molecular mechanisms developed in solid cancer 1 leading to the development of solid cancers and the associated genomic testing.
This module will focus on patients with lung, ovarian, breast, central nervous system (CNS) and sarcoma tumours and will provide trainees with the knowledge to understand the organisation and delivery of a diagnostic cancer genomic service. This module will provide trainees with the skills to recognise the sample diagnostic pathway, the relevant testing strategies, including NGS and non-NGS assays, as well as the importance of bioinformatic/NGS quality metrics. This module will also provide the trainees with the skills to analyse and interpret patient results, to understand the implications of somatic and germline variants in specific cancers and to understand the importance of pharmacogenomics.
Work-based content
Training activities
| # | Learning outcome | Training activity | Type | Action |
|---|---|---|---|---|
| # 1 | Learning outcome 1 |
Training activities
Receive samples and referral information for a range of solid cancers, to include:
|
Type ETA | Action View |
| # 2 | Learning outcome 1 |
Training activities
Select laboratory molecular assay for patients referred for solid tumour investigation for:
|
Type ETA | Action View |
| # 3 | Learning outcome 2 |
Training activities
Perform morphological assessment of cellularity and neoplastic cell content for two of the following:
|
Type DTA | Action View |
| # 4 | Learning outcome 2,4 |
Training activities
Analyse and interpret data to include fusion gene translocations and variant interpretation for:
|
Type ETA | Action View |
| # 5 | Learning outcome 2,8 |
Training activities
Prepare a range of interpretative reports for:
|
Type ETA | Action View |
| # 6 | Learning outcome 2,3,7,8 |
Training activities
Prepare a range of interpretative reports including somatic and germline variants for ovarian and breast tumours |
Type ETA | Action View |
| # 7 | Learning outcome 2,8 |
Training activities
Prepare a range of interpretative reports for CNS and sarcoma tumours |
Type DTA | Action View |
| # 8 | Learning outcome 2,4,5,8 |
Training activities
Analyse and interpret genomic results from circulating tumour DNA (ctDNA) testing in lung cancer |
Type DTA | Action View |
| # 9 | Learning outcome 2,4,5,8 |
Training activities
Prepare a range of interpretative reports for ctDNA testing in lung cancer |
Type DTA | Action View |
| # 10 | Learning outcome 2,4,5,6 |
Training activities
Analyse, interpret and report pharmacogenetic testing in oncology patients, to include
|
Type DTA | Action View |
| # 11 | Learning outcome 2,8 |
Training activities
Assist with the preparation of cases to be discussed and reviewed in a multidisciplinary team meeting or tumour board meeting with other healthcare professionals |
Type DTA | Action View |
| # 12 | Learning outcome 2,4 |
Training activities
Review an EQA report, recommend corrective actions and draft a plan to action recommendations |
Type ETA | Action View |
| # 13 | Learning outcome 4 |
Training activities
Assist in the preparation and take part in ISO surveillance visit for solid cancers |
Type DTA | Action View |
| # 14 | Learning outcome 4 |
Training activities
Perform and document an audit, make recommendations and agree actions |
Type ETA | Action View |
| # 15 | Learning outcome 2,4 |
Training activities
Perform and document a validation or verification for solid cancers |
Type ETA | Action View |
Assessments
Complete 3 Case-Based Discussions
Complete 3 DOPS or OCEs
Direct Observation of Practical Skills Titles
- Perform morphological assessment for lung, ovarian, breast, CNS cancer, or sarcoma.
- Perform tumour genotype analysis using bioinformatic pipelines and associated tools for lung, ovarian, breast, CNS cancer, or sarcoma.
- Perform gene fusion analysis using bioinformatic pipelines and associated tools for lung, ovarian, breast, CNS cancer, or sarcoma.
- Produce a diagnostic clinical report for a patient with hotspot mutation(s) for lung, ovarian, breast, CNS cancer, or sarcoma.
- Produce a diagnostic clinical report for a patient with a gene fusion for lung, ovarian, breast, CNS cancer, or sarcoma.
- Interpret ctDNA data.
- Interpret a somatic variant, discuss the relevance for diagnosis for lung, ovarian, breast, CNS cancer, or sarcoma.
- Interpret a germline variant, and discuss the relevance for diagnosis for ovarian and breast.
Observed Clinical Event Titles
- Discuss patient results with another healthcare professional for lung, ovarian, breast, CNS cancer, or sarcoma.
- Present a lung, ovarian, breast, CNS cancer, or sarcoma case at a multidisciplinary team meeting.
- Raise an ISO finding a quality meeting.
- Present findings of an audit at a quality meeting.
Learning outcomes
| # | Learning outcome |
|---|---|
| 1 | Select the relevant testing strategy for patients referred for diagnostic genomic testing for lung, ovarian, breast, central nervous system (CNS) and sarcoma tumours. |
| 2 | Analyse, interpret and prepare interpretive reports of clinically relevant findings for patients with lung, central nervous system (CNS), sarcoma tumours, and somatic and germline variants in ovarian and breast cancer. |
| 3 | Evaluate the clinical significance of variants identified for ovarian and breast tumours using a range of bioinformatics tools following best practice guidelines. |
| 4 | Interpret QC data including bioinformatic and NGS quality metrics in relation to assay performance, EQA and ISO:15189 standards. |
| 5 | Analyse, interpret and prepare interpretive reports for circulating tumour DNA (ctDNA) testing in lung cancer. |
| 6 | Analyse, interpret and prepare interpretive pharmacogenetic reports in oncology patients. |
| 7 | Describe the implications of the identification of somatic and germline variation in tumour samples for the patient and their family. |
| 8 | Practice with relevant specialties for the diagnosis and treatment of cancer patients, and contribute to multidisciplinary team meetings. |
Clinical experiences
Clinical experiences help you to develop insight into your practice and a greater understanding of your specialty's impact on patient care. Clinical experiences should be included in your training plan and you may be asked to help organise your experiences. Reflections and observations from your experiences may help you to advance your practice and can be used to develop evidence to demonstrate your awareness and appreciation of your specialty.
Activities
- Observe the submission of EQA data to appreciate the process and importance of EQA in maintaining quality and patient safety.
- Observe preparation of ctDNA.
- Observe histopathological preparation of samples for IHC.
- Attend a genetic counselling appointment where information on a germline variant is provided to a patient to appreciate the impact on patients and their family.
- Observe the preparation of assays for methylation testing.
Academic content (MSc in Clinical Science)
Important information
The academic parts of this module will be detailed and communicated to you by your university. Please contact them if you have questions regarding this module and its assessments. The module titles in your MSc may not be exactly identical to the work-based modules shown in the e-portfolio. Your modules will be aligned, however, to ensure that your academic and work-based learning are complimentary.
Learning outcomes
On successful completion of this module the trainee will be able to:
- Apply integrative knowledge of the aetiology and biological processes leading to the development of the following solid tumours; lung, breast, ovarian, central nervous system (CNS) and sarcomas.
- Describe the genomic mechanisms underpinning the development of the following solid tumours; lung, breast, ovarian, central nervous system (CNS) and sarcomas.
- Critically evaluate the appropriate technologies and their application to the analysis of solid tumours; lung, breast, ovarian, central nervous system (CNS) and sarcomas.
- Evaluate further testing strategies in the context of disease monitoring, metastasis, relapse and resistant genomic aberrations in cancer.
- Apply integrative knowledge of the patient pathway for solid tumours from sampling to reporting of laboratory findings, including integrated reporting and feedback of results.
- Demonstrate extended understanding of the clinical treatment pathway for patients including the use of clinical therapeutics and their role in precision medicine.
- Apply integrative knowledge of epigenetic change and its influence on targeted therapies and outcomes.
- Explain the importance of Genomics and other clinical specialism partnerships for appropriate genomic investigations in the patient pathway.
Indicative content
- Aetiology of lung, breast, ovarian, CNS and sarcomas.
- Molecular and underlying mechanisms, including epigenetics.
- Signalling pathways and associated genes.
- Mechanisms of genomic aberrations in lung, breast, ovarian, CNS and sarcomas, including relapse, metastasis, and resistance and secondary mutations.
- Associated genomic aberrations and role within diagnosis, prognosis and disease management.
- Germline associations.
- Epigenetic change e.g. methylation and its influence on targeted therapies and outcomes and clinical trials using current examples e.g. CNS.
- Current nomenclature used to describe genomic alterations.
- Current laboratory techniques and methodologies employed for tumour genotyping in identifying aberrations such as point mutations, deletions, insertions and fusions/translocations.
- Histopathological sample processing requirements for genotyping and impact on upstream testing.
- The use of protein expression to classify tumours.
- Extraction methodologies for less-invasive sampling techniques such as liquid biopsies.
- Modern sequencing technologies employed and troubleshooting, including panel based testing and whole genome analysis using both DNA and RNA as analytes.
- An understanding of genomic testing of cell free tumour DNA in blood, for diagnosis, monitoring and treatment of solid cancers.
- Quality control, validation and verification, and external quality assessment schemes.
- Analytical and clinical sensitivity and specificity of these tests.
- Bioinformatics tools, relevant genomic databases, pathways for reporting variants of unknown significance.
- Analysis, interpretation and reporting of genomic alterations in a clinical context.
- Potential application of relevant emerging technologies e.g. digital pathology.
- Therapeutics available for primary and secondary disease and how these are used in the clinical setting.
- The use of medical imaging in cancer.
- Primary and secondary disease monitoring, reflex testing in the context of metastases, resistant genomic aberrations and available therapeutics.
- Clinical trials and their role in a diagnostic setting.
- Precision medicine e.g. the role of tyrosine kinase inhibitors, detection of hotspot mutations (such as EGFR), intracellular signalling targeted therapy (such as RAS, BRAF), translocated genes targets (such as ALK, ROS1, NTRK) in lung cancer and the role of PARP inhibitors in ovarian cancers.
- Epigenetic change and role within targeted therapies for common CNS tumours.
- Multidisciplinary team working,including pathology, histopathology, genomics laboratory, clinical genetics and disease specific multidisciplinary teams.
- Impact of genomics on patients and their families, including ethical considerations, such as consent.
- Best practice guidelines, national guidance, clinical trials, advisory and regulatory bodies, NICE guidelines and standard of care testing.