Training activity information
Details
Analyse and interpret results for a range of genome wide copy number assays for paediatric patients, and select appropriate reflex tests
Type
Entrustable training activity (ETA)
Evidence requirements
Evidence the activity has been undertaken by the trainee repeatedly, consistently, and effectively over time, in a range of situations. This may include occasions where the trainee has not successfully achieved the outcome of the activity themselves. For example, because it was not appropriate to undertake the task in the circumstances or the trainees recognised their own limitations and sought help or advice to ensure the activity reached an appropriate conclusion.
Reflection at multiple timepoints on the trainee learning journey for this activity.
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 does success look like?
- Identify what is expected of you in relation to analysing and interpreting genome-wide copy number assay results for paediatric patients.
- Consider how the learning outcomes apply, specifically concerning the performing of targeted and whole genome analysis, interpreting genomic variants including copy number changes, and interpreting / reporting results with recommendations.
- What does accurate analysis and interpretation of copy number variants look like, contributing to diagnosing paediatric patients with rare inherited disorders?
- Discuss with your training officer to gain clarity on expectations for analysing and interpreting these results.
What is your prior experience of this activity?
- Think about what you already know about analysing and interpreting data from genome-wide copy number assays (e.g., arrays) for paediatric patients.
- Consider possible challenges you might face during the activity, such as complex or small variants, mosaic findings, or VUS, and think about how you might plan to handle them.
- Recognise the scope of your own practice for this activity i.e. know when you will need to seek advice or help with analysis, interpretation and selection of appropriate reflex tests
- Acknowledge how you feel about analysing and interpreting the results for a range of genome wide copy number assays for paediatric patients. How confident do you feel about selecting the appropriate reflex tests?
What do you anticipate you will learn from the experience?
- Consider the specific skills you want to develop related to analysing and interpreting data from genome-wide copy number assays, classifying variants, and selecting appropriate reflex tests.
- Identify specific insights you hope to gain regarding the challenges and nuances of interpreting copy number variants in paediatric patients, particularly in the context of developmental disorders or dysmorphism.
What additional considerations do you need to make?
- Consult actions identified following previous experience of analysing and interpreting results and selecting appropriate testing.
- Identify important information you need to consider before embarking on the activity, such as the principles of genome-wide copy number assays (e.g., microarray) and established guidelines for interpreting copy number variants. You should also review what bioinformatic tools are used, how to assess clinical significance, and in what scenarios reflex tests (e.g., FISH, parental studies, sequencing) are appropriate.
In action
Is anything unexpected occurring?
- Are you noticing anything surprising or different from what you anticipate while analysing and interpreting the genome-wide copy number assay results?
- Are you encountering situations such as:
- Identifying a small CNV or a finding in a region of variable penetrance that makes assessing its clinical significance complex or unclear?
- The identified CNV potentially requiring a reflex test e.g., FISH, targeted sequencing that was not initially budgeted for or planned, necessitating an immediate decision on the appropriate follow-up strategy?
- Dealing with data quality issues or artefacts e.g., in log R ratio or B allele frequency plots that complicate the clear delineation of a potential gain or loss?
How are you reacting to the unexpected development?
- How is this impacting your actions? For example, are you responding to the situation appropriately? Are you adapting or changing your approach to CNV evaluation?
- Consider the steps you are taking in the moment, such as:
- Immediately checking relevant CNV databases or reviewing parental data to clarify the clinical significance of a complex finding?
- Are you actively deciding which specific reflex tests are appropriate based on the initial copy number findings?
- Do you need to discuss the interpretation of a complex case or the selection of reflex tests with a senior colleague or clinical scientist?
- How are you feeling in that moment? For instance, are you finding it difficult to adapt when distinguishing pathogenic variants from benign ones? Is it affecting your confidence in assessing the clinical significance based on genomic content and patient phenotype?
What is the conclusion or outcome?
- Identify how you are working within your scope of practice. For example, are you successfully classifying the CNV and recommending the reflex test, or needing support because the finding is novel or the clinical significance is too uncertain for you to proceed independently?
- What are you learning as a result of the unexpected development? For example, are you learning the specific workflow for selecting appropriate reflex testing based on CNV size/location, or gaining crucial insight into the reliable interpretation of specific data metrics (e.g., log R ratio)?
On action
What happened?
- Begin by summarising the key points of the experience of analysing and interpreting results from genome-wide copy number assays and selecting reflex tests.
- Consider specific events, actions, or interactions which felt important, such as identifying complex or novel copy number variants (CNVs) or determining the necessity for a specific reflex test based on pathogenicity.
- Include any ‘reflect-in-action’ moments where you had to adapt to the situation as it unfolded, for instance, immediately checking relevant CNV databases or consulting a colleague to clarify the significance of a complex finding before recommending a reflex test. How did you feel during this experience?
How has this experience contributed to your developing practice?
- Identify what learning you can take from this experience regarding CNVs, their role in paediatric disorders, and the selection of appropriate reflex tests.
- What strengths did you demonstrate e.g., systematic approach to CNV analysis? What skills and/or knowledge gaps were evident e.g., difficulty classifying CNVs of uncertain significance or justifying the clinical necessity of certain reflex testing strategies?
- Compare this experience against previous array or CNV analysis activities – were any previous identified actions for development achieved? Has your practice in analysis and interpretation improved?
- Identify any challenges you experienced e.g., ambiguity in CNV boundaries or limited phenotypic correlation and how you reacted to these. Did this affect your ability to deal with the situation? Were you able to overcome the challenges?
- Identify anything significant about the activity, such as needing to seek advice or clarification on CNV pathogenicity or escalating the need for a non-standard reflex test to ensure that you were working within your scope of practice.
- Acknowledge any changes in your own feelings about analysing and interpreting such results. How do you now feel about selecting appropriate reflex tests, without direct supervision?
What will you take from the experience moving forward?
- Identify the actions or ‘next steps’ you will now take to support the assimilation of what you have learnt, including from any feedback you have received regarding your ability to analyse and interpret results for a range of genome wide copy number assays for paediatric patients. What feedback have you received about your ability to select appropriate reflex tests?
- What will you do differently next time you analyse genome-wide copy number data and select reflex tests? Has anything changed in terms of what you would do if you were faced with a similar situation again?
- Do you need to practise any aspect of the activity further, such as mastering the use of specific resources or tools for CNV analysis, or exploring specific types of complex CNVs or reflex testing strategies in depth?
Beyond action
Have you revisited the experiences?
- Have you reviewed your actions from your previous reflections for this activity? What specific actions did you previously identify you would need to take to improve your practice related to performing whole genome analysis, interpreting genomic variants including copy number changes, and selecting appropriate reflex tests?
- Have you completed these previously identified actions? For example, if you planned to review the established guidelines for interpreting copy number variants, how did completing this action impact your ability to confidently assess a complex or small copy number variant (CNV)?
- Engage in professional storytelling with peers, near peers, or colleagues about challenging CNV interpretations. Have complex cases encountered since this initial activity, such as those involving regions of variable penetrance, refined your skills in interpreting copy number variants and selecting appropriate reflex tests (e.g., FISH, parental studies)?
How have these experiences impacted upon current practice?
- Consider how the accumulated learning from performing or reflecting on CNV analysis will support you in preparing for observed ‘in-person’ assessments for the module, such as a DOPS titled ‘Classify a variant’.
- How has your practice related to analysis and interpretation developed and evolved over time? For example, how have the analytical and interpretative skills developed here (interpreting genomic variants, selecting appropriate reflex tests) been transferable to your analysis of other types of structural variants or genomic data, such as those found during whole genome analysis?
- As genome-wide technologies evolve, how will your foundational understanding from this activity help you to interpret and integrate new types of copy number information, perhaps from evolving bioinformatic tools, in the future?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 2 |
Outcome
Perform targeted analysis for patients referred with paediatric conditions. |
| # 3 |
Outcome
Perform whole genome analysis for patients referred for paediatric disorders. |
| # 4 |
Outcome
Interpret genomic variants, including copy number changes, and investigate the clinical significance of variants using bioinformatic tools using best practice guidelines. |
| # 5 |
Outcome
Interpret and report genomic testing relevant to paediatric conditions, including appropriate recommendations for patient management. |