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

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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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14

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

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Loca

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Inte

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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)