100,000 genomes project and its potential for rare disease research
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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
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 pre-existing 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
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
Clinical Features Developmental delay ACC Not much in common with CSS Although mechanism of haploinsufficiency is the same
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
The International Journal of Biochemistry & Cell Biology, Volume 52, 2014, 83–93
What about going beyond diagnosis?
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 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-Polydactyly-Hydrocephalus 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
GLG1: c.1229A>G p.H410R
Confirmed
CCND2: c.838A>G p.T280A
Confirmed
JT144
11/5 JT145
15/0 JT146
18/0
JT144
34/17 JT145
46/0 JT146
55/1
Additional MPPH Patients
JT210 CCND2: c.842C>G
p.P281R
JT232 CCND2: c.839C>A
p.T280N
JT238 CCND2: c.851T>G
p.V280G
P
CCND2 CCND2
P
P
GSK3B
Ubiquitin-mediated
degradation
Proliferation
T280A prevents phosphorylation of CCND2
HyperActive
P CCND2 CCND2
P
GSK3B
Ubiquitin-mediated
degradation
P
GSK3B
P
AKT3
P
Proliferation
P
P P P P
Active
Inactive
Active
PI3K hyper-activation and CCND2 Stabilisation
PIK3CA
PIK3R2
P
AKT3
P
P
P
(PI3K)
Inactive
P P
P P
P P
HyperActive Active
PIP2
PIP3
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
Array CGH
qPCR
FISH
Karyotype
Conventional PCR/Sanger sequence
[Custom]
[Custom]
Long PCR NGS
Targetted panel NGS
MLPA
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