Training activity information
Details
Generate a genomic sequence alignment in an appropriate format
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.
Considerations
- Alignment methodologies e.g., against a reference sequence, indel realignment or de novo
- SAM/BAM/CRAM files
- Genomic architecture e.g., genes, introns, exons etc.
- Reference genome and different genome builds
- Quality metrics used for sequence alignment and any caveats of e.g., difficulties with short reads, pseudogenes, soft/hard-clipping, CIGAR strings etc.
- Store data in appropriate formats according to local and national standards, taking into consideration patient confidentiality
- Data integrity and patient safety
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 1 |
Outcome
Explain the structure of the human genome and the impact of variation on human development, health, and disease. |
| # 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. |
| # 4 |
Outcome
Analyse NGS data in a clinical setting applying appropriate quality control and data validation. |