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Anna Schuh Niamh Appleby
Schuh Anna NiamhAppleby.jpg


Learning Outcomes

By the end of this module the student will be able to:

1. Understand the process of developing a biomarker into a diagnostic test. Critically appraise the types of tests available with reference to guidelines for test standardisation and clinical application with reference to

  • Chronic Myeloid Leukaemia and BCR-ABL
  • Chronic lymphocytic leukaemia and TP53

2. Understand the potential of novel diagnostic technologies to alter the patient journey and clinical decision making practices. Be able to discuss examples with reference to

  • Whole Genome Sequencing
  • Minimal residual disease testing
  • Non-invasive biopsy such as circulating tumour DNA

3. Recognise the potential of precision diagnostics in resource limited healthcare settings and global health.

4. Specifically for sequencing based testing,

  • Understand the principals of quality control of sequencing data
  • Describe the steps undertaken after sequencing to convert raw data into a clinical report including

                                                     i.     Quality control

                                                   ii.     Alignment to the reference genome (and choice of reference)

                                                  iii.     Calling and annotating variants

                                                  iv.     Variant filtering strategies

                                                   v.     Describe how the pathogenicity of a variant is determined

  • Appreciate the limitations of the above strategies

5. Appreciate the role of the different regulatory frameworks governing genomic medicine in clinical and research practice from informed consent, professional practice guidelines, tissue handling regulations and clinical laboratory accreditation systems. For example

  •  CLIA; IsoStandards,
  • the UK’s Human Tissue Act and Information Governance.
  • American College of Medical Genetics and Genomics (ACMG)
  • the American College of Pathologists and the Global Alliance for Genomics and Health (GA4GH).

Indicative Content

This module covers the identification and development of molecular testing and its application in clinical oncology and haematology, supported by examples from specific cancers. Students will learn the principals underlying a selection of molecular tests, the steps required in data interpretation and how test results influence the patient journey. The module provides an overview of the clinical, scientific, quality assurance and regulatory frameworks guiding laboratory testing and clinical interpretation of -omics data.