Applied Genomics and Bioinformatics in Advanced Clinical Care

Module details

Title

Applied Genomics and Bioinformatics in Advanced Clinical Care

Type

Specialist

Module code

SLS427

Credits

15

Requirement

Compulsory

Aim of this module

This module will provide the trainee with an in-depth understanding of the role of genomic testing in establishing a genetic diagnosis. They will develop the expertise to support the diagnostic process (as part of a multidisciplinary team approach) through exploration of the relationship between genotype and phenotype. The  trainee will also extend their understanding of genomics, how the patient’s  phenotype and the family history can contribute constructively, together with expertise from clinical geneticists, clinical scientists in the laboratory and in bioinformatics, as well as other specialist colleagues, in determining the  pathogenicity of variants.

 In their work-based learning they will further develop their skills to support advanced genetic and genomic counselling practice and shared decision making in partnership with the patient. They will demonstrate their ability to autonomously handle cases that include pre-symptomatic testing, prenatal diagnosis, cascade screening and the management of rare and complex genetic and genomic disease within the context of the multidisciplinary team.

Competencies

#	Learning outcome	Competency	Action
# 1	Learning outcome 1	Competency Prepare and deliver advanced genetic counselling for three complex scenarios including pre- symptomatic testing, prenatal testing and cascade testing.	Action View
# 2	Learning outcome 1	Competency Prepare and deliver advanced genomic counselling consultations involving the use of genomic technologies in a range of rare and complex conditions.	Action View
# 3	Learning outcome 1,2	Competency Synthesise and critically analyse literature from reputable sources to compile information on the clinical presentation and course of a range of rare and/or complex inherited diseases and established clinical phenotypes, in readiness for three consultations.	Action View
# 4	Learning outcome 1,3	Competency Synthesise and relay condition-and life-stage-specific information to patients in five consultations, using appropriate language and communication aids where applicable.	Action View
# 5	Learning outcome 3	Competency Within a consultation, describe the existing non-genomic diagnostic pathways within reproductive, paediatric and adult settings.	Action View
# 6	Learning outcome 2	Competency Observe the work of experienced genetic counsellors in an MDT in an adult, paediatric and reproductive setting.	Action View
# 7	Learning outcome 1,2	Competency Support the use of genomic testing within the diagnostic pathway in a range of body systems and life stages.	Action View
# 8	Learning outcome 1,2	Competency Ascertain relevant family history and psychosocial information and contribute to the use of this alongside medical information to determine appropriate genomic testing approaches within MDT settings.	Action View
# 9	Learning outcome 1	Competency Describe, in MDTs or consultations, the way results of genomic tests are generated and filtered, as well as the challenges and limitations of bioinformatics techniques.	Action View
# 10	Learning outcome 1,2,3	Competency Provide advanced genetic counselling input for management of genomic test results in the reproductive setting.	Action View
# 11	Learning outcome 1,2	Competency Synthesise patient information/medical records with information gained from exome/whole genome analysis to determine diagnosis, penetrance or prognosis for three examples of common and/or rare inherited conditions [phenotype to genotype].	Action View
# 12	Learning outcome 1,4	Competency Within three genomic counselling sessions, describe, in lay terms, how genomic tests contribute to management of a range of conditions, both currently and how this is anticipated in future healthcare.	Action View
# 13	Learning outcome 4	Competency Explain, to service users and/or professionals, the principal of genomic screening and the specific challenges this presents.	Action View
# 14	Learning outcome 5	Competency Observe and reflect on educational sessions for a range of non-genetic health professionals, facilitating widespread genetics and genomics knowledge. This may include educational sessions delivered at both undergraduate and post graduate level.	Action View
# 15	Learning outcome 5	Competency Deliver and reflect on an educational session for a group of non-genetic health professionals at undergraduate level. May include education on family history taking, management of specific genetic conditions, or genomic test results including ethical and psychosocial issues.	Action View
# 16	Learning outcome 5	Competency Deliver and reflect on an educational session for a group of non-genetic health professionals at postgraduate level. May include education on family history taking, management of specific genetic conditions or genomic test results including ethical and psychosocial issues. This may include educational sessions delivered at both undergraduate and post graduate level.	Action View

Assessments

You must complete:

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

Co ordinate discussion of molecular findings from a panel, exome or whole genome sequencing test at an MDT meeting	DOPS
Deliver a teaching session with attention to specific needs of the audience and reflect on the experience and evaluation	DOPS
Interpret the results of a panel test or whole genome screen, including considering the likelihood of findings explaing the phenotype observed	DOPS
Using language appropriate to a patient, explain a VUS, including its classification and how bioinformatic tools help to provide evidence for against pathogenicity.	DOPS
In an MDT setting, discuss the results of a patients genomic test and the implications of this for management, personalised medicine, therapeutic opportunity or involvement in research.	DOPS
Explain WGS and counsel patient about implications of incidental and additional looked for findings for individual and family, facilitating decision making about disclosure of findings and enabling informed consent	OCE
Explain the results of panel, exome or WGS test to patient and reflect on the episode and how it influenced understanding	OCE
Provide genetic counselling to facilitate decision making through presymptomatic testing	OCE
Provide genetic counselling to facilitate decision making through prenatal testing	OCE

Learning outcomes

1. Lead, under supervision, complex consultations involving genetic testing in complex scenarios, and consultations involving the use of genomic technologies.
2. Contribute Genetic Counsellor expertise to multidisciplinary teams (MDT) by assimilating knowledge of patient pathways in a range of healthcare settings with genomics expertise.
3. Discuss very rare and/or complex genetic and genomic conditions with patients in an easy to understand format centred on the needs of the patient.
4. Advise patients and professionals on current and potential future use of genomic screening for risk prediction, including in multifactorial disease and explain the benefits and limitations of such approaches.
5. Prepare, deliver and evaluate teaching sessions in genetics and genomics for healthcare colleagues using a range of teaching methods.

Learning outcomes

1. Describe and critically evaluate the selection and differentiation of a range of current genomic testing strategies used to sequence targeted parts of the genome or the whole exome/genome and their application within prenatal, childhood and adult settings.
2. Explain the way genomic results are generated and how data is filtered using bioinformatic pipelines.
3. Evaluate and utilise approaches for the interpretation of genomic results and the use of genotype and phenotype data in establishing pathogenicity.
4. Describe the use of genomic results in personalised/precision medicine, pharmacogenetics and emerging therapeutics.
5. Explain and critically appraise the broader use of genomic screening for disease risk prediction.
6. Describe the role of the Genetic Counsellor in the partnership of genetics with other clinical specialisms in the diagnosis of genetic disorders.
7. Critique theories and approaches to adult education and how to apply these to genetics and genomics.

Indicative content

Advanced Genomic Counselling

• Pre-conception and    reproductive    genetic    counselling   that    use    genomic technologies, including prenatal diagnostic support
• Genomics in the fetal medicine clinic
  • Diagnostic challenges of antenatal scanning
  • NIPT
  • RCPath guidance on the sharing of incidental findings picked up in pregnancy
• The diagnostic odyssey and the specific benefits and challenges of genomics in a range of settings
• The use of sources for researching the natural history of rare diseases including:
  • OMIM
  • Orphanet
  • Gene Review
  • Pubmed
  • Eurogentest
  • Support groups such as Unique

 Genomic testing strategies

• Genomic testing strategies such as: gene focused, multiple genes or whole genome or exome and for detection of sequence, copy number or rearrangements, including when these might be applied by laboratory clinical scientists
• How laboratory clinical scientists determine the analytical sensitivity and specificity of genomic tests
• The health economic limitations of testing in a publicly funded health service
• Have an appreciation of the necessary interplay between genomics delivered via clinical services and subsequently research services (when the limits of what can be offered clinically have been reached)

Bioinformatic pipelines

• Principles applied to quality control of sequencing data, alignment of sequence to the reference genome, calling and annotating sequence variants and filtering strategies to identify pathogenic mutations in sequencing data
• Use of multiple database sources, in silico tools and literature for pathogenicity evaluation and familiarity with the statistical programmes to support this (e.g. EVS, dbSNP, polyphen )
• Principles of integration of laboratory and clinical information, including knowledge of best practice guidelines for indicating the clinical significance of results

 Evaluating pathogenicity

• Approaches to the evaluation of pathogenicity of variants in the context of an NHS clinical report
• The value and importance of phenotype and inheritance information alongside sequence analysis to determine diagnosis and pathogenicity [phenotype to genotype]
• Prediction of phenotype from variants obtained from a hypothesis free whole exome/genome analysis [genotype to phenotype] in established genetic conditions
• Analytical challenges in genomics as applied to rare inherited diseases including:
  • the benefits and potential risks of sharing, integrating and aggregating clinical data and information
  • the potential of electronic health records to enrich patient data
  • importance of phenotyping and use of databases such as ClinVar, OMIM and Decipher
  • use of large population datasets, e.g. ExAC
  • sharing information, e.g. Human Variome Project

 The role of the Genetic Counsellor in the MDT

• Interpreting variant data in the clinic: the role of a Genetic Counsellor in the MDT to discuss pathogenicity of possible variants linked to a specific phenotype
• The role of the Genetic Counsellor and other members of the MDT in communicating uncertain information, variants of uncertain significance and incidental findings and counselling approaches to this
• Approaches to the management of incidental findings and the difference between this and opportunistic genomic screening
• The role of the Genetic Counsellor in facilitating supporting investigations including segregation analysis
• Approaches to and implications of the release of differing extents of genomic information

Use of genomic diagnosis

• Examples of the utility of a genomic diagnosis in establishing treatment strategies and personalised medicine, including in oncology, adult medicine, paediatrics and prenatal settings
• Non-invasive prenatal diagnosis
• Preimplantation genetic diagnosis
• Current uses of pharmacogenetics
• The role of genomics and other omics technologies in the development of new therapeutics, including gene therapy

 Genomic screening for risk prediction

• Existing population screening programmes in antenatal, newborn and adult settings (e.g. Down syndrome screening, cystic  fibrosis, haemoglobinopathies, familial hypercholesterolaeimia, breast, cervical and bowel cancer)
• Emerging strategies of genomic screening for disease risk prediction in reproductive (e.g. panels for carrier testing) and adult settings (e.g. cancer, neuropsychiatric), including application in specific ethnic groups
• Approaches to opportunistic genomic screening internationally and the risks and merits of these approaches
• How to take ‘broad consent’, together with the pros and cons of this approach
• The challenges of genomic screening for risk prediction in multifactorial disease and evaluate current approaches to combining risk factors
• The evidence on how patients manage their behaviour in light of risk stratification information
• The differing impact of genomic screening within private healthcare and in the direct to consumer market, including the impact of such testing on the NHS

 Clinical Education

• Major theoretical approaches to adult learning
  • Student centred and teacher centred learning
  • Learning styles
  • Active teaching and learning
• Teaching methods and generation of teaching resources
  • Planning and preparing to teach
• Teaching methods:
  • clinical skills
  • lecturing
  • small group teaching
  • problem based learning
  • Public engagement and education
  • e-learning
  • m-learning
• Core Teaching Skills
  • Questioning
  • Giving and receiving feedback
• Principles of assessment

Activities

• Present a complex case within a multidisciplinary review meeting, lead the discussion and critically reflect on the experience and importance of a multidisciplinary approach for the patient
• Use bioinformatics tools and databases by replicating the process for interpretation of one or more variants identified through genomic
• Observe multidisciplinary team clinics across a range of specialisms, for example fetal medicine, cardiology, paediatrics, endocrinology, assisted reproduction, neurology, ophthalmology or oncology and reflect on the role of the Genetic
• Develop an appreciation of genomic testing through recruitment of patients to genomic testing projects including gaining informed
• Assist in a genetics community, school or patient engagement event and critically reflect on the teaching and facilitation skills required.