Back Module: S-G-S7-1

Rare Disease 2

Module information

Module details

Title
Rare Disease 2
Type
Specialist
Module code
S-G-S7-1
Credits
20
Phase
3
Requirement
Compulsory

Aim of this module

This module aims to provide the trainee with further knowledge and skills 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.

This module includes the following conditions as exemplars: newborns who present as dysmorphic, hypotonic or with ambiguous genitalia, patients referred for cystic fibrosis (CF), myotonic dystrophy, fragile X, spinal muscular atrophy, Prader-Willi and Angelman syndrome, Duchenne and Becker muscular dystrophies, learning disabilities or delayed puberty.

Work-based content

Training activities

# Learning outcome Training activity Type Action
# 1 Learning outcome 1, 7, 8 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 arising with sample preparation
  • Liaison with external healthcare professionals to resolve matter arising e.g. clinical information to support test eligibility, sample issues
 Type ETA Action View
# 2 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of testing for Spinal Muscular Atrophy (SMA) to include:

  • Diagnostic testing
  • Carrier/familial testing
 Type DTA Action View
# 3 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of testing for Duchenne Muscular Dystrophy or Becker Muscular Dystrophy (DMD/BMD) to include:

  • Diagnostic testing
  • Carrier/familial testing
 Type DTA Action View
# 4 Learning outcome 1, 2 ,3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of testing for Prader-Willi syndrome.

 Type DTA Action View
# 5 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of testing for Angelman syndrome referrals.

 Type DTA Action View
# 6 Learning outcome 2 ,7, 8 Training activities

Perform risk calculations for modes of inheritance to include:

  • autosomal recessive
  • X-linked
 Type DTA Action View
# 7 Learning outcome 5 Training activities

Participate in population health testing relevant to your local laboratory or region.

 Type DTA Action View
# 8 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of sanger sequencing analysis for cascade testing to include:

  • predictive/presymptomatic testing
  • carrier testing
  • family studies
 Type ETA Action View
# 9 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report results from Whole Genome Sequencing (WGS) testing to include,

  • coding variation
  • non-coding variation
 Type ETA Action View
# 10 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report genome-wide copy number assays from WGS and/or microarray testing for patients with chromosomal disorders.

 Type ETA Action View
# 11 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

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

  • diagnostic testing
  • presymptomatic testing.
 Type DTA Action View
# 12 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

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

  • diagnostic testing
  • presymptomatic testing
 Type DTA Action View
# 13 Learning outcome 1, 2, 3, 4, 7, 8 Training activities

Review referrals; analyse, interpret and report the results of diagnostic, presymptomatic and carrier testing for FMR1 related conditions to include:

  • Fragile X syndrome
  • Premature Ovarian Failure (POF)
  • Fragile X- associated tremor/ataxia syndrome
 Type DTA Action View
# 14 Learning outcome 2, 3, 4, 7, 8 Training activities

Analyse, interpret and report repeat expansions detected by WGS.

 Type ETA Action View
# 15 Learning outcome 2, 3, 4, 7, 8 Training activities

Analyse and interpret mitochondrial variants detected by WGS.

 Type DTA Action View
# 16 Learning outcome 6, 7, 8 Training activities

Investigate an incident and perform a root cause analysis, recommend corrective and preventative actions and document the findings.

 Type DTA Action View
# 17 Learning outcome 6 Training activities

Review a recent UKAS visit in your department. Consider the preparation required, the findings and how the findings were cleared.

 Type DTA Action View
# 18 Learning outcome 7, 8 Training activities

Liaise with multidisciplinary specialists to inform clinical decision making related to genomic rare disease investigations.

 Type DTA Action View
# 19 Learning outcome 1, 2, 3, 4, 6, 7, 8 Training activities

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

  • Communication with other healthcare professionals
  • Troubleshooting of testing
 Type DTA Action View

Assessments

Complete 4 Case-Based Discussions

Complete 4 DOPS or OCEs

Direct Observation of Practical Skills

  • Analyse and interpret results for a genomics investigation for rare disease using a copy number assay.
  • Analyse and interpret results for a genomics investigation for rare disease using WGS.
  • Analyse and interpret results for a genomics investigation for a rare disease repeat expansion disorder.
  • Prepare a report for a genomics investigation for rare disease.
  • Perform a risk calculation for a rare disease investigation.
  • Triage a rare disease sample received into the laboratory.
  • Classify a variant identified in investigation of rare disease.

Observed Communication Event Titles

  • Provide advice to another healthcare professional on the requirements for a sample for investigation of a rare disease.
  • Provide an urgent result from an investigation for rare disease to another healthcare professional.
  • Discuss patient results from an investigation for rare disease with healthcare professionals at a multidisciplinary meeting.

Learning outcomes

# Learning outcome
1

Review referrals for patients referred for rare disease genomic testing.
2

Analyse, interpret and report results for diagnostic, presymptomatic and familial/carrier rare disease genomic testing.
3

Perform targeted analysis, whole genome analysis, and chromosomal analysis for patients referred for rare disease genomic testing.
4

Interpret genomic variants to investigate their clinical significance for patients referred for rare disease genomic testing.
5

Engage in genomic population health testing.
6

Outline how the principles of quality management contribute to the delivery of high-quality rare disease genomics services.
7

Employ specialist knowledge of rare disease genomic testing to deliver a safe and high-quality service.
8

Demonstrate appropriate communication skills with healthcare professional colleagues to inform the clinical management of patients referred for rare disease genomic testing.

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

  • Observe the set-up of assays for investigation.
  • Observe rare disease genetics clinics to appreciate the consent discussion required with the patient prior to testing, ethical issues and implications or the family for example an adult-onset neurological clinic.

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 critical understanding of the principles of the NHS newborn screening programme, including current biochemical and genomic screening strategies.
  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. Understand and apply knowledge of risk calculations for multiple modes of inheritance.
  5. Critically evaluate the ethical, legal, and professional issues associated with genomic testing in the context of rare disease, including informed consent, familial implications, equity of access, and safeguarding considerations.
  6. Describe how integrated working between laboratory genetics and other clinical specialisms supports patient-centred care, including diagnosis and treatment strategies for patients and their families.

Indicative content

  • Clinical presentation, genetic mechanisms and testing strategies relevant to rare genomic disorders; to include:
    • Duchenne muscular dystrophy/Becker muscular dystrophy.
    • Spinal muscular atrophy.
    • Prader-Willi and Angelman syndrome.
    • Fragile X syndrome, FXTAS and FXPOI.
    • Mitochondrial disorders.
    • Neurogenetic conditions associated with short tandem repeats; to include Huntington Disease and Myotonic Dystrophy.
    • Developmental Disorders/Intellectual disability.
  • Diagnostic testing strategies for acutely unwell children with a likely monogenic disorder.
  • Variant 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.
  • The importance of counselling, e.g. in predictive testing of late onset disorders such as Huntington’s disease and the importance of distinguishing between diagnostic and predictive test requests.
  • Safeguarding children and vulnerable adults
  • The application of targeted and disease‑modifying therapies for disorders listed above.
  • Follow-up management for affected families including recurrence risks and Bayesian calculations.

Module assigned to

Specialties

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