Module information
Module details
- Title
- Introduction to Clinical Bioinformatics Genomics
- Type
- Rotation
- Module code
- S-BG-R1
- Credits
- 10
- Phase
- 1
- Requirement
- Compulsory
Aim of this module
This module will introduce trainees to the principles, application, impact on care and wider multidisciplinary team involved in the practice of Clinical Bioinformatics Genomics.
Work-based content
Training activities
| # | Learning outcome | Training activity | Type | Action |
|---|---|---|---|---|
| # 1 | Learning outcome 1,2,3,6 |
Training activities
Attend a lab meeting for Clinical Bioinformatics Genomics and reflect on the meeting |
Type OTA | Action View |
| # 2 | Learning outcome 1,2,3,6 |
Training activities
Shadow a Clinical Scientist in Bioinformatics – Genomics and reflect on their role |
Type OTA | Action View |
| # 3 | Learning outcome 1,2,3,6 |
Training activities
Observe running an internal pipeline and reflect on the process |
Type OTA | Action View |
| # 4 | Learning outcome 1,2,3,6 |
Training activities
Follow patient bioinformatics data through the healthcare pathway and reflect on the journey |
Type OTA | Action View |
| # 5 | Learning outcome 1,3,4,6 |
Training activities
Explore a potential upcoming change in practice in Clinical Bioinformatics Genomics and reflect on the impact this will have on practice |
Type OTA | Action View |
| # 6 | Learning outcome 1,3,5,6 |
Training activities
Review the effect of a guideline or piece of legislation within Clinical Bioinformatics Genomics and reflect on how this guides practice |
Type OTA | Action View |
| # 7 | Learning outcome 1,2,3,6 |
Training activities
Follow the software development cycle and reflect on the process |
Type OTA | Action View |
| # 8 | Learning outcome 1,2,3,6 |
Training activities
Observe retrieval of information from a database and reflect on the process |
Type OTA | Action View |
| # 9 | Learning outcome 1,2,3,6 |
Training activities
Shadow a Technologist or Clinical Scientist in Genomics and reflect on their role |
Type OTA | Action View |
| # 10 | Learning outcome 1,2,3,6 |
Training activities
Observe the use of external data sources or pipelines in local practice and reflect on the process and use |
Type OTA | Action View |
Assessments
Complete Case-Based Discussion
Complete 1 DOPS or OCE
Direct Observation of Practical Skills Titles
- Prepare a command to initiate a pipeline.
- Check the progress of a pipeline.
- Interpret the data quality metrics for a stage/aspect of a pipeline.
- Extract and visualise subset from a BAM file.
- Write a database query.
Observed Clinical Event Titles
- Gather a patient history relevant to the specialty from a patient, patient representative, or a member of the multidisciplinary team.
- Present a patient history relevant to the specialty to a member of the multidisciplinary team.
Learning outcomes
| # | Learning outcome |
|---|---|
| 1 | Explore the contribution of Clinical Bioinformatics Genomics to patient care. |
| 2 | Identify the roles and relationships of the multidisciplinary team in Clinical Bioinformatics Genomics. |
| 3 | Describe the working practices of Clinical Bioinformatics Genomics. |
| 4 | Examine the impact of innovation in Clinical Bioinformatics Genomics. |
| 5 | Review the effect of legislation in Clinical Bioinformatics Genomics. |
| 6 | Compare and contrast the practice of Clinical Bioinformatics Genomics with other specialties. |
Clinical experiences
Activities
There is no clinical experiential learning associated with this module.
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:
- Discuss the governance and ethical frameworks in place within the NHS and how they apply to bioinformatics.
- Analyse genomic data in line with current standards, best practice guidelines and standard operating procedures and demonstrate a critical awareness of how they are developed, improved and applied to clinical bioinformatics.
- Describe the partnership of clinical bioinformatics and genomics to other clinical specialisms in the investigation and management of genetic disorders and the contribution to safe and effective patient care.
- Apply integrative knowledge of the development, implementation strategies, file and data formats and operation of bioinformatic analysis pipelines.
- Apply bioinformatics pipelines to analyse genomic and variant data and interrogate its quality.
- Demonstrate a critical awareness of the purpose and practice of clinical genetic/genomic variant testing.
- Interpret evidence from bioinformatic tools and resources and integrate this into the sum of genetic information for the interpretation and reporting of test results from patients.
- Demonstrate extended understanding of sources of data used in clinical genomics and how they are accessed and applied.
Indicative content
Sequencing
- Understanding of the different data formats and file types used, and an overview of how these are processed in sequence within a bioinformatics pipeline
- Raw sequencing data, FASTQ, SAM / BAM, CRAM, VCF and gVCF
- Analysis, annotation and interpretation of sequencing data
- Panel versus exome versus whole-genome sequencing
Genomic variants
- Visualise single nucleotide variants (SNV)/indels/copy number variants (CNV), and structural variants (SV) in an appropriate genome viewer
- Understanding of the annotation and concepts of read depth, insert size and read/base quality
- Review the difference between somatic and germline variants
Pipelines and workflows
- Observe a diagnostic workflow from referral of patient, activation of relevant test in LIMS, processing of sequencing data and production of diagnostic quality report via a pipeline
- Understand quality control, sensitivity and specificity of test, use of controls and logs
- Annotation of results and filtering strategies
- Annotation file formats (BED/GFF)
- Annotation sources (including: gnomad, OMIM, ClinVar, HGMD, GTEx, COSMIC, dbSNP and VeP)
- Reproducibility, handling and reporting of errors (error logging, for example: QPulse)
Software development
- Use of appropriate best practice and industry guidelines (PEP8 and ACGS best practice)
- Develop and deploy a change to a current piece of software, applying version control, testing and documentation, alongside an experienced programmer as part of a pair-programming team
- Different types of testing (unit, integration and end-user)
Standards and governance
- Creating and tracking a sample through the laboratory information management system (LIMS)
- Introduction to ISO standards, data protection and medical device regulations
Patient care
- Patient confidentiality and incidental findings
- Understand how the appropriate testing strategies are decided on to reduce diagnostic odyssey: exome/whole genome versus panel or single gene, and family trio testing versus proband only
- Clinical risk guidelines
Module assigned to
Specialties
| Specialty code | Specialty title | Action |
|---|---|---|
| Specialty code SBI1-1-22 | Specialty title Clinical Bioinformatics Genomics [2022] | Action View |
| Specialty code SLS4-1-22 | Specialty title Genomics [2022] | Action View |
| Specialty code SLS4-2-22 | Specialty title Genomic Counselling [2022] | Action View |
| Specialty code SLS4-3-23 | Specialty title Cancer Genomics [2023] | Action View |
| Specialty code SBI1-3-22 | Specialty title Clinical Informatics [2022] | Action View |
| Specialty code SLS4-3-22 | Specialty title Cancer Genomics [2022] | Action View |
| Specialty code SBI1-1-23 | Specialty title Clinical Bioinformatics Genomics [2023] | Action View |
| Specialty code SBI1-3-23 | Specialty title Clinical Informatics [2023] | Action View |
| Specialty code SLS4-2-23 | Specialty title Genomic Counselling [2023] | Action View |
| Specialty code SLS4-1-23 | Specialty title Genomics [2023] | Action View |
| Specialty code SLS4-3-24 | Specialty title Cancer Genomics [2024] | Action View |
| Specialty code SBI1-1-24 | Specialty title Clinical Bioinformatics Genomics [2024] | Action View |
| Specialty code SBI1-3-24 | Specialty title Clinical Informatics [2024] | Action View |
| Specialty code SLS4-2-24 | Specialty title Genomic Counselling [2024] | Action View |
| Specialty code SLS4-1-24 | Specialty title Genomics [2024] | Action View |