Rare Disease 2 —
Training activity: 15

Details

Analyse and interpret mitochondrial variants detected by WGS.

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.

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 are the intended outcomes of the training activity?

• How will this activity demonstrate your ability to perform whole genome analysis and interpret genomic variants to investigate their clinical significance in the context of the mitochondrial genome?
• How does this task support the requirement to analyse, interpret, and report results for diagnostic or familial cases?
• What do you need to know before embarking on the activity? Consider the unique genetic basis of mitochondrial disorders, such as maternal inheritance, heteroplasmy, and the threshold effect.
• What specific specialist knowledge is required to deliver a safe and high-quality service when dealing with the complexities of the mitochondrial genome?

What do you anticipate you will learn from the experience?

• What insights do you hope to gain regarding the WGS bioinformatic pipeline for mitochondrial DNA (mtDNA) and the strategies used for variant filtering and prioritisation?
• What do you anticipate learning about the limitations of WGS in detecting low-level heteroplasmy or distinguishing true mtDNA variants from Nuclear Mitochondrial DNA segments (NUMTs)?
• How do you anticipate this will improve your ability to communicate findings to healthcare professional colleagues to inform patient management?

What actions will you take in preparation for the experience?

• How have you planned to gain clarity on the laboratory’s specific mitochondrial WGS analysis protocols?
• Will you review relevant literature, ACMG/AMP variant interpretation guidelines (specifically for mtDNA), or specialist databases such as MITOMAP?
• What potential difficulties might arise? Consider challenges such as interpreting variants of uncertain significance (VUS) in the mtDNA, dealing with varying heteroplasmy levels across different tissue types, or managing incidental findings.
• How do you feel about embarking on this activity, given the technical complexity and the significant clinical implications of mitochondrial results for the patient and their wider family?
• Under what circumstances (e.g., encountering a novel variant or complex heteroplasmy pattern) will you seek immediate advice or clarification to ensure your interpretation remains within established laboratory protocols and your current level of training?

In action

What are you doing?

• How are you currently approaching the analysis of mitochondrial WGS data, and why have you chosen specific steps such as focusing on heteroplasmy thresholds or filtering against MITOMAP?
• What decisions are you making in the moment to determine if a finding is a true mitochondrial variant or a Nuclear Mitochondrial DNA segment (NUMT)?
• Which aspects of the analysis feel intuitive, and which—such as applying specialised ACMG/AMP criteria for the mitochondrial genome—require more conscious effort?

How are you progressing with the activity?

• How effective are your current filtering and prioritisation strategies in identifying causative variants that explain the patient’s clinical presentation?
• How are you managing real-time challenges, such as interpreting VUS in mtDNA, handling low-level heteroplasmy, or correlating levels with the threshold effect for a specific condition?
• What are you learning as the data progresses regarding unexpected findings, and how do these results connect to your existing knowledge of maternal inheritance and mitochondrial biology?

How are you adapting to the situation?

• Which alternative approaches, such as broadening filtering criteria or reviewing raw sequencing reads, are you considering if your initial assessment remains unclear?
• How are you identifying the point where you require immediate support or guidance regarding the clinical significance of a specific mitochondrial variant?
• How are you ensuring that your real-time interpretation remains strictly within the scope of established laboratory protocols and your current professional level of training?
• In what ways are you ensuring your interpretation accurately considers the clinical information provided in the referral to deliver a safe and high-quality service?

On action

What happened?

• How would you summarise your experience with the mitochondrial WGS analysis, and what were the primary clinical indications for the cases you reviewed?
• What specific mitochondrial variants and heteroplasmy levels did you identify, and did you encounter any unusual findings like Nuclear Mitochondrial DNA segments (NUMTs)?
• How did you feel while managing the technical complexity and significant clinical implications of these mitochondrial results for the patient and their wider family?

How has this experience contributed to your developing practice?

• In what ways has your ability to navigate mitochondrial-specific bioinformatic pipelines and apply specialised ACMG/AMP interpretation guidelines improved?
• How did you successfully manage unexpected challenges, such as interpreting a VUS with a heteroplasmy level near a suspected clinical threshold?
• What did these challenges teach you regarding the clinical necessity for tissue-specific testing or parental studies in mitochondrial diagnostics?
• How did your ‘reflection-in-action’ (e.g., real-time decisions to adjust filters or consult specific databases) influence the final accuracy and quality of your interpretation?
• How does mastering this analysis relate to the requirements for your future practice as a Clinical Scientist responsible for high-complexity WGS data?

What will you take from the experience moving forward?

• Do you require a deeper understanding of the threshold effect in mitochondrial disease or the nuances of maternal inheritance patterns?
• How will you apply a more systematic approach to distinguishing true mtDNA variants from NUMTs in future WGS investigations?
• Which specific ‘next steps’—including reviewing latest literature, attending MDT meetings, or seeking senior feedback on interpretive reports—will you take to consolidate your learning?
• What additional support or resources, such as specialised bioinformatic tools or expert mentorship, have you identified as necessary to further develop your expertise in mitochondrial genomics?

Beyond action

Have you revisited the experiences?

• How has your understanding of heteroplasmy levels and the threshold effect evolved as you have gained experience with a wider variety of mitochondrial WGS cases since your initial training?
• Which technical strategies for distinguishing true mitochondrial variants from NUMTs—observed during senior scientist shadowing or OTAs—have you now assimilated into your routine workflow?
• In what ways has professional storytelling with peers regarding challenging mitochondrial VUS or low-level heteroplasmy transformed your interpretative perspective?
• What overarching themes regarding your ability to manage high-complexity datasets have emerged from reviewing your reflections across all WGS-related training activities?

How have these experiences impacted your current practice?

• How has this activity supported your development of broader high-level skills, such as writing complex interpretive reports, clinical reasoning, and navigating specialist databases like MITOMAP?
• How are you applying your knowledge of maternal inheritance patterns and the impact of tissue-specific heteroplasmy to other genomic investigations in your routine practice?
• In what ways is this learning supporting your preparation for ‘in-person’ assessments, such as a Case-based Discussion (CBD) regarding the clinical significance of a mitochondrial finding?

How might these contribute towards your future practice?

• Which transferable skills, such as bioinformatic pipeline navigation and variant prioritisation, do you recognise as vital for your future career as a Scientist?
• Which clear next steps for continued development—including attending specialised workshops, reviewing updated national guidelines, or exploring tools for complex mitochondrial rearrangements—will you take to stay at the forefront of the field?

Relevant learning outcomes

#	Outcome
# 2	Outcome Analyse, interpret and report results for diagnostic, presymptomatic and familial/carrier rare disease genomic testing.
# 3	Outcome Perform targeted analysis, whole genome analysis, and chromosomal analysis for patients referred for rare disease genomic testing.
# 4	Outcome Interpret genomic variants to investigate their clinical significance for patients referred for rare disease genomic testing.
# 7	Outcome Employ specialist knowledge of rare disease genomic testing to deliver a safe and high-quality service.
# 8	Outcome Demonstrate appropriate communication skills with healthcare professional colleagues to inform the clinical management of patients referred for rare disease genomic testing.