| Programme | Scientist Training Programme |
| Specialty | Clinical Bioinformatics Genomics |
| Year of review | 2025 – 2026 |
| Curriculum | Click link to access Clinical Bioinformatics Genomics curriculum |
| Specialty Lead Editor | Sam Nalty |
Current priority areas
Stakeholder feedback
Feedback collecting through the Curriculum Library survey collected between January 2024 and November 2025. All stakeholder feedback is presented verbatim.
Programme
- I would like to propose a curriculum review for the specialty Bioinformatics Genomics to develop it into a specialty named ‘Bioinformatics and Genomic Informatics’ In genomic/genetic laboratories there are STPs following the Bioinformatics Genomics specialty there are also Informatics and IT staff who are undertaking work in Computer Science / Software and Systems Development and Data Management and Analysis. Some of these staff may align to the STP in Clinical Informatics and at least one Genomics Laboratory Hub has a trainee following that curriculum, other genetics labs also offer rotational modules to Clinical Informatics trainees. We have also considered offering this training programme, However, genetics laboratories only have enough Bioinformatics or Informatics work for a small number of staff in each of these areas compared to the number of staff in the Genomics and Cancer Genomics specialisms. A far better solution would be to merge the Bioinformatics and Informatics staff groups into one specialism that allows a robust and flexible workforce to develop that would be able to work on both Bioinformatic an Informatic solutions in Genomics depending on the needs and priorities of the department. Please can the proposal for the specialism to be reviewed to develop it into ‘Bioinformatics and Genomic Informatics’ be raised for consideration.
- I’d like to suggest that S-HI-R1 Introduction to Health Informatics be an alternative option in the Core modules to S-GC-R1 Introduction to the Principals and Practice of Genetic and Genomic Counselling. For the Bioinformatics Genomics Curriculum Only. This would be in keeping with another course offered in Clinical Bioinformatics – The PGCert. PG Cert Clinical Bioinformatics (Distance Learning) – BMH 2018-19 (manchester.ac.uk). This would also be in keeping with the post training work of staff in the Bioinformatics field who tend to have a closer working relationship with Clinical/Health Informatics staff than they do with Genetic Councillors.
- With the change in name of Bioinformatics (Physical Sciences) to Clinical Scientific Computing and Bioinformatics (Health Informatics) to Clinical Informatics. Consider if the name of the Specialty should be changed from Clinical Bioinformatics Genomics to just Clinical Bioinformatics. The programme title already contains Genomics ie. currently Programme title: Genomics Sciences – Clinical Bioinformatics Genomics to Programme title: Genomics Sciences – Clinical Bioinformatics. In the Specialty modules in the 2nd / 3rd year, I wonder if there’s scope to cover some of the work of the broader informatics team that work in Genomics. Eg Genomic LIMS development, Interoperability between Genomic LIMS and Electronic Patient Records, The National Genomic Test Directory (including the Genomic Testing Reporting Specification and Patient Level Contract Monitoring)
- The first year I don’t believe the first year is fit for purpose. The activities solely consisting of observe and reflect mean that the trainees don’t develop any bioinformatics skills during their first year unless they do significant work outside the curriculum. Additionally while I think it’s useful that the first years are now exposed to genomics, cancer genomics and counselling, this has been at the expense of cutting essential material from the first year curriculum (the previous module in computing delivered essential skills in databases and software development, and the other modules provided the only exposure to any kind of infrastructure information that was received in the program). I think the first years would benefit from a shorter genomics science combined rotation and a reintroduction of these missing components. Additionally, if the curriculum must be assessed by observation and reflection only, then this should be delivered over much shorter timescales to allow the trainees to develop more work based skills.
Inappropriate OCEs Any OCEs involving patient histories (notably S-BG-R1 OCEs) aren’t appropriate for bioinformatics modules – it is never appropriate for a bioinformatician to be gathering a patient history.
S-BG-S2 TA9 This training activity “Validate a Pipeline” seems more appropriate for third year than second, as this is an enormous amount of work. If there is any kind of expectation trainees finish the phase 2 modules at the end of second year, this would be better placed in S-BG-S4 or replaced with “Validate or verify a pipeline”.
S-BG-S3 Specifying R and Pandas throughout this module is useful if those are skills we want bioinformaticians to developed, but do not necessarily reflect how data is analysed in labs – I think it would be better if these skills were specialised for one competency and then the trainee is allowed to use whatever appropriate language to statistically analyse data for the rest of their competencies.
For TA-13, the wording is a little confusing – selecting an unestablished metric for variant interpretation has little practical use unless there are about to be new guidelines introduced which contain a new metric, as most labs should be using standardised guidelines for variant interpretation.
Other comments Overall I think the specialist content of the curriculum works well, and covers the major skills required to be a bioinformatician in the NHS. I think the curriculum would benefit from some training or education (probably through the university) on things like Cloud which are being rapidly adopted by many trusts – and that this content should be kept up to date as the field evolves.
Programme learning outcomes
- 1 – “Evaluate variation in the human genome and assess pathogenicity” – this probably needs rephrasing as evaluating pathogenicity is the job of genomics clinical scientists and not bioinformaticians. Additionally it does seem to tie in to just rare disease (cancer variants are looking at oncogenicity).
- S-BG-S1 (Diagnostic Sequencing) TA10: Is vague and overlaps with other training activities. Clarification and differentiation would be good. S-BG-S2 (Software) There is significant overlap with the Service Delivery module (e.g. validation). Recommend: Making TAs more technically focused. Introducing a TA specifically on containerisation (e.g. Docker). Making TA3, TA4, and TA10 more generic and inclusive of software, allowing them to be fulfilled via database or pipeline projects. S-BG-S4 (Service Delivery) Is good S-BG-S3 (Statistics) TA2, TA5, TA6, TA11, and TA12 have a lot of overlap and stats is not a major part of clinical bioinformatics so it seems a lot to have 5 TA on this Suggest including: A focus on how results are displayed to clinical scientists. Include TA relating to automation. Overall For some modules the DOPs and OCEs feel misaligned with the learning objectives or module content.
S-BG-R1 Introduction to Clinical Bioinformatics Genomics
Module aim
- This module is compulsory for genomics and cancer genomics trainees but contains more detailed information than they need. It would be better to have a few training activities relating to bioinformatics in the other first year modules or to have a single large introductory module with introductions to genomics, cancer, bioinformatics, counselling covered over 6 months leaving 2 and half years for trainees to focus on their specialism, each of which has so much specialist content.
Training activities
- 7 – Not relevant to genomics trainees. 9 is a duplication of a training activity in the genomics module.
- 9 – Duplicated from the Genomics Rotation (S-G-R1 TA2 & 7). Difficult to fulfil within bioinformatics as requires staff from other teams.
- 9 – This TA is to shadow a technologist or genomics clinical scientist so can’t be done in our team and we always have to ask the trainees to complete it in another rotation or arrange for the trainees to meet with a scientist in the lab
- 9 – TA9: The current requirement to “shadow a technician/clinical scientist” is covered in another rotational module (Introduction to Genomics) and cant be delivered by a bioinformatics team. Recommend replacing it with a focus on how bioinformatics integrates with other teams.
Direct Observation of Practical Skills (DOPS)
- “Prepare a command to initiate a pipeline”. “Check the progress of a pipeline.”- not relevant to genomics trainees.
Observed Communication Events (OCE)
- These feel unrelated to the module content
- “Gather a patient history relevant to the specialty from a patient, patient representative, or a member of the multidisciplinary team.” “Present a patient history relevant to the specialty to a member of the multidisciplinary team.”- Not relevant to bioinformatics. bioinformaticians don’t meet patients or gather history.
S-BG-S1 Diagnostic Sequencing
Training activities
- 2 – Generate a genomic sequence alignment in an appropriate format. Evidence the activity has been undertaken by the trainee repeatedly, consistently, and effectively over time, in a range of situations. Annotate genomic variation data in the context of inherited and acquired disease Evidence the activity has been undertaken by the trainee repeatedly, consistently, and effectively over time, in a range of situations. The requirement to demonstrate that the activity has been carried out repeatedly does not reflect current bioinformatics practice where these steps are carried out as part of a pipeline rather than being carried out repeatedly by individual bioinformaticians. in practice trainees carry out the activity once as part of their training to ensure they understand the process that forms part of the pipeline rather than carrying it out repeatedly.
S-BG-S2 Software
- no feedback received
S-BG-S3 Applied Statistics, Data Science and Quality in Clinical Bioinformatics
- no feedback received
S-BG-S4 Service Delivery and Development
- no feedback received
Changes made
Module level changes
| Change ID | M1 |
| Module code | S-BG-R1 |
| Module content | Training Activity |
| Original | Shadow a Technologist or Clinical Scientist in Genomics and reflect on their role |
| Change | Observe a Bioinformatician interacting with a professional from another discipline and reflect on the role of bioinformaticians.
Considerations:
Mapped LO: 1, 2, 3, 6 |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M2 |
| Module code | S-BG-R1 |
| Module content | OCE |
| Original | Add a new OCE |
| Change | Describe a bioinformatics pipeline in the laboratory and how this meets good practice and regulatory requirements. |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M4 |
| Module code | S-BG-S1 |
| Module content | Training Activity |
| Original | 2 – Generate a genomic sequence alignment in an appropriate format |
| Change | This should be a DTA |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M5 |
| Module code | S-BG-S1 |
| Module content | Training Activity |
| Original | 5 – Annotate genomic variation data in the context of inherited and acquired disease |
| Change | This should be a DTA |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M6 |
| Module code | S-BG-S2 |
| Module content | Training Activity |
| Original | 9 – Validate a pipeline |
| Change | Change this to “Validate a change to a pipeline or verify a pipeline release.” |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M7 |
| Module code | S-BG-S3 |
| Module content | Training Activity |
| Original | 1 – Retrieve data from a REST application programming interfaces (API) and manipulate to create dataframes in both python 3 (pandas) and R |
| Change | Retrieve and parse data from a REST application programming interface (API) |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M8 |
| Module code | S-BG-S3 |
| Module content | Training Activity |
| Original | 2 – Hold genomics data in dataframes and perform statistical analyses using both python 3 (pandas) and R |
| Change | Perform programmatic statistical analysis of parsed data |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M9 |
| Module code | S-BG-S2 |
| Module content | Training Activity |
| Original | Gather user requirements for a pipeline and select appropriate tools and scripting language for the pipeline and justify selection. |
| Change | Gather user requirements for a piece of software or pipeline and select appropriate tools and scripting language for the pipeline and justify selection. |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M10 |
| Module code | S-BG-S2 |
| Module content | Training Activity |
| Original | Gather user requirements for a pipeline and select appropriate tools and scripting language for the pipeline and justify selection. |
| Change | Gather user requirements for a piece of software or pipeline and select appropriate tools and scripting language for the pipeline and justify selection. |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M11 |
| Module code | S-BG-S2 |
| Module content | Training Activity |
| Original | Produce appropriate documentation for a pipeline, provide training and gather user feedback |
| Change | Produce appropriate documentation for a piece of software or pipeline, provide training and gather user feedback |
| Change category | Minor |
| Implementation cohort | 2026 |
| Change ID | M12 |
| Module code | S-BG-S3 |
| Module content | Training Activity |
| Original | |
| Change | Introduce a new training activity “Plan, develop and implement a visualisation of data not derived from a statistical test for an end user”
Type: DTA Reflective guidance: |
| Change category | Major |
| Implementation cohort | 2027 |
Programme level changes
| Change ID | P1 |
| Component | Module substitution |
| Original | Current phase 1 rotations are S-BG-R1, S-G-R1, S-CG-R1, S-GC-R1 |
| Change | Replace S-GC-R1 with S-HI-R1 |
| Change category | Major |
| Implementation cohort | 2027 |
| Change ID | P2 |
| Component | Programme LO |
| Original | Evaluate variation in the human genome and assess pathogenicity |
| Change | Reword to “Evaluate variation in the human genome and predict variant effect programmatically” |
| Change category | Major |
| Implementation cohort | 2027 |
Periodic review
This specialty curriculum requires significant change beyond the scope of an annual review.
Response – no
Rationale
Please provide an overview of the rationale for why the proposed changes are needed or why changes were not needed, with reference to stakeholder feedback.
Response
| Change | Rationale |
| M1 | The current shadowing requirement duplicates S-G-R1 and cannot be delivered within bioinformatics teams, requiring external coordination. Multiple sites report difficulty fulfilling this in-house. The replacement focuses on interdisciplinary collaboration directly deliverable within bioinformatics placements and reflects actual bioinformatician work. |
| M2 | Bioinformaticians never gather patient histories in clinical practice, making this activity fundamentally inappropriate for a bioinformatics module so a new additional option for an activity that that is directly relevant to the scope of a bioinformatician is useful. |
| M4 | Current assessment requirement states activity must be undertaken “repeatedly, consistently, and effectively over time.” In modern bioinformatics practice, sequence alignment is pipeline-automated; trainees perform it once to understand the process. ETA better captures single-performance demonstration of competency aligned with contemporary practice. |
| M5 | Like M4, stakeholders note annotation is typically automated; trainees learn it once as part of pipeline understanding rather than repeatedly. Changing to ETA assessment reflects actual bioinformatics practice where these steps are one-off learning activities, not repeated actions. |
| M6 | Full pipeline validation is enormous workload inappropriate for second year if phase 2 completion is expected by year-end. The reworded activity captures realistic second-year scope: verification of released pipelines and validation of incremental changes. Proportionate scope allows reasonable phase 2 completion timing. |
| M7 | Stakeholders noted mandatory specification of both R and Pandas doesn’t reflect how data is actually analysed in NHS labs, which use varied languages depending on available expertise. Simplifying to API retrieval generic to any language removes prescriptive burden while maintaining core competency. |
| M8 | See above |
| M9 | Current wording narrowly prescribes pipelines as the only acceptable project type, excluding legitimate software development (databases, analysis tools, automation scripts, etc.). Bioinformaticians develop diverse software beyond pipelines. Rewriting to allow database projects, analysis tools, or other software types enables broader skill development while maintaining core competencies and allows STPs to directly address current clinical priorities and service needs. Inclusive scope better reflects real bioinformatics work. |
| M10 | See above |
| M11 | See above |
| M12 | Stakeholder feedback |
| P1 | Bioinformatics STPs work more closely with Informatics staff than genetic counsellors post-training, yet mandatory genetic counselling training is included. S-HI-R1 aligns with established clinical bioinformatics training programs (e.g., Manchester’s PGCert). Offering it as an alternative allows appropriate specialisation while maintaining breadth. |
| P2 | Current wording misrepresents bioinformatician role—pathogenicity assessment is a clinical scientist responsibility, not bioinformatician. Outcome also artificially ties to rare disease only; cancer variants assess oncogenicity. Reworded outcome accurately reflects core competency: predicting computational effects of variants, aligning with actual bioinformatics practice. |
I confirm I have reviewed the Reflective Practice Guidance for ETAs and DTAs and have made any changes necessary.
Specialty Lead Editor signature: Sam Nalty
Date: 5 January 2026
Change control - completed by the school
Programme structure
| Change ID | Programme structure maintained | Comments |
| M1 | Yes | |
| M2 | Yes | |
| M3 | n/a | |
| M4 | Yes | |
| M5 | Yes | |
| M6 | Yes | |
| M7 | Yes | |
| M8 | Yes | |
| M9 | Yes | |
| M10 | Yes | |
| M11 | Yes | |
| M12 | Yes | |
| P1 | Yes | |
| P2 | Yes |
Completed by: Chris Fisher
Date: 15 January 2026
Health and Care Professions Council (HCPC) mapping
- No module level learning outcomes changed. Mapping to 13.04 select and use appropriate assessment techniques and equipment and 13.06 undertake or arrange investigations as appropriate revisited due to changes in the core modules. HCPC mapping maintained.
Completed by: Chris Fisher
Date: 15 January 2026
Major change control
School Lay Representative Collaborative Review
- Lay feedback
Stakeholder survey
- Survey period: TBC
- Unique page views: TBC
- Survey responses: TBC