Paediatric Genomics

Module details

Title

Paediatric Genomics

Type

Specialist

Module code

SLS421

Credits

10

Requirement

Compulsory

Aim of this module

This module will provide the trainee with knowledge and understanding of the role and application of genetic and genomic testing in the diagnosis  and management of paediatric patients with rare inherited diseases, including the implications for other family members.

 The content for this module will focus on (as exemplars): newborns who present as dysmorphic, failure to thrive, ambiguous genitalia or who are hypotonic. those patients who have a clinical suspicion of Duchenne muscular dystrophy, spinal muscular atrophy, Prader-Willi and Angelman syndrome, fragile X syndrome, myotonic dystrophy, cystic fibrosis, disorders of sexual differentiation, children with developmental delay or delayed puberty.

Competencies

#	Learning outcome	Competency	Action
# 1	Learning outcome 1	Competency Select the correct genetic test(s) for samples from patients referred with learning disability.	Action View
# 2	Learning outcome 2,4,5	Competency Perform and interpret whole genome analysis from patients with learning disabilities.	Action View
# 3	Learning outcome 1,3,4,5	Competency Select an appropriate reflex test and the interpretation within the context of the primary analysis.	Action View
# 4	Learning outcome 2,3,4,5	Competency Perform the analysis and interpretation of genomic dosage and targeted analysis for the detection of genome anomalies associated with learning disability.	Action View
# 5	Learning outcome 3,5	Competency Interpret results from methylation studies for PWS/AS syndrome.	Action View
# 6	Learning outcome 4,5	Competency Prepare full and accurate interpretative clinical reports for patients referred with learning disabilities.	Action View
# 7	Learning outcome 1,3,4,5	Competency Select the correct genetic tests for patients referred with a suspected neuromuscular disorder.	Action View
# 8	Learning outcome 3,4,5	Competency Perform dosage analysis on a patient sample referred for DMD or SMA and analyse the result of molecular testing using appropriate software.	Action View
# 9	Learning outcome 5	Competency Perform simple Bayesian analysis to calculate carrier probability in BMD/DMD and SMA.	Action View
# 10	Learning outcome 4,5	Competency Prepare a range of full and accurate reports relevant to the referrals for testing of neuromuscular disorders.	Action View
# 11	Learning outcome 3	Competency Perform a PCR-based test to detect common CFTR mutations.	Action View
# 12	Learning outcome 4,5	Competency Prepare a range of full and accurate interpretative clinical reports for paediatric patients referred for Cystic Fibrosis testing.	Action View

Assessments

You must complete:

• 3 case-based discussion(s)
• 3 of the following DOPS/ OCEs:

Bisulphite modification and PCR to detect methylation	DOPS
FISH analysis using microscopy	DOPS
Processing samples for FISH	DOPS
Karyotype by image analysis	DOPS
Microarray analysis for a patient referred with learning disability	DOPS
Analyse results of MLPA analysis	DOPS
Interpret and report MLPA data	DOPS
Sample preparation for array analysis	DOPS
Use bioinformatics tools to interpret clinical significance of array result	DOPS
Analyse the results of CF testing	DOPS
Perform laboratory set up of CF test	DOPS
PCR amplification of a triplet repeat	DOPS
Analyse results of FMR1 gene analysis	DOPS
Perform basic risk calculation	DOPS
Prepare a clinical report for a paediatric patient referred with learning disability	DOPS
Prepare a clinical report for a paediatric patient referred for cystic fibrosis	DOPS
Prepare a clinical report for a paediatric patient referred with a neuromuscular disorder	DOPS
Participate in an MDT meeting with other healthcare professionals	OCE
Take a patient history can be undertaken in virtual patient environment	OCE
Discuss patient results with a healthcare professional telephone or in person	OCE

Learning outcomes

1. Apply an appropriate testing strategy relevant to patients referred for paediatric disorders.
2. Perform appropriate whole genome analysis for patients referred for paediatric genomic testing.
3. Perform targeted testing for patients referred with paediatric genetic conditions.
4. Investigate the clinical significance of variants using a range of bioinformatics tools, following current best practice guidelines.
5. Interpret and report a range of genetic and genomic testing relevant to paediatric conditions, including the results of diagnostic testing which should encompass appropriate recommendations for patient management.

Learning outcomes

1. Explain the clinical presentation and assessment of patients with paediatric genetic and genomic disorders.
2. iscuss and evaluate appropriate genomic laboratory testing strategies for paediatric patients according to current best practice.
3. Describe the design, operation and performance of a range of genomic tests relevant to the investigation of these disorders.
4. Discuss and debate the relevant clinical scientific, ethical and legal considerations in the field of paediatric genomics.
5. Describe the purpose and evaluate 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 and assessment of patients

• Clinical presentation and types of inheritance, including pedigree analysis
• Importance of accurate phenotyping

 Genetic laboratory testing strategies

• Laboratory testing pathway including reflex testing
• The potential advantages of trio testing design, operation and performance of a range of genetic tests
• The principles of cost effectiveness in regards to the tests used
• Testing methodology including limitations and sensitivity
• PCR based methods including triplet repeats and methylation and kit based testing
• Copy number variation detection (e.g. Multiplex Ligation- dependent Probe Amplification (MLPA), chromosomal microarray, FISH and G-band analysis)
• Sequencing – using all current methods in clinical use
• Validation and verification of sequencing results
• The importance of appropriate internal quality control and external quality assurance
• Bioinformatics for the processing of large datasets
• Awareness of the importance of turnaround time in the pathway of care
• Interpret archived results based on older technologies and discuss the implication and limitation of these results for the patient and  family

 Clinical scientific, ethical and legal considerations 

• Consent for paediatric testing, storage of patient material and parental involvement
• National guidelines for testing in children
• Follow-up management including prenatal testing for subsequent pregnancies (of future siblings)
• Safeguarding children and young people

Interpretation and reporting of results to include:

• Analysis and interpretation including the relationship of the genetic alteration to the phenotype
• Clinical reporting

• The categories of genetic variation observed within this patient group
• The mechanisms of pathogenesis in paediatric genetic disorder
• Diagnostic and prognostic significance of genetic abnormalities found in this group of patients
• The use of linkage analysis and the risk of recombination to include Bayesian calculation
• The importance of appropriate internal quality control and external quality assurance
• Use of standardised nomenclature to describe genetic and genomic variation
• How to critically appraise relevant literature and databases to develop an awareness of the need for any further testing
• Role of multi-disciplinary team (MDT) meetings to aid interpretation and guidelines such as Improving Outcomes Guidance and NICE guidelines

Activities

• Attend a genetics dysmorphology clinic or multidisciplinary (MDT) meetings and critically reflect on and review experiences in terms of service delivery and patient investigations and management.
• Attend a school for children with learning disabilities and critically reflect and discuss the interaction between the laboratory services and facilities for children in terms of investigation and management, taking into account appropriate governance issues, such as safeguarding children and young people.
• Attend a ward round with a consultant geneticist/paediatrician and discuss the process and outcomes in relation to the information and action points, resulting in your supervisor identifying the challenge of obtaining paediatric samples.
• Contact with a patient group society/charity (e.g. attending a conference or open day). Reflect and report on the importance and role of these organisations in patient care.
• Observe the laboratory quality management system and perform examination and other audits as part of the laboratory accreditation process.
• Review a selection of archived cases, focussing on the laboratory results from earlier technology, including Southern Blotting.
• Process a blood sample to obtain chromosome preparations suitable for analysis for patients with learning disabilities.