100,000 Genomes Project and its potential
for rare disease research
Eamonn Sheridan
Professor of Clinical Genetics
University of Leeds
100,000 genomes project
• Launched 2012 by the Prime Minister
• Genomes England (DoH owned) will sequence 100,000 whole
genomes by 2017
• Aims
– Create ethical and transparent programme based on consent
– Benefit patients and set up a genomic medicine service for the NHS
– Enable new scientific discovery and medical insights
– Kick start the development of a UK genomics industry
Rare diseases
• 50,000 genomes
– Three per patient
• (proband + two relatives)
• Genome sequence not exome
• Deliver clinically meaningful results
– Analytical challenge
• Store data
– 200GB per genome
– Total 10-20 petabytes
– 30000-50000 CDs –tower 250-500m
high
– Facebook 300PB!!
• Research in the 100,000
genomes project
– Genomics England Clinical
Interpretation Partnerships (GeCIP)
– bring together researchers,
clinicians and trainees from
academia and the NHS
– main focus of GeCIP is on clinical
interpretation
• research will also be undertaken
Now with added:
Paed sepsis
Inherited cancer
Hepatology!!!!
Serum and plasma for proteomics and
metabolomics.
Cell free serum for circulating tumour
DNA and to assess tumour
recurrence.
Germ-line RNA for transcriptomics.
Lymphocyte DNA for epigenetics.
Tumour for RNA expression profiles,
tumour epigenetics and proteomics.
How is all this going to help research?
• Traditional approach to gene
discovery
– Targetted at patients with preexisting clinical diagnoses
– Eg De novo dominant Mutations in
ARID1B cause Coffin Siris syndrome
• Developmental delay, Absent speech,
Coarse facies, hypertrichosis, fingernail
abnormalities, ACC
• Includes three patients with deletions
of 6q25 including ARID1B
– Haploinsufficiency is the disease
mechanism
Santen et al 2012
The ARID1B phenotype: What we have learned so far
Clinical Features
Developmental delay
ACC
Not much in common
with CSS
Although mechanism of
haploinsufficiency is the
same
American Journal of Medical Genetics Part C: Seminars in Medical Genetics
Volume 166, Issue 3, pages 276-289, 28 AUG 2014 DOI: 10.1002/ajmg.c.31414
http://onlinelibrary.wiley.com/doi/10.1002/ajmg.c.31414/full#ajmgc31414-fig-0001
ARID1B
• Subsequently reported in DDD as
cause of 1% of delay in recruits
– Much broader phenotype in these
patients
• Core CSS phenotype still valid
predictor of mutations in ARID1B
– CSS is also caused by mutations in
SMARCB1
What about going beyond diagnosis?
The International Journal of Biochemistry & Cell Biology, Volume 52, 2014, 83–93
Genome wide analysis of modifiers
100,000 genomes
• Promiscuous approach to
mutation discovery
• Linked to very deep phenotyping
– May broaden phenotypes
– Better identification of core
components
– Better data on natural history
• Presently often a snapshot
• All patients have detailed
genome sequence available
• Can be re-interrogated in light of
subsequent knowledge
–
–
–
–
Technology
Disease
Natural history
Pathogenetic pathways
100,000 genomes
•
Serum and plasma for proteomics and
metabolomics.
•
Cell free serum for circulating tumour
DNA and to assess tumour recurrence.
•
•
•
Germ-line RNA for transcriptomics.
Lymphocyte DNA for epigenetics.
Tumour for RNA expression profiles,
tumour epigenetics and proteomics.
100,000 genome – trio sampling strategy
100,000 genome – trio sampling strategy
100,000 genomes – biological insight
MPPH syndrome
• Early overgrowth (brain > somatic tissues)
• Progressive megalencephaly
• Ventriculomegaly/Hydrocephalus
• Cerebellar tonsillar ectopia
• Mega-corpus callosum
• Polymicrogyria
Distal limb anomalies
• Postaxial polydactyly
• Familial recurrences rare
•
Megalencephaly-Polymicrogyria-PolydactylyHydrocephalus Syndrome
(MPPH)
• No recurrence in all reported families.
• Exome sequencing of one trio:
• 5,980 heterozygous ‘functional’ variants identified in
proband
• 5 candidate de novo variants
• 4 true de novo variants validated by Sanger
sequencing
Potential Denovos
JT144
JT144
34/17
11/5
JT145
JT145
46/0
15/0
JT146
JT146
55/1
18/0
GLG1: c.1229A>G
p.H410R
Confirmed
CCND2: c.838A>G
p.T280A
Confirmed
Additional MPPH Patients
JT210
CCND2: c.842C>G
p.P281R
JT232
CCND2: c.839C>A
p.T280N
JT238
CCND2: c.851T>G
p.V280G
CCND2 Mutations in MPPH Patients
Cyclin D2 Regulates G1-S Cell-Cycle
Transition
P
RB1
RB1
P
E2F
CDK4/6
E2F
P
CCND2
G1
Cell Cycle
S
T280A prevents phosphorylation of CCND2
Proliferation
P
CCND2
CCND2
P
P
GSK3B
Ubiquitin-mediated
degradation
Genetic data allows you generate hypotheses and
answer those questions
But you still have to get on with stuff
PI3K hyper-activation and CCND2
Stabilisation
(PI3K)
PIK3R2
Active
HyperActive
PIK3CA
Inactive
PP
P
PIP2
P
Proliferation
GSK3B
P
P
PIP3
P
P
P
P
P
P
P
P PP
P
P
AKT3
AKT3
GSK3B
Inactive
CCND2
CCND2
P
P
Active
HyperActive
Active
Ubiquitin-mediated
degradation
Summary
• 100000 genomes will provide basic genetic data on large
numbers of patients
• This will allow the generation of novel disease hypotheses
• It is up to us to further investigate those
• Provide new disease paradigms
July 2015, 30× coverage
$1363 = £888
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100,000 genomes
•
•
•
•
•
•
Radically alter NHS provision of genomic services
Single platform
Common workflows
Deep phenotyping
Clinically relevant results
Qucikly!