Training activity information
Details
Select appropriate tools for identifying different types of genomic variation in inherited disease
Type
Developmental training activity (DTA)
Evidence requirements
Evidence the activity has been undertaken by the trainee.
Reflection on the activity at one or more time points after the event including learning from the activity and/or areas of the trainees practice for development.
An action plan to implement learning and/or to address skills or knowledge gaps identified.
Considerations
- For example: SNVs, Indels, CNVs, structural variants, mitochondrial heteroplasmy, mosaicism, sort tandem repeats (STR) and transposable elements in inherited disease
- Quality metrics
- Storage of data in appropriate formats according to local and national standards, taking into consideration patient confidentiality
- Data integrity and patient safety
Reflective practice guidance
The guidance below is provided to support reflection at different time points, providing you with questions to aid you to reflect for this training activity. They are provided for guidance and should not be considered as a mandatory checklist. Trainees should not be expected to provide answers to each of the guidance questions listed.
Before action
- What specific types of genomic variation in inherited diseases will you be focusing on (e.g., SNVs, CNVs, structural variants)? What are the key characteristics and functionalities that a tool should possess to effectively identify these variations in the context of inherited disease? What prior knowledge of genomic variation in inherited disease and available bioinformatics tools do you need for this activity?
- What specific bioinformatics tools do you hope to learn more about for identifying variations in inherited diseases? What criteria will you use to evaluate the appropriateness of different tools? What challenges do you anticipate in selecting the most suitable tools for different types of inherited disease variation?
- Will you research different bioinformatics tools and databases used for identifying genomic variation in inherited diseases? Will you discuss with your training officer the specific types of inherited diseases or variations you might focus on? Have you considered any specific resources or literature you might need to review beforehand? How do you feel about the task of selecting appropriate bioinformatics tools?
In action
- Are you systematically reviewing tool documentation, comparing features, or trying out different tools with example data? Why did you start with a particular type of tool or a specific approach to evaluation?
- Are you finding suitable tools for all types of inherited disease variation you are considering? Are there specific types of variation for which it is proving more difficult to identify appropriate tools? What new insights are you gaining about the capabilities and limitations of different tools as you evaluate them? How does this tool selection process align with what you already know about analysing inherited disease?
- If your initial search for tools isn’t yielding suitable options, are you refining your search terms or considering different categories of tools? Are you thinking about seeking guidance on specific types of variation or tool functionalities?
On action
- Summarise the key steps you took in selecting tools for identifying different types of genomic variation in inherited disease. What types of tools did you consider? What were the key features or functionalities you focused on? What were the main sources of information you used to identify potential tools (e.g., literature, databases, colleagues)? Did you encounter any unexpected challenges or points of interest during the tool selection process?
- What skills or knowledge did you develop or improve through this activity related to tool selection for inherited disease variant identification? Were there any unexpected challenges or successes during the activity? What did you learn from these? For example, did any tools perform differently than expected based on their documentation? Were there any specific types of inherited variation for which it was harder to find suitable tools? In what ways did your reflection-in-action (during the activity) influence how the tool selection unfolded? For example, did you change your search strategy or evaluation criteria based on your immediate observations? How does this experience relate to the requirements for post-programme practice? How might the ability to select appropriate tools impact your future work? Did you gain a better understanding of the databases and tools available for this task?
- What areas for continued development have been identified as a result of this activity? For example, do you need to improve your understanding of specific types of genomic variation or certain categories of bioinformatics tools? How can you apply the learning from this activity to your routine practice? How will you approach similar tool selection tasks in the future? Identify the actions / ‘next steps’ you will now take to support the assimilation of what you have learned. For example, will you explore the documentation of specific tools in more detail or discuss your choices with your training officer? What support or resources might you need to further develop in the areas identified through this reflection?
Beyond action
- Consider evaluating and re-evaluating your experience of selecting tools for identifying different types of genomic variation in inherited disease in light of your subsequent learning and experiences.
- Have you since engaged in training activities that involved using or evaluating similar bioinformatics tools? How does your experience in this DTA compare with those later experiences? What observable behaviours and practices have you adopted as a result of this initial tool selection activity and subsequent experiences? Have you revisited your initial reflections on this training activity as part of a broader review of the S-BG-S1 module or your overall training? What new learning or actions have emerged from this re-evaluation? Have you discussed your approach to tool selection for inherited disease with peers or colleagues? Has your understanding or perspective changed as a result of these discussions?
- Recognise that this training activity is not an isolated incident but contributes to your overall training experience. How has this specific training activity supported the development of broader skills applicable to other training activities, such as critical evaluation of resources or understanding the principles behind different analysis methods? How have you applied the knowledge and skills gained from this training activity in subsequent work, whether in selecting tools for other analyses or understanding the rationale behind tool choices made by others? How have your skills in this area developed over time? How has subsequent experience influenced your approach to similar tool selection tasks?
- Identify the transferable skills you are developing through this training activity. How might the skills and knowledge gained from this training activity (e.g., understanding different types of genomic variation, evaluating tool features and limitations) be relevant to future challenges or roles in your career as a Clinical Bioinformatician? Identify clear actions for the continued development of the skills introduced through this activity. What steps will you take in the future to further enhance your ability in selecting appropriate bioinformatics tools for inherited disease variant identification?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 2 |
Outcome
Evaluate sources of information about variation in the human genome including access, application and clinical impact. |
| # 3 |
Outcome
Select appropriate tools for next generation sequencing (NGS) analysis of inherited and acquired disease. |