Back Module: S-G-S5-1

Rare Disease 1

Module information

Module details

Title
Rare Disease 1
Type
Specialist
Module code
S-G-S5-1
Credits
10
Phase
2
Requirement
Compulsory

Aim of this module

This module aims to provide the trainee with the knowledge required to diagnose patients with rare inherited disorders using genomics. Trainees will develop the skills to apply genomic testing for patients with rare inherited disorders and understand the implications of results on family members.

Work-based content

Training activities

# Learning outcome Training activity Type Action
# 1 Learning outcome 1, 5 Training activities

Perform duty scientist tasks for rare disease investigations to include:

  • Triage of referrals
  • Liaison with internal colleagues to resolve matters arising e.g. issues with sample preparation
 Type DTA Action View
# 2 Learning outcome 3 Training activities

Perform interpretation of sequence variants for patients referred for investigation of rare disease and make recommendations for further testing required to reclassify variants, to include:

  • missense,
  • nonsense,
  • splice site,
  • indels
  • frameshifts.
 Type ETA Action View
# 3 Learning outcome 1, 2, 3, 4 Training activities

Review referrals; analyse, interpret, and report results for Next Generation Sequencing (NGS) panels for patients referred for investigation of rare disease using HGVS nomenclature to describe genomic sequence changes.

 Type ETA Action View
# 4 Learning outcome 3 Training activities

Perform variant interpretation of copy number changes and other structural variation (for example inversions and translocations) for patients referred for rare disease investigations.

 Type ETA Action View
# 5 Learning outcome 2, 3, Training activities

Perform full chromosome analysis for patients referred for infertility testing or recurrent miscarriage using International System for Human Cytogenomic Nomenclature (ISCN) to describe genomic structural variant changes and select appropriate reflex testing.

 Type DTA Action View
# 6 Learning outcome 2 Training activities

Perform analysis of the segregation of chromosomes following chromosomal rearrangements; determine implications for recurrence risk and future testing.

 Type DTA Action View
# 7 Learning outcome 1, 2, 3, Training activities

Review referrals; analyse, interpret and report the results of testing for Cystic Fibrosis to include:

  • Diagnostic (classical and non-classical) testing
  • Presymptomatic testing
  • Carrier/familial testing
 Type DTA Action View
# 8 Learning outcome 5 Training activities

Review an External Quality Assessment (EQA) report, recommend corrective actions and draft a plan to action recommendations.

 Type DTA Action View
# 9 Learning outcome 5 Training activities

Draft a plan to introduce a change that needs to be made in your department to include:

  • Requirements for validation and verification
  • Management of risks
  • Stakeholder engagement
  • Accreditation requirements (ISO 15189)
 Type DTA Action View
# 10 Learning outcome 1, 2, 3 Training activities

Participate in service delivery for rare disease services, to include:

  • Communication with other healthcare professionals
  • Troubleshooting of testing

 

 Type DTA Action View

Assessments

Complete 2 Case-Based Discussions

Complete 2 DOPS or OCEs

Direct Observation of Practical Skills

  • Analyse and interpret results for a genomics rare disease investigation.
  • Prepare a report for a Next Generation Sequencing (NGS) panel for investigation of rare disease.
  • Classify a variant identified in investigation of rare disease.
  • Perform chromosome analysis for investigation of rare disease.

Observed Communication Event Titles

  • Communicate a result or finding of a rare disease investigation to a healthcare professional
  • Provide advice to another healthcare professional on the requirements for a sample provided for investigation of rare disease.

Learning outcomes

# Learning outcome
1

Triage referrals for rare disease genomic investigations.
2

Perform targeted and chromosomal analysis for patients referred for investigation of rare disease.
3

Interpret genomic variants to investigate the clinical significance using appropriate nomenclature.
4

Interpret and report genomic testing for Next Generation Sequencing (NGS) panels.
5

Employ specialist knowledge of quality management within a Genomics laboratory.

Clinical experiences

Clinical experiences help you to develop insight into your practice and a greater understanding of your specialty’s impact on patient care. Clinical experiences should be included in your training plan and you may be asked to help organise your experiences. Reflections and observations from your experiences may help you to advance your practice and can be used to develop evidence to demonstrate your awareness and appreciation of your specialty.

Activities

  • Attend multidisciplinary meetings to appreciate the role of genomics in the patient pathway.
  • Observe the set-up of assays for investigation of rare diseases.
  • Attend a Quality Meeting where change management and/or EQA within the laboratory are discussed.
  • Observe an element of newborn screening (NBS) in another healthcare science specialty to appreciate the pathway and process for NBS.

Academic content (MSc in Clinical Science)

Important information

The academic parts of this module will be detailed and communicated to you by your university. Please contact them if you have questions regarding this module and its assessments. The module titles in your MSc may not be exactly identical to the work-based modules shown in the e-portfolio. Your modules will be aligned, however, to ensure that your academic and work-based learning are complimentary.

Learning outcomes

  1. Demonstrate advanced understanding of the clinical landscape and national policies relating to rare genomic disease within the NHS; including the role the Genomic Laboratory Hubs (GLHs), and partnerships with other clinical specialisms.
  2. Explain the molecular mechanisms and clinical features associated with a range of rare genomic disorders.
  3. Critically evaluate the technical principles, capabilities, and limitations of laboratory testing strategies for rare disease diagnosis in NHS clinical genomics.
  4. Critically evaluate the implementation of next-generation sequencing (NGS) and whole genome sequencing (WGS) in the NHS, including historical development, key milestones, drivers for adoption, and future directions.
  5. Critically appraise ethical, legal, and professional issues associated with NGS and WGS testing, with particular emphasis on consent, data sharing, incidental findings, and testing in paediatric versus adult populations.

Indicative content

  • Clinical presentation, genetic mechanisms and testing strategies relevant to rare genomic disorders; to include:
    • Paediatric CNV disorders (eg. Williams syndrome and DiGeorge syndrome)
    • Chromosomal causes of infertility and recurrent miscarriage
    • Familial Hypercholesteremia
    • Disorders of sexual differentiation
  • Different types of variation identified by genomic testing
  • Testing strategies to include: NGS/WGS, chromosome analysis, in situ hybridisation and whole genome CNV analysis
  • SNV and CNV interpretation according to current best practice guidelines.
  • The role of multidisciplinary team meetings to aid interpretation.
  • Follow up testing for variants of uncertain significance and how these can alter classification.
  • Bioinformatics for the processing of large datasets.
  • Consent for rare disease testing, storage of patient material, data sharing and secondary findings, with reference to appropriate best practice guidelines
  • The importance of appropriate internal quality control and external quality assurance.
  • Awareness of the importance of turnaround time in the pathway of care.

 

Module assigned to

Specialties

Specialty code Specialty title Action
Specialty code SLS4-1-27 Specialty title Genomics [2027] Action View
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