The  100,000  Genomes  Project

Richard  ScottClinical  Lead  for  Rare  Disease14th September  2015

Four  main  aims

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1.  To  bring  benefit  to  NHS  

patients

2.  To  create  an  ethical  and  transparent  

programme  based  on  consent

3.  To  enable  new  scientific  

discovery  and  medical   insights

4.  To  kickstart the  development  of  a  UK  genomics  industry

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Timeline

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What  will  we  be  telling  participants?• Information  about  a  patient’s  main  condition

• Information  about    ‘serious  and  actionable’  conditions  (optional)

• Carrier  status  for  non  affected  parents  of  children  with  rare  disease  (optional) Image  courtesy  of  Health  Education  England

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Principal  Partners

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NHSEand  GMCs

GeCIP

IndustryPartnerships

Genomics  England

Illumina

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Rare  diseases  studied

• A  growing  repertoire

• 131  disorders  to  date• each  with  specific  eligibility  criteria• each  with  tailored  clinical  data  collection  models• each  with  diagnostic-­‐grade  gene  panel  for  initial  report

• Pattern  of  family  members  recruited  reflects  likely  pattern  of  inheritance:• Proband-­‐mother-­‐father  trio  in  simplex  cases• Multiple  affected  individuals  +-­‐ parents  in  other  scenarios

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NHS Genomic Medicine Centres• Clinical samples and hospital data• Laboratory processing including molecular pathology• Broad consent for research and re-contact

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DNA & samples for multi-omics

Clinical Data

• Identifiable clinical data• Longitudinal • Linked to genomic data

Research Data• Pseudonymised• GeCIP and industry partners

work within data centre

Clinicians & Academics

TrainingIndustry

Part

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Fire wall

Existing Clinical DataCancer &RD registries, HES, Mortality data, etc

Data and Analysis Improvement

• Annotation & QC• Scientists/SMEs• Product comparison

Oversight: Funding:

Establishment  Phase• Illumina  -­‐ NHS  Genomic  Medicine  Sequencing  Centre  in  Hinxton• UK  Data  Infrastructure  for  Genomic  Medicine  (with  MRC)• NIHR  National  Biosample Centre  -­‐ £24  million  state-­‐of-­‐the-­‐art  facility  to  store  the  samples  • 11  NHS  Genomic  Medicine  Centres  in  England  to  enrol,  validate  and  feedback  to  patients

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Data  CentreNHS  Genomic  Medicine  Sequencing  Centre NIHR  Biosample centre

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NHS  Genomic  Medicine  Centres• Eleven  Genomic  Medicine  Centres  (GMCs)  established  in  December  2014  by NHS  England.  These  centres  will  lead  the  way  in  delivering  the  100,000  Genomes  Project.

• Track-­‐record  of  providing  excellence  in  genomic  services.• Eligible  patients  will  be  referred  to  GMCs  by  their  clinicians.• First  patients  recruited  by  Manchester  GMC  in  March.  

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Genomics  England  Clinical  Interpretation  Partnership  (GeCIP)  

• Launched  at  the  Wellcome Trust  in  June  2014• Partnership  between  over  2,000  researchers  from  academia  and  the  NHS,  trainees,  plus  international  collaborators.  

• Designed  to  accelerate  academic/industry  partnership  and  development  of  diagnostics  and  therapies

• Over  30  topics  (domains)  of  research  and  most  domains  cover  a  single  disease  or  group  of  diseases  and  some  are  wider.  These  include  epigenomics,  health  economics  and  technology.

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Working  with  the  research  community

• All  data  generated  contributes  to  the  Genomics  England  Dataset

• Second  round  of  applications  Aug-­‐Oct.  New  domains  announced  in  December  2015

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GENE  Consortium

• Ten  companies  have  come  together  to  create  the  Genomics  Expert  Network  for  Enterprises  (GENE)  Consortium  to  oversee  a  year-­‐long  Industry  Trial• Aims  to  identify  most  effective  and  secure  way  of  bringing  industry  expertise  into  the  100,000  Genomes  Project  in  order  to  realise  the  potential  benefits  for  patients.• AbbVie,  Alexion,  AstraZeneca,  Berg,  Biogen,  Dimension  Therapeutics,  GSK,  Helomics,  Roche,  Takeda

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Working  with  industry

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Health  Education  England

• 9  University  providers  of  MSc  in  Genomic  Medicine  – aimed  at  NHS  healthcare  professionalsworking  in  England

• HEE  -­‐ Genomics  Education  Programme,  online  training  courses  and  resources  • University  of  Birmingham• Newcastle  University• University  of  Manchester• University  of  Sheffield• Imperial  College  London• Queen  Marys  University  of  London• St  Georges,  University  of  London• University  of  Cambridge• University  of  Southampton

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Upskilling  the  workforce

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What  can  we  expect  from  this  Project?

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Patients • Feedback  on  min  findings  – which  will  get  quicker  and  better  informed  as  the  project  progresses

• If  the  patient  opts  for  it,  feedback  on  secondary    findings  – again  this  will  develop  as  the  project  progresses

• Access  under  strict  governance  rules  to  the  increasing  dataset  and  a  suite  of  best  in  class  tools

• Engagement  in  a  collaborative  programme  with  leading  scientific  and  clinical  experts

• Opportunity  to  share  in  the  publication  of  findings• Opportunity  to  engage  in  translation  opportunities  

with  industry  collaborators

Research  Collaborators

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What  can  we  expect  from  this  Project?

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Industry

General  Public

• A  number  of  mechanisms  to  gain  access  to  the  dataset  and  tools  under  strict  governance  rules

• Engagement  with  the  research  collaborators  and  access  to  expert  clinical  and  bioinformatics  support

• Opportunity  to  address  relevant  patient  cohorts  both  through  the  Genomics  England  dataset  and  through  other  UK  collaborations

• Possibility  of  significant  advances  in  diagnostic  markers  of  genetic  diseases

• Possibility  of  new  understanding  of  mutations  causing  progress  of  common  cancers

• Possibility  of  fresh  insights  into  genetic  markers  for  common  diseases

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Progress  so  far

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• Over  5,000  participants  have  already  agreed  to  take  part  as  part  of  the  pilots:  3,500  in  rare  diseases  and  almost  2,000  in  cancer.

• We  have  already  delivered  over  2,300  whole  genome  sequences,  and  we  are  starting  to interpret  these  to  help  patients.

• Dependent  on  samples  passing  quality  control,  we  will  have  5,000  whole  genome  sequenced  by  the  end  of  August  2015  

• These  first  5,000  sequences  are  from  the  pilot  phase  and  ourGeCIPdomains and GENE  Consortiumpartners  will  shortly  begin  working  with  this  data

• http://www.genomicsengland.co.uk/100000-­‐genomes-­‐project-­‐update/

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