Educating for genomics Wessex and Genomic Medicine
Deborah MackayProf of Medical EpigeneticsFaculty of Medicine, University of SouthamptonProgramme Leader: MSc Genomic Medicine
Innovations•Massive data: eg DNA sequencing at unprecedented speeds and low cost•Massive cohorts•Massive computing: eg informatic approaches to data integration
The drivers for genomics
Challenges•Chronic and noncommunicable disease•Ageing populations•Insufficiency of current disease models•Rising costs of treatment (drug development & prescription)
PotentialsChanging focus of healthcare…Stratification of diagnosisPersonalisation of treatmentDefinition of risk – prediction / preventionEngagement of population – participation
The public and NHS staff and students are learning about genomics at the same time
THEN…
Information & knowledge
Health practitioner
Patient
Information & knowledge
NOW…
Health practitionerPatient
Perceptions of genomics
The mission of Genomics England
• 100,000 whole genome sequences in NHS patients in England with rare inherited disease, cancers and pathogens
• Whole Genome Sequencing• Generation of health and wealth• Legacy of infrastructure, human capacity and capability• World-leadership in the application of Genomic Medicine for
healthcare (massively increased rate of translation from discovery to clinical practice)
• Rare Disease 5/10,000 people 3 million in the UK, 7000 rare disorders
• Cancer Disease of disordered genomes Lung, breast, colon, ovary, prostate, CLL
• Infection Pathogens and severe response to infection
The focus of the 100,000 Genomes Project
The programme for genomicsNHS Genomic Medicine Centres (GMCs)Rare diseases, cancers and pathogens
Broad consent, characteristics, molecular pathology and samples
MRC £24m Research Data Infrastructure (GeCIP)Sequential builds of pseudonymised data and WGS
Safe haven- users work within
Refreshable identifiableClinical Data Life-course registry
Linked to anonymised Whole Genome SequenceSequencing Centre
Wellcome Trust £27m
DNA & multi-omicsRepository
Primary Care Hospital episodes
Cancer RegistriesRare Disease
RegistriesInfectious Disease
Mortality dataPatient entry
Annotation & QCScientists & SMEs
Product comparison
Clinicians &
AcademicsIndustry
Training & capacity
Fire wallPatient data stays in safe haven
Only processed results pass outside
Oxford Big Data
The establishment of genomics(central vs local implementation)
• Illumina Partnership• New NHS Sequencing Centre £27m
from WT, at Sanger Centre• £24m from MRC for UK Data Infrastructure
for Genomic Medicine
• 11 New NHS Genomic Medicine Centres in England to enrol, validate and feedback to patients
• 700 person years of Masters, PhD and short course training - £25m
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Wessex Genome Medicine Centre – pathway to implementation Continual Monitoring / Audit / Patient Feedback
Collection Stage
RecruitmentClinical/Research/Patients/Family
Consent
Phenotyping Data
DNA/RNA extraction
Central Gel Hub
XML & Samples
Primary Reporting Stage
GMC core team including manager/ rare /cancer/ lab / clinical + UoS informatics / cell pathology/ transformation / education / ethics
Wessex GECIP Leads
Education opportunities for staff to learn
GMC linked Researchers
GMC linked Clinicians
Confirmation Stage
Clinically Significant results validated
EQA Approved Wessex Genomics Hub
Clinical Reporting Stage
Patient result discussed at relevant MDT in the Region
Patient informed of results as part of routine clinical practice [with feedback from patient]
Referral to clinical genetics for cascade testing where appropriate
All information with clear explanation of what can and cannot be inferred from result
Genomics “Hot Line” available for support
Wessex Education Program for Health Professionals
Partnering with Patients
Inte
grat
ed In
form
atics
and
Dat
a St
anda
rds
Results sent to referring healthprofessional with written information for patient/relative
Cancer Ellen Copson
University Hospital Southampton Foundation Trust Board
Clinical Diagnosis and Treatment Panel
Wessex Genomic Medicine Centre
UHSFT CEO Genomics Strategy group
South Coast Genomic Medicine BoardUHS Medical Director
GMC Directors – A Williams/ IK TempleGMC Project Manager – G Baljinder
NHS genetics lead – K Lachlan; Ethics GMC Lead – A LucassenIntegrated Informatics GMC Lead – J Batchelor/ D Cable
Nursing GMC Lead – E MunroWessex AHSN GMC Lead – B Vearncombe
Rare Disease /Cancer Patient Rep – Jac Samuels, Kate SonpalFoM lead – S Ennis; Education lead – D Mackay; Training lead –
M Watson
South Coast Genomic Medicine Core TeamGMC Directors
Rare Disease Lead/ Cancer leadClinical Informatics Lead/ Ethics Lead
Molecular Laboratory Lead/ Cellular Pathology Lead/ Clinical Genetics Lead / Cancer Nursing Lead/ Rare
Disease Nursing Lead/ PPI&E Lead / GMC Project Manager/ GMC administrator
Communications lead
GMC Clinical
Staff
GMC Laboratory
Staff
GMC R&D Staff
Rare Disease Catherine Mercer/ Emma Baple/ Justin Davies
Area Clinical Pathology
Lung C Ottensmeier
S Jogai
Colon A Mirnezami A Bateman
Breast R Cutress H Roche
Ovary S Crawford N Singh
Prostate S Crabb H Markham
Oesophagus
T Underwood TBA
Pancreas J Primrose TBA
Paed J Gray TBA
Haem onc M Jenner/A Duncombe
M Aston-Key
CLL F Forconi M Aston-Key
Head &Neck
E King G Thomas
Area Clinical
CVS Aisling Carroll/?
Endocrine Justin Davies
Ophthalmology A Lottery/ Jay Self
Tumour Predisposition
Muna Ahmed/ Diana Eccles/ J gray
Immunology Saul Faust/ Williams
Hearing T Mitchell/?
Dermatology M Arden jones/?
Neurology S Hammans/ ?
Gastrointestinal M Beattie/?
Sepsis R Read/?
Skeleton/ Bone dysplasia
M Uglow/ C Edwards/ Dennison/ Davies
Congenital anomal.
Nigel Hall/ N Foulds
Respiratory Lucas/CarrollUHS Clinical Recruiters
All clinical staff within UHS
Research
Southampton Centre for Biomedical Research
NHS R and D
Faculty of Medicine
Informatics committee
genomes and clinical
informatics
NHS Transformation
committee
NHS engagement with genomics:the background
• A 2013 National Genomics and Genetics Education Centre review of 187 UK healthcare trainees' curricula, showed that there was significant disparity in the content and amount of genomics teaching across professions
• In a study of medical schools in USA and Canada in 2015, most respondents felt the amount of time spent on genetics was insufficient preparation for clinical practice
1. Plunkett-Rondeau J, Hyland K, Dasgupta S. Training future physicians in the era of genomic medicine: trends in undergraduate medical genetics education: Genet Med. 2015 Feb 12. doi: 10.1038/gim.2014.208. [Epub ahead of print] 2. Baars MJ, Scherpbier AJ, Schuwirth LW, et al. Deficient knowledge of genetics relevant for daily practice among medical students nearing graduation. Genet Med 2005;7:295–301. 3. Challen K, Harris HJ, Julian-Reynier C, et al.; GenEd Research Group. Genetic education and non-genetic health professionals: educational providers and curricula in Europe. Genet Med 2005;7:302–310. 4. www.hee.nhs,uk
MSc Genomic Medicine
Higher Specialist Scientist Training - Genetics
CPPD MSc Modules
HSST - Molecular Pathology of Acquired
Disease
Online educational resources:•Consent & ethics•Sample processing & DNA extraction•Introducing Genomics in Healthcare video•Introduction to Genomics•Introduction to Bioinformatics•Rare Diseases videos
www.hee.nhs.uk/ : http://www.genomicseducation.hee.nhs.uk/
Health Education England:national perspective on NHS training for genomics
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Birmingham
Newcastle Manchester
QMUL/UCL:
KCL/StGeorge’s:
Imperial:
Cambridge
Southampton
And MSc providers
Ethical, Legal & Social Implications of Genomics
Counselling Skills for Genomics
Health Economics
EpigenomicsAdvanced Informatics
Work Based Learning
Clinical Research Skills
OptionalIntroduction to Human
Genetics & Genomics
Omic technologies in Genomics Medicine
Genomics of common & rare disease
Molecular Pathologyof Cancer
Pharmacogenomics& stratified medicine
Genomics of Infectious disease
Genomic Informatics
Research Project /Dissertation
Core
Clin
ical
+ n
on-c
linic
al m
odul
e le
ads
Loca
l exp
ertis
e /
Inte
rnati
onal
repu
tatio
n
IRIDISHigh Performance Computing Facility
Winchester
Wessex expertise in genomicsEducation, Clinical, Research, Public Health, IT
Education for genomics: Pathways flexible to the needs of working professionals
Optional Modules CompletionCore Modules
2015Introduction & Omics
* Full time 1 year or part time 2 years
CPD for individual modules
Repeated Core Modules Research Project
2016
5-7 weeks of study per module
REMOTE LEARNINGONSITE TEACHING
ASSESSMENT
ONSITE TEACHING
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 … … 42
Blended learning for NHS professionals: Intensive direct teaching combined with independent remote study
• Onsite teaching• Lectures, workshops, group work
• Remote Learning• Virtual patient tasks, online tutorials, assignments, online forum, data analysis
• Assessments• Written assignments including critical appraisal, case reports, literature review; data
analysis & interpretation; oral presentations, short note assessments, virtual patient tasks (including MCQ)
PRE-LEARNING
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Genomics at a distance
Virtual Learning environment• Electronic Blackboard• Online student forum• E-assignment submission• Virtual patients
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Wessex ethos in genomic medicineCommunication! Talk / interrupt / ask / object!
Collaboration! There is a LOT of expertise here. MDT.
Curiosity! Learn from module leaders / one another
Creativity! This is an evolving programme in an evolving network of programmes, in an evolving educational project within an evolving field. This is a time of change and creativity and we can help create the field.
The Wessex MSc cohort in Genomic Medicine
• 42 admitted (22 to this programme intake)
• 29 programme students - 18 of whom NOT trainees• 13 modular - 9 of whom NOT trainees
• 18 clinicians (4 NOT genetics; 10 clin genet trainees)
• 21 clinical scientists / technologists
• 2 research nurses• 1 trials manager• 0 bioinformaticians
• 28 from 'traditional' genetics
Doctorate and post-doctorate training programmes in Genomic Medicine to develop future clinical academic leaders.
Post-graduate MSc courses, funded to ensure adequate outputs on workforce numbers.
Increased teaching of genomics and bioinformatics in undergraduate curricula for students of medicine, nursing, allied health professions and healthcare science.
General awareness of bioinformatics non-genetic/genomic specialist workforce in e.g. rare diseases and cancer, first-contact professionals e.g. GPs and commissioners of services.
The strategy for education in genomics
• Wessex GMC – genomes transforming clinical practice in the region
• GeCIPs – an opportunity to learn how to get the most out of a genome
• Training opportunities for NHS staff including MSc• Laboratories fit for 21st century diagnosis, to take on
genome sequencing after project – NHS England genetics laboratory reconfiguration
• NIHR/ University research and enterprise in genomics
The strategy for genomics – the next 5 years
The public and NHS staff / students are learning how to use genomics at the same time
Perhaps genomics is just the beginning
Genome EnglandClinical InterpretationPartnerships
(GeCIPs)
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