Training activity information
Details
Perform at least one quality measure for an NGS assay, and assess all quality measures from initiation to sequencing
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 performing at least one quality measure and assessing all quality metrics for an NGS assay. This includes interpreting the bioinformatic and NGS quality metrics in relation to assay performance and External Quality Assessment (EQA).
- Discuss with your training officer to gain clarity of what is expected of you in relation to the acceptable thresholds for specific quality metrics (e.g., read depth, coverage uniformity) and validation procedures.
What is your prior experience of this activity?
- Think about what you already know about performing quality control measures or assessing NGS quality metrics, such as those related to validation and verification.
- Consider possible challenges you might face during the activity, such as interpreting complex quality reports or troubleshooting issues, distinguishing acceptable assay performance from technical failures, and think about how you might handle them.
- Recognise the scope of your own practice for this activity i.e. know when you will need to seek advice or help, and from whom. You will need to seek advice from your Training Officer when required, for example if required quality measures deviate significantly from defined pass criteria.
- Acknowledge how you feel about performing quality measures in the context of this training activity. How do you feel about assessing all quality measures in the process?
What do you anticipate you will learn from the experience?
- Consider the specific skills you want to develop, such as systematic assessment of NGS quality control reports and troubleshooting bioinformatic quality metrics.
- Identify the specific insights you hope to gain into the impact of different quality metrics on assay performance or the critical importance of EQA schemes and standardisation protocols.
What additional considerations do you need to make?
- Consult actions identified following previous experiences of quality control, assay validation, or equipment performance checks.
- Identify important information you need to consider before embarking on the activity, such as standardisation protocols, validation/verification procedures, and the specific use of relevant bioinformatics tools for quality metric analysis.
In action
Is anything unexpected occurring?
- Are you noticing anything surprising or different from what you anticipate whilst monitoring and reacting to quality metrics during the NGS assay process?
- Are you encountering situations such as:
- Quality metrics (e.g., Q30 scores, cluster density, or coverage uniformity) falling unexpectedly outside the established performance range?
- Issues flagged by the instrument or software during the run that challenge the interpretation of quality metrics?
- Unexpected variability or poor performance compared to previous External Quality Assessment (EQA) or validation runs?
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 immediately troubleshooting, repeating a step, or pausing the run? Are you adapting or changing your approach to assessing quality measures due to the unexpected flag?
- Consider the steps you are taking in the moment, such as immediately documenting the failure metric and consulting a guide on acceptable thresholds before proceeding with the sequencing run.
- How are you feeling in that moment? For instance, are you finding it difficult to adapt your standard quality assessment protocol? Is it affecting your confidence in determining if the assay run is diagnostically acceptable?
What is the conclusion or outcome?
- Identify how you are working within your scope of practice. For example, are you successfully troubleshooting a minor cluster density issue by adjusting the workflow? Or are you needing support because a major equipment or software failure compromises the run integrity and requires senior technical review?
- What are you learning as a result of the unexpected development? For example, are you mastering a more efficient technique for relating specific bioinformatic flags to assay performance and reliability?
On action
What happened?
- Begin by summarising the key steps you took when performing or assessing quality measures for the NGS assay from initiation (e.g., DNA/RNA QC) to sequencing.
- Consider specific events, actions, or interactions which felt important, such as how you assessed the bioinformatic/NGS quality metrics (e.g., read depth, uniformity) or how you documented the results of the quality checks.
- Include any ‘reflect-in-action’ moments where you had to adapt to the situation as it unfolded, for instance, immediately adjusting the QC threshold when unexpected low read depth was detected for a critical gene region, requiring consultation with the bioinformatics team.
- How did you feel during this experience, e.g., did you feel acutely aware of the risk to assay performance or confident in troubleshooting technical issues?
How has this experience contributed to your developing practice?
- Identify what learning you can take from this experience regarding interpreting the bioinformatic and NGS quality metrics in relation to assay performance and EQA. What strengths did you demonstrate, e.g., systematic adherence to quality check documentation requirements?
- What skills and/or knowledge gaps were evident, e.g., unfamiliarity with the specific quality criteria applied to newly implemented sequencing platforms?
- Compare this experience against previous engagement with similar activities – were any previously identified actions for development achieved? Has your practice improved in identifying quality issues throughout the NGS workflow?
- Identify any challenges you experienced, such as needing to seek advice or clarification on scope of practice regarding the failure of a specific quality measure that required senior sign-off before data release, and how you reacted to this.
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, with regards to performing and assessing NGS quality measures.
- What will you do differently next time you approach quality assessment of a sequencing run, for instance, by proactively reviewing the historical quality performance of the assay against EQA results?
- Do you need to practise any aspect of the activity further, such as troubleshooting common NGS quality control failures or key learning outcomes related to interpreting bioinformatic and NGS quality metrics?
Beyond action
Have you revisited the experiences?
- How have your subsequent experiences of performing and assessing NGS quality measures since completing this specific training activity led you to revisit your initial approach or decisions during that activity? For example, how a subsequent sequencing run suffering persistent failures in coverage uniformity forced you to re-evaluate the meticulousness of your pre-run quality measure performance and documentation you applied during your first attempt at this training activity?
- Considering what you understand about interpreting bioinformatic and NGS quality metrics now, were the actions or considerations you identified after your initial reflection on this training activity sufficient? How have you since implemented or adapted improvements in your technique for performing quality measures or assessing quality reports based on further learning and experiences? For example, how you proactively reviewed and integrated external quality assessment (EQA) metrics into your internal assessment workflow to standardise performance checks.
- Has discussing instances where specific quality metrics (e.g., read depth) indicated a problem or the significance of EQA schemes with colleagues, peers, or supervisors changed how you now view your initial experience in this training activity? For example, how professional storytelling with a senior staff member about a time when complex metrics were misinterpreted, refined your understanding of the critical nature of data integrity verification across the entire sequencing workflow?
How have these experiences impacted upon current practice?
- How has the learning from this initial training activity, in combination with subsequent experiences, contributed to your overall confidence and competence in assessing NGS quality and interpreting metrics, particularly in preparing for assessments? For example, how your integrated understanding of NGS quality metrics now enables you to confidently perform quality checks and troubleshoot assay performance during a Direct Observation of Practical Skills (DOPS)?
- How has reflecting back on this specific training activity, combined with everything you’ve learned since, shaped your current approach to quality assessment? How does this evolved understanding help you identify when something is beyond your scope of practice or requires escalation? For example, how your evolved approach means you now routinely seek advice immediately when performance metrics fall below defined validation criteria or suggest systematic equipment failure?
- Looking holistically at your training journey, how has this initial experience, revisited with your current perspective, contributed to your development in meeting the learning outcomes related to interpreting bioinformatic and NGS quality metrics?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 5 |
Outcome
Interpret the bioinformatic and NGS quality metrics in relation to assay performance and EQA. |