Introduction to Cancer Genomics

Module details

Title

Introduction to Cancer Genomics

Type

Rotation

Module code

SLS404

Credits

20

Requirement

Compulsory

Aim of this module

This module will provide the trainee with an introduction to the principles and practice of cancer genomics including elements of both haematology and histopathology in the context of the pathogenesis of neoplastic disorders. They will understand the organization and delivery of laboratory services for patients referred with a differential cancer diagnosis. They will understand the principles and practices of common methods used in the processing of clinical samples and gain an understanding of the interpretation of patient results in a variety of clinical settings.

Competencies

#	Learning outcome	Competency	Action
# 1	Learning outcome 1,2,5,6,7	Competency Receive, assess and store common haematology specimens	Action View
# 2	Learning outcome 1,2,5,6,7,8	Competency Interpret laboratory data in light of clinical details and prepare basic interpretive written reports on patients with at least two of the following: Polycythaemia Peripheral blood with >20% blast cells Pancytopenia Lymphocytosis Thrombocytosis	Action View
# 3	Learning outcome 1,2,5,6,7,8	Competency Identify one case requiring urgent intervention and describe relevant clinical advice on follow-up and/or further management	Action View
# 4	Learning outcome 1,2,3,4, 5,6,7,8	Competency Perform at least three of the following methods to specified quality standards: prepare blood and bone marrow aspirate films peripheral blood cell microscopy automated analysers to quantify erythrocytes, leucocytes, platelets, reticulocytes and white cell differentiation Flow cytometry to enumerate blast cells and identify their lineage Immunomagnetic cell selection	Action View
# 5	Learning outcome 1,2,4, 5,6,7	Competency Perform a range of methods for diagnosing and monitoring treatment of haematological malignancy, including: fluorescence in-situ hybridisation molecular diagnostics, including: IGH gene rearrangement and/or TCR gene rearrangement BCRABL	Action View
# 6	Learning outcome 2,3,4,	Competency Perform a basic chromosome analysis on a minimum of three ‘simple’ cases that demonstrate different chromosomal syndromes or anomalies	Action View
# 7	Learning outcome 4,7,8	Competency Interpret haematology data in order to aid the classification of haematological malignancies	Action View
# 8	Learning outcome 1,2,3,4,5,6,	Competency Receive, label and store of a wide range of histopathology specimens (includes haematological malignancy tissue samples)	Action View
# 9	Learning outcome 1,6,	Competency Prepare and use a microtome on a range of tissue samples within different embedding materials	Action View
# 10	Learning outcome 1,2,3,	Competency Apply the haematoxylin and eosin staining technique to a variety of tissue samples	Action View
# 11	Learning outcome 1,2,3,	Competency Set up and use light microscopy at various magnifications in the investigation of a range of tissue specimens	Action View
# 12	Learning outcome 3,5,	Competency Select the appropriate immunohistochemical and/or immunofluorescence techniques and antibodies to demonstrate a specific disease process	Action View
# 13	Learning outcome 4, 5	Competency Select the appropriate molecular techniques, markers and reagents required to demonstrate a specific disease process using current best practice for cancer diagnosis	Action View
# 14	Learning outcome 8	Competency Produce a basic interpretative report on histopathology investigations	Action View
# 15	Learning outcome 4, 5,6,	Competency Observe and assist with the range of laboratory methods and their application to generate genetic test results for cancer patients	Action View
# 16	Learning outcome 4, 5,6,	Competency Perform a copy number analysis using chromosomal microarray	Action View
# 17	Learning outcome 1,3,6,	Competency Observe the dissection of at least 3 different tissue types and sample cancer resection specimens received in accordance with local protocols	Action View
# 18	Learning outcome 3,4,5,6,7,8	Competency Interpret the histological or cytological findings of a sample in the correct clinical context and discuss in detail with a senior colleague	Action View

Assessments

You must complete:

• 2 case-based discussion(s)
• 2 of the following DOPS/ OCEs:

Perform Haematoxylin and eosinstaining technique on tissue samples	DOPS
Label and store a wide range of cancer specimens	DOPS
Prepare and use a microtome on a range of tissue samples within different embedding material	DOPS
Set up and use light microscopy at various magnifications in the investigation of tissue specimens	DOPS
Set up and use light microscopy at various magnifications in the investigation of blood	DOPS
Spread bone marrow smears and stain with a stain prior to microscopic examination.	DOPS
Review a small number of referrals and samples received for cancer diagnosis assessing their appropriateness	DOPS
Perform a basic molecular analysis for a sample referred for cancer diagnosis	DOPS
Participate in a ward round	OCE
Participate cancer MDT	OCE
Discuss implications of receiving an unlabelled sample with a healthcare professional.	OCE
Discuss an oncology referral with another healthcare professional	OCE
Telephone a clinician to discuss details of an oncology referral	OCE

Learning outcomes

1. Receive, prepare and process specimens for solid tumour investigation To include supervised dissection, tissue selection cutting, fixation and staining, as appropriate
2. Receive, prepare and process specimens for haematological malignancy investigation To include sampling methods, correct sample procedures, collection and storage of samples nucleic acid extraction and quality assessment
3. Use microscopic and/or digital imaging examination techniques to investigate specimens
4. Recognise normal cellular morphology of representative tissues and organs and common pathobiological processes associated with them
5. Perform a range of laboratory techniques used in screening and investigating histopathological and haematological malignancy disorders
6. Apply the principles of internal quality control and external quality assessment and draw conclusions about assay performance
7. Use laboratory IT systems for the safe handling, processing and storage of patient data
8. Interpret results of clinical diagnostic tests
9. Prepare basic clinical reports for the patients based on the outcome of genomic investigation

Learning outcomes

1. Understand and explain the basics of cell cycle control, proliferation and death
2. Understand the molecular mechanisms of oncogenesis, and how changes within genes of various categories may result in an altered phenotype
3. Understand the molecular basis of tumour growth, angiogenesis, tissue invasion and metastasis
4. Describe and recognise the normal cellular morphology of specified tissues and organs and relate these to the pathobiological processes associated with them
5. Explain the haemopoeitic pathways and normal haemostatic mechanisms, and discuss how deregulation by mutation, deletion or other genetic mechanism may be implicated in causing neoplasia
6. Understand the importance of sample quality for cancer genomic analysis
7. Understand genomic testing of cell free tumour DNA in blood, for the diagnosis and monitoring of solid cancers
8. Evaluate the design, operation and performance of the tests and procedures required to enable selection of safe and appropriate analysis for patients with suspected cancer
9. Describe and evaluate the application of quality assurance methodologies cancer genomics
10. Discuss the partnership of cancer genomics with routine histopathology, haematology and with other clinical specialisms in investigation and contribution to patient pathway

Indicative content

Haematological malignancy

• Normal haemopoiesis and bone marrow function in the development and differentiation of blood cells
• Normal lymphopoiesis and lymph node structure and function
• Principles, scientific basis and clinical application of commonly performed analytical procedures in haematological malignancy
• Principles and scientific basis of automated cell counters and flow cytometers
• Understanding of multi-parametric flow cytometry and its role in diagnosis and disease monitoring post treatment
• Presentation, diagnosis and management of common haematological malignancy disorders
• Blood film preparation, staining and interpretation in normal and pathological conditions
• Bone marrow aspiration, trephine biopsy, preparation and staining techniques for the morphological identification of cells in bone marrow in normal and pathological conditions
• Immuno-magnetic cell selection for liquid sample
• Non-molecular techniques such as conventional karyotyping (liquid samples)
• Presentation of haematological malignancy patients, recognising that many will present with solid tumours and that individual patient pathways may be complicated
• Principles and application of internal quality control and external quality assurance programmes

 Histopathology (solid tumours)

• Normal cellular morphology of specified tissues and organ systems, including skin, lung, GI tract building on basic anatomy and physiology
• Basic principles of pathobiology, to include inflammation, fibrosis, necrosis, hypertrophy, hyperplasia, atrophy, metaplasia and apoptosis
• Introduction to tissue preparation techniques
• Specimen acquisition, viability, collection and delivery
• Principles and practice of fixation (important for downstream molecular testing understand the effect of formalin fixation on DNA structure)
• Principles of specimen dissection and block selection
• Tissue processing and embedding techniques
• Pre-treatment, eg decalcification
• Microscopy principles and practice
• Haematoxylin and eosin; special stains to identify individual tissue/cellular components, eg connective tissues, nucleic acids, mucins, lipids, pigments; histochemical techniques; microtomy, cryotomy, ultramicrotomy
• The use of digital imagery for the assessment of samples
• Immunocytochemistry and its role in diagnosis
• Molecular diagnostics nucleic acid extraction (DNA and RNA)
• Measurement of DNA and RNA concentration
• PCR methods
• FISH methods
• Introduction to arrays and high throughput sequencing
• Quality assurance
• Artefacts

 Haematological malignancy and histopathology (solid tumours)

• Principles and scientific basis of international cancer classification schemes (WHO 2016)
• Principles and scientific basis of international cancer clinical staging schemes
• Understanding of the role radiology imaging studies have in the diagnostic and staging pathway (x-ray, CT, MR and PET)

 The Role of Laboratory Tests in Guiding Therapy

• Understand the use of expression profiling to generate prognostic and predictive signatures; to aid treatment stratification and guide adjuvant therapy choices
• Use of point of care molecular testing to guide surgical decisions
• The importance of multidisciplinary team working in providing integrated cancer reports

Activities

1. Attend a cancer MDT in both solid tumour and haematological malignancy (adult and paediatric to cover suitable range of diseases) and reflect on the discussions
2. Observe a bone marrow aspirate and trephine biopsy and reflect on the process
3. Observe a sample being taken by surgical technique both resection and biopsy and reflect on the process
4. Observe a sample being taken by Radiological guided technique and reflect on the process
5. Shadow a Consultant Histopathologist, Oncologist and Haematologist and reflect on the role these health professionals play
6. Observe the process of cell suspension and downstream testing and analysis
7. Observe immunophenotyping/immunohistochemistry on suspected cancer samples
8. Carry out DNA and RNA extraction on fresh samples and FFPE processed samples
9. Set up a simple PCR test (single mutation DNA PCR)
10. Set up a FISH test on tissue
11. Karyotype an expected ‘simple’ result (example new CML)