Transcript Cancer Research UK Stratified Medicine Programme

Recent Advances in
Laboratory Genetic Testing
Rachel Butler
[email protected]
The Impact of Genomics on Public Health
The Impact of Genomics on Public Health 06/11/2014
Where are we now?
• Single gene disorders
• Antenatal screening by QF-PCR
• Arrays for LD
April
2013
Where are we going?
• Free-fetal DNA
• Next generation sequencing
• Personalised medicine
The Impact of Genomics on Public Health 06/11/2014
What’s changed? Nov ‘14
•
•
•
•
NHS England and Genomics England
NIPT has progressed
Real clinical applications of NGS
Applications and further opportunities of
stratified medicine in oncology
The Impact of Genomics on Public Health 06/11/2014
NHS and Genomics England
Genomics England set up in 2013 by
DH
• Cameron announcement to
sequence 100,000 genomes
• Focus on cancer and rare
diseases
• ~75,000 people will be consented
to give samples (a few will directly
benefit)
• External contract of sequencing
The Impact of Genomics on Public Health 06/11/2014
NHS England:
Genetic lab reconfiguration
•
•• •••
•• •
•• • ••••
•
• Currently 17 Genetic labs,
plus many specialist
genetic services
(Haematology,
Biochemistry, molecular
pathology)
• Aim to reduce costs by
20%, and increase future
capacity
• Drive clinical-laboratory
specialist services
The Impact of Genomics on Public Health 06/11/2014
The bigger picture…
Sequencing
facility
•
•
•• ••
•• •
•• • ••
•
Genomic
Medicine
Hub
Samples
Data
Questions:
• How many GMCs?
• What about the devolved nations?
The Impact of Genomics on Public Health 06/11/2014
NHS and Genomics England: Benefits
Patients
• Increased access to genetic diagnosis and
treatments (now and in the future)
NHS
• New diagnostic platforms and technologies
• Improved capability for genetic analysis and
interpretation
UK economy
• (currently unforeseen) Economic
benefits in technology development and
provision
The Impact of Genomics on Public Health 06/11/2014
Free fetal DNA analysis or NIPT
• Clinical applications
– Sexing
– Rhesus D
– Single gene disorders
– Aneuploidy analysis
The Impact of Genomics on Public Health 06/11/2014
Extraction of cell free fetal nucleic acids from
maternal plasma
Cell free maternal DNA (96.6%)
Cell free fetal DNA (3.4%)
Plasma
Amount of cell free
fetal DNA extracted
is equivalent to 25
cells / ml plasma
Cell free maternal RNA
Cell free fetal RNA
Maternal blood cells
The Impact of Genomics on Public Health 06/11/2014
Detecting ffDNA in maternal
blood….
The Impact of Genomics on Public Health 06/11/2014
Taken from Cell free fetal nucleic acids for non-invasive prenatal
diagnosis; PHGF, 2009
The Impact of Genomics on Public Health 06/11/2014
Fetal sexing
Taken from CMGS Audit 2011-12
The Impact of Genomics on Public Health 06/11/2014
Single gene disorders
• Services now available for achondroplasia and
thanatophoric dysplasia
• Others being piloted through RAPID for:
– Aicardi Goutiere, Alagille, Barth, Cockayne, Craniosynostoses,
Dominant Ataxias, Ectodermal dysplasia, Ellis van Creveld,
Fragile X, Friedrich’s ataxia, Gylcogen storage diseases,
Huntington’s, Holt Oram, Inborn errors of metabolism, IPEX,
Lissencephaly, Meckel gruber, Myotonic dystrophy, Neonatal
diabetes/familial hyperinsulinaemias, Neurofibromatosis ½,
Okihiro, Ornthine transcarbamylase deficiency, Osteogenesis
imperfecta, Polycystic kidney disease, Rett syndrome,
Retinoblastoma, Skeletal dysplasias, Smith Lemli Opitz, Spinal
muscular atrophy, Spondylocostal dysostosis, TAR, Treacher
Collins, Tuberous sclerosis 1/2, UPD 14, Wolcott-Rallison, Xlinked Adrenoleukodystrophy and X-linked myotubular myopathy
The Impact of Genomics on Public Health 06/11/2014
Roll-out of commercial NIPT…
MATERNIT21® PLUS
Better results born of better science.
Fan et al., PNAS Oct 2008
The Impact of Genomics on Public Health 06/11/2014
Sources of error:
• Early gestational
age
• Maternal obesity
• Multiple
pregnancies
• Placental mosaicism
• Shotgun or targeted sequencing
• Sensitivity and specificity close to 100%
• Comparison with combined screening:
– Combined = 90% detection with 3% false +ve
– Combined implementation has already
reduced the no. of invasive procedures
The Impact of Genomics on Public Health 06/11/2014
NIPT: Patient and healthcare benefits
Noninvasive
testing
Reduced
risk of
miscarriage
Earlier
testing
availability
Reduced
cost of
PND
The Impact of Genomics on Public Health 06/11/2014
Next Generation Sequencing (NGS)
• Ability to sequence whole genome or
selected regions of the genome
– On a scale massively larger than Sanger
sequencing
• Applications
– Whole genome
– Whole exome
– Targeted (panels)
The Impact of Genomics on Public Health 06/11/2014
Next Generation Sequencing
1. Whole
Genome
sequencing
(WGS)
2. Exome sequencing
(WES); 2% genome is
coding, subtract the
introns
3. Targeted
gene panels
Gene panels adopted in NHS
2013-14
2014-15
Familial hyperparathyroidism
Paediatric cardiomyopathy
Alport syndrome
Familial hypertrophic
cardiomyopathy
Chromosome breakage
Methymalonic acidemia
CMT hereditary neuropathy
Inflammatory bowel disease
Inherited ataxias
Phaeochromocytoma and
paraganglioma
Syndromic and nonsyndromic hearing loss
Osteopetrosis
Retinal degeneration
Urea cycle disorders
Disorders of sexual
development
Noonan spectrum
Monogenic diabetes
Neurogenetic disorders
Brain malformation
(Lissencephaly)
Neonatal diabetes
Congenital anaemia
Nucleotide excision repair
Primary ciliary dyskinesia
Iron regulatory
Congenital myopathy
Hereditary cancer and FA
Early infantile epileptic
encephalopathy
Bardet-Biedel syndrome
Connective tissue disorders
Primary immune deficiencies
The Impact of Genomics on Public Health 06/11/2014
Targeted analysis: EOIE (Cardiff)
ALDH7A1
CNTNAP2
MAPK10
PLCB1
SCN2A
SPTAN1
ARHGEF9
FOXG1
MECP2
PNKP
SCN9A
SRGAP2
ARX
GABRG2
MEF2C
PNPO
SLC25A22
STXBP1
BTD
GLUD1
NRXN1
POLG
SLC2A1
TCF4
CDKL5
KCNQ2
PCDH19
SCN1A
SLC9A6
UBE3A
ZEB2
Detection of an SCN1A mutation
• Confirmation of diagnosis (Dravet
syndrome)
• Altered management – medication
• Analysis of at-risk family members
The Impact of Genomics on Public Health 06/11/2014
Whole exome analysis (Exeter)
Diagnosing lethal fetal disorders is difficult
large number of potential genes
phenotypic variability associated with many known genetic causes
challenges of defining phenotype and pathology in a mid-gestation fetus
fetal DNA samples often limited quantity/quality and irreplaceable
Family referred with fetal akinesia syndrome with contractures, pterygia,
pulmonary hypoplasia and hydrops
1 in 4 risk of recurrence but no molecular prenatal test possible
The Impact of Genomics on Public Health 06/11/2014
Options:
Candidate genes, aCGH
WES – tiny amounts fetal DNA (plenty of parental)
- genes by phenotype
Time: Wait to 20 week scan, 2nd trimester termination
Exome sequencing
Genes with heterozygous
variants in both parents
CLIP1
GLE1
GLE1 co-segregation testing
p.R569H/N
p.V617M/N
P
Male
Female
6/40
Co-segregation testing
P
p.R569H/p.V617M
p.R569H/p.V617M
Both previously reported as Finnish founder mutations causing
recessive lethal congenital contracture syndrome
lethal arthrogryposis with anterior horn disease
The Impact of Genomics on Public Health 06/11/2014
Bioinformatics
Library
preparation
Bioinformatic
analysis
Alignment
Reference
seq
Variation
Determination of
detection
causation
The Impact of Genomics on Public Health 06/11/2014
The problems of NGS…
•
•
•
•
Detection of unclassified variants
Unexpected findings
ELSI
Data storage
The Impact of Genomics on Public Health 06/11/2014
NGS: Patient and healthcare benefits
Reduced
anxiety for
patients and
families
Vastly
reduced
reporting
times
Opportunity
for testing
rare
“unknown”
genetic
disorders
NGS
services:
WGS, WES
and targeted
gene panels
Increased
sensitivity of
genetic
analysis for
rare inherited
disorders
Reduction
in tests (£)
before
clinical
diagnosis is
made
Potential to
develop
new
diagnostic
services
The Impact of Genomics on Public Health 06/11/2014
Stratified Medicine
Challenge: drugs don’t work for most cancer patients
Drug Response Rate, %
80
60
Analgesics
Cancer
40
20
0
Source: Spears et al., Trends Mol Med, 2001; Lazarou et al., JAMA, 1998,
26
The Impact of Genomics on Public Health 06/11/2014
What’s better for patients?
…benefits of stratified medicine
The Impact of Genomics on Public Health 06/11/2014
Crizotinib and EML4- ALK fusions
The Impact of Genomics on Public Health 06/11/2014
Biomarkers that predict response in solid tumours
Biomarker
Tumour
Drug / biomarker approved
HER2
Breast / gastric
Yes
EGFR
NSCLC
Yes
KRAS
mCRC
Yes
c-KIT / PDGFRA
GIST
Yes
1p36 / 19q13, MGMT, IDH1/2
Multiforme glioblastoma
In common use
BRAF
Metastatic melanoma
Yes
ALK-EML4
NSCLC
Yes
MSI
mCRC
Being adopted
The Impact of Genomics on Public Health 06/11/2014
Validated biomarkers
predicting treatment or
prognosis
Solid tumours where
either no or significant
proportion of patients
have no predictive or
prognostic biomarker
Tumour
Germline
The Impact of Genomics on Public Health 06/11/2014
Molecular strategies for NSCLC
The Impact of Genomics on Public Health 06/11/2014
Diagnostic
biopsy
mCRC
First line
chemo 16
wks
Stable/
responding
A
B
BRAF
PIK3CA
REGISTER
on FFPE tumour block
BRAF, PIK3CA, KRAS, NRAS
mutation; mRNA EREG;
IHC MMR, PTEN
Biomarker
analysis
C
KRAS/
NRAS
D
N
All WT
NONE
ALLOCATE
RANDOMISE
P
Novel
oral
P
Novel
oral
P
Novel
oral
P
Novel
oral
N
CAP
rebiopsy
Primary endpoint
PFS
in the interval
Restart first line chemo on progression
rebiopsy
The Impact of Genomics on Public Health 06/11/2014
Diagnostic
biopsy
mCRC
First line
chemo 16
wks
Stable/
responding
A
B
BRAF
PIK3CA
REGISTER
on FFPE tumour block
BRAF, PIK3CA, KRAS, NRAS
mutation; mRNA EREG;
IHC MMR, PTEN
Biomarker
analysis
C
KRAS
D
N
All WT
NONE
ALLOCATE
RANDOMISE
P
BRAFi
Novel
MEKi
oral
EGFRi
PI3K
P
Novel
aspirin
mTOR
oral
i
P
Novel
AKTi +
vaccine
MEKi
oral
AZD
Novel
8931
oral
P
N
E
F
ATM
loss
MMRd
P
Novel
PD1
ab
oral
CAP
Novel
ATR i
oral on Public Health 06/11/2014
The Impact of Genomics
P
MATRIX
SCC PIK3CA mutant
SCC PIK3CA amplified
SCC PTEN loss, not mutated
SCC PTEN mutant
Ad - PI3kinase/AKT deregulated
NSCLC - AKT1 mutation
NSCLC - FGFR mutations
NSCLC - TSC1/2 mutations
NSCLC - LKB1 mutations
SCC with proficient Rb and p16 loss
CDK4 amplified NSCLC
CCND1 amplified NSCLC
Adeno - KRAS mutations
Met amplified NSCLC
NSCLC - ROS fusions
EGFR mutation and T790M+
SCC - NF1 mutations
Ad - NF1 mutations
NSCLC - N-RAS mutations
Biomarker negative cohorts
AZD5363
AZD4547
AZD2014
Palbociclib
Crizotinib
AZD9291 Selumetinib
+ docetaxel
MEDI
4736
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The Impact of Genomics on Public Health 06/11/2014
Longitudinal sampling: ctDNA
From Gonzalez et al. Clin Pharmacol Ther. Mar 2013; 93(3): 252–259
Tumours change at the molecular level,
ctDNA analysis:
• Determines molecular mechanisms
of relapse and resistance
• Identifies potential new treatment
targets
The Impact of Genomics on Public Health 06/11/2014
Stratified Medicine: Benefits for
patients and Healthcare
Treatment is
tailored to the
individual
• Considerably improved survival
• Reduced side-effects
Significant cost- • Patients more likely to respond
saving on drugs • Reduced side-effects and associated
readmissions
and re-admissions
• Oral drugs can be taken at home
Longitudinal
sampling
• ctDNA analysis to monitor molecular
response
• And resistance
The Impact of Genomics on Public Health 06/11/2014
UK Laboratory Genetics
• Time of uncertainty / anxiety for Genetic
laboratories
• New technologies and their application
offer many new opportunities
• Significant opportunities for healthcare
through genetic and genomic service
developments