Module information
Module details
- Title
- Diagnostic Sequencing
- Type
- Specialist
- Module code
- S-BG-S1
- Credits
- 10
- Phase
- 2
- Requirement
- Compulsory
Aim of this module
This module will help trainees develop an understanding of the human genome and techniques for analysing genomic data. The module will provide the trainee with tools and strategies for converting genomic data into clinically useful information and an awareness of how this might impact the patient.
Work-based content
Training activities
| # | Learning outcome | Training activity | Type | Action |
|---|---|---|---|---|
| # 1 | Learning outcome 1,2,3,4 |
Training activities
Produce a functional genomic sequence data file in an appropriate format and perform quality analysis of the sequence data |
Type ETA | Action View |
| # 2 | Learning outcome 1,2,3,4 |
Training activities
Generate a genomic sequence alignment in an appropriate format |
Type ETA | Action View |
| # 3 | Learning outcome 2,3 |
Training activities
Select appropriate tools for identifying different types of genomic variation in inherited disease |
Type DTA | Action View |
| # 4 | Learning outcome 2,3 |
Training activities
Select appropriate tools for identifying different types of genomic variation in acquired disease |
Type DTA | Action View |
| # 5 | Learning outcome 1,2,3,4 |
Training activities
Annotate genomic variation data in the context of inherited and acquired disease |
Type ETA | Action View |
| # 6 | Learning outcome 1,2,3,4,5 |
Training activities
Identify and interpret the consequence of a genomic variant |
Type ETA | Action View |
| # 7 | Learning outcome 3,4 |
Training activities
Identify and visualise target genomic regions and variation |
Type ETA | Action View |
| # 8 | Learning outcome 2,3,4 |
Training activities
Apply the appropriate analytical strategies for rare disease cases |
Type ETA | Action View |
| # 9 | Learning outcome 2,3,4 |
Training activities
Apply the appropriate analytical strategies to solid cancer and haematological malignancy cases |
Type ETA | Action View |
| # 10 | Learning outcome 3,4 |
Training activities
Develop a strategy to modify or assemble tools, pipelines or processes |
Type DTA | Action View |
Assessments
Complete 2 Case-Based Discussions
Complete 2 DOPS or OCEs
Direct Observation of Practical Skills Titles
- Assess the quality of sequencing from an NGS sequencing run.
- View a sequence alignment BAM file and assess either the alignment, variant or structural variant.
- Annotate a variant and provide a functional interpretation.
- Interpret a variant in context of the patient’s family, ancestry and medical history.
Observed Clinical Event Titles
- Present and explain NGS quality control checks to data users.
- Present the findings of a variant interpretation, commenting on the effect on protein function.
- Discuss with a Genomic Scientist the effect of different modes of variation on protein structure and function and the impact on disease.
- Discuss the impact of CNVs and SVs on the expression of a gene.
Learning outcomes
| # | Learning outcome |
|---|---|
| 1 | Explain the structure of the human genome and the impact of variation on human development, health, and disease. |
| 2 | Evaluate sources of information about variation in the human genome including access, application and clinical impact. |
| 3 | Select appropriate tools for next generation sequencing (NGS) analysis of inherited and acquired disease. |
| 4 | Analyse NGS data in a clinical setting applying appropriate quality control and data validation. |
| 5 | Interpret and analyse various types of variants from single nucleotide variants (SNVs), through to large structural variants. |
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
- Attend a multidisciplinary team meeting reviewing a rare disease and cancer case.
- Follow the process for preparation of sequencing samples from DNA to sequencing data.
- Attend a Clinical Genetics appointment with a patient to appreciate the impact the data analysis has on the clinical outcome and the patient.
- Observe the process of generating integrated reports to appreciate how bioinformatics data is applied to cancer cases and the role of genomics in the multidisciplinary approach to cancer care.
- Shadow a Genomics Clinical Scientist while they interact with decision support systems and identify clinical risks.
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:
- Describe the structure of DNA and the human genome, the transcription of DNA to mRNA and the protein synthesis process, and the functions of coding and non-coding DNA.
- Discuss the impact of genetic variation on development, health and disease (acquired and inherited) and the biological background to diagnostic genetic testing.
- Demonstrate a critical awareness of databases and tools which provide information relevant to the implementation, analysis and interpretation of NGS.
- Apply integrative knowledge of applications of NGS in the clinical setting, including targeted genes, panels, whole exome and whole genome sequencing.
- Critically appraise NGS platforms and the methodologies that they use and their strengths for solving different biological problems.
- Discuss the concept and measurement of quality applied to bioinformatic resources, data and analysis in the clinical setting, and the representation and use of metadata.
- Describe the development, implementation strategies and operation of bioinformatic analysis pipelines for NGS data.
- Justify the importance of standards, validation, best practice guidelines and standard operating procedures.
Indicative content
Genomics and healthcare
- Brief history of sequencing strategies
- Application of next generation data in genetics/genomics and medicine and the impact on patient care, including somatic and inherited diseases
NGS Platforms
- The genome science behind NGS – short/long reads, sequencing and assembly
- Different sequencing platforms and the physical chemistry they deploy
- Applications of NGS and application strategies/techniques
- The background to sample preparation and problems that can occur
NGS analysis
- Next generation alignment strategies
- Data formats for next generation data – BAM, SAM, FASTQ and VCF
- Sequence annotation and interpretation
- SNP detection and CNV detection
Data handling and data governance
- Workflows for bioformatic analysis
- Data quality in genetic and genomic data
- Annotation, prioritisation and interpretation of next generation data
- Models of use of next generation technology within the NHS
- Issues of patient consent, governance and ethics
Current literature and practice around the impact of NGS tools in clinical medicine and genomics
Module assigned to
Specialties
| Specialty code | Specialty title | Action |
|---|---|---|
| Specialty code SBI1-1-22 | Specialty title Clinical Bioinformatics Genomics [2022] | Action View |
| Specialty code SBI1-1-23 | Specialty title Clinical Bioinformatics Genomics [2023] | Action View |
| Specialty code SBI1-1-24 | Specialty title Clinical Bioinformatics Genomics [2024] | Action View |