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News & Views
ISSN 1462-241610.2217/PGS.13.73 © 2013 Future Medicine Ltd Pharmacogenomics (2013) 14(8), 861–867 861
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The Wolfson Centre for Personalised Medicine (WCPM) [101] was established in 2009 through joint investment by the Wolfson Foundation and The University of Liverpool (UoL). The Centre is housed in a Grade II listed building designed in 1887 by Alfred Waterhouse, a famous British architect, associated with Victorian Gothic Revival architecture. His most notable work being the Natural History Museum (London, UK).
The Centre is integral to the Depart-ment of Molecular and Clinical Phar-macology at the UoL, which also hosts the Medical Research Council (MRC) Centre for Drug Safety Science (CDSS) [102]. The two centers undertake funda-mental basic and clinical research into the causes, characteristics and consequences of drug efficacy and toxicity, aiming to improving the benefit:risk ratio of drugs through improved drug design and drug and patient selection. The WCPM cur-rently employs 73 scientists, medics, research nurses and administrators, who are largely funded through research grants from governmental organizations (Department of Health, National Insti-tute of Health Research (NIHR), MRC, Wellcome Trust, European Commission) and charities (Epilepsy Research UK among others).
Crucial to the WCPM research strategy is the ‘bench to bedside’ concept, whereby the discovery of a biomarker associated with variable drug response is taken on a
long journey to its clinical implementation and assessment of its impact on population health [1]. Although biomarker discovery still heavily dominates the field of phar-macogenomics and personalized medicine, the Centre is paving the way to assessing the clinical utility of pharmacogenetic test-ing and investigating clinical outcomes of interventions in targeted patient popula-tions. This is important for drug efficacy where response rates vary widely among patients, leading to unnecessary and waste-ful therapies with consequences to patient health and economic wealth. This is also true for adverse drug reactions (ADRs) where there is a need to understand the mechanistic reasons for drug toxicity and also to develop better biomarkers that can aid the stratification of individuals sus-ceptible to such toxicity, as well as develop intervention strategies that can help man-age such individuals. Here we describe examples of our orchestrated efforts to incorporate clinical and basic research, training of clinicians and scientists, pub-lic engagement and regulatory authorities’ involvement with the aim of facilitating implementation of personalized medicine into clinical practice.
Translation of a biomarker into clinical practice can be broadly divided into four translational phases: T1: discovery phase; T2: clinical validity/utility; T3: imple-mentation; and T4: assessing the effect of testing on public health [1]. WCPM has an interest in the identification of
Institutional Profile
The Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool, UKThe Wolfson Centre for Personalised Medicine is part of the Institute of Translational Medicine at the University of Liverpool (Liverpool, UK). It houses a multidisciplinary team of personalized medicine researchers engaged in collaborative research with partners across the globe. The primary focus of the centre is the identification of predictive biomarkers of drug safety and efficacy with the aim of translation from ‘bench-to-bedside’. Studies utilizing the latest genotyping and phenotyping, and point-of-care technologies, are undertaken with the ultimate aim of developing easy access for patients to truly personalized medicine. In addition to translation into clinical practice, the Centre puts significant emphasis into education of clinicians and scientists alike, as well as public engagement activities to promote personalized medicine.
Ana Alfirevic1, Daniel F Carr1, Fabio Miyajima1, Sudeep Pushpakom1, Laura Sutton2, Andrea L Jorgensen2 & Munir Pirmohamed*1
1Department of Molecular & Clinical Pharmacology, University of Liverpool, Block A: Waterhouse Buildings, 1–5 Brownlow Street, Liverpool, L69 3GL, UK 2Department of Biostatistics, The University of Liverpool, Shelley’s Cottage, Brownlow Street, Liverpool, L69 3GS, UK *Author for correspondence: Tel.: +44 151 794 5549 Fax: +44 151 794 5540 [email protected]
Pharmacogenomics (2013) 14(8)862 future science group
News & Views – Institutional Profile
both genetic and nongenetic biomark-ers of drug safety and efficacy and their clinical utility.
Biomarker discovery�� Drug safety
Of particular interest is identification of predictive genetic biomarkers for predispo-sition to ADRs. In recent years the WCPM has identified strong associations between genetic biomarkers and predisposition to ADRs (Table 1). Collaboration with bio-technology and academic partners is now aimed at developing simple, reliable com-panion genotyping diagnostics with the ultimate aim of translation into clinical practice (Figure 1).
ADR biomarker identif ication can be aided by deep, accurate standardized phenotyping of patients. The WCPM has had a key role in the preparation of international standardization guidelines for three important ADRs: skin injury [2], liver injury [3] and torsades de pointes [4].
As the coordinating center for the Inter-national Consortium of Drug Hyper-sensitivity (ITCH), part of the Interna-tional Serious Adverse Event Consortium (iSAEC) [103], and the repository for DNA from worldwide sufferers of severe drug-induced skin injury, we are well placed to further elucidate the genetic basis of drug hypersensitivity. Understanding the mechanisms of drug hypersensitiv-ity is important and collaboration with the MRC CDSS has led to the develop-ment of a DNA archive in 400 volunteers, HLA-typed and linked to a cell archive, allowing the investigation of the HLA-restriction, which underlies many of these severe immune mediated reactions [5]. Drug-induced liver injury (DILI) is a leading cause of liver failure requiring liver transplantation. The WCPM has par-ticipated in a number of consortia-based projects such as DILIGEN, which led to the identification of HLA-predisposing factors for flucloxacillin and co-amoxiclav. The €32.4 million Innovative Medicines Initiative Project to develop mechanism-based integrated systems for prediction of DILI (MIP-DILI) [104] is a multidis-ciplinary consortium led by the MRC CDSS including key opinion leaders from academia (nine partners), biotechnology (six) and pharmaceutical industry (11).
Consistent with the underlying WCPM aim of undertaking translational research, we have developed a program on the cardio-vascular and/or metabolic safety of drugs, such as antiretrovirals. The work under-taken on HIV utilizes in vitro and in vivo disease models, which are interrogated in parallel by multiple omic approaches. A similar strategy has been employed for bio-marker discovery and mechanistic valida-tion to explain antiretroviral drug-induced adipose and renal toxicity.
The WCPM is a major hub for a GB£2.4 million MRC Programme Grant on nosocomial infection, focusing on establishing approaches for investigating host–pathogen interactions during Clos-tridium difficile infection, a severe diar-rheal condition associated with bacterial resistance to antibiotics. Using prospec-tively recruited patients, the WCPM aims to identify and validate host–pathogen biomarkers predictive of outcomes such as disease severity and prolonged hospital-ization, which significantly impact health and economics. The approach, combined with clinical and epidemiological infor-mation, supports the development of pre-dictive tools for early identification and intervention of at-risk patients. Candidate biomarkers include bacterial genomic sig-natures linked with pathogenicity to host immune response markers [6].
In addition to traditional recruitment and sample collection methods, we have also collaborated with the Clinical Practice Research Datalink (CPRD) [105] to utilize electronic medical records for identifica-tion of rare ADRs, such as statin-induced myopathy. Patients were identified from the CPRD database, which at the time consisted of 5 million patients from 688 participating primary care practices, and recruited directly by their own general prac-tice physician who also collected biological samples. This represents the first example of acquiring biological samples in associa-tion with CPRD – there were many chal-lenges identified, and solutions developed (to be reported in a future paper). This is important as this type of recruitment has enormous potential in aiding genetic bio-marker discovery and determining validity in rare ADR research.
As part of our multidisciplinary team, we have access to expertise in clinical trial
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Tab
le 1
. Exa
mp
les
of
Wo
lfso
n C
entr
e fo
r Pe
rso
nal
ised
Med
icin
e st
ud
ies
focu
sed
on
bio
mar
ker
dis
cove
ry a
nd
clin
ical
uti
lity.
Dru
gIn
dic
atio
nPh
eno
typ
ePo
pu
lati
on
Fun
din
gD
escr
ipti
on
Dru
g s
afet
y
Car
bam
azep
ine
Epile
psy
Hyp
erse
nsiti
vity
Cau
casi
anD
oHH
LA-A
*31:
01 id
entifi
ed a
s pr
edic
tive
mar
ker
of m
ultip
le p
heno
type
s of
car
bam
azep
ine-
indu
ced
hype
rsen
sitiv
ity [13]
Nev
irapi
neH
IVH
yper
sens
itivi
tyM
alaw
ian
Wel
lcom
e Tr
ust
iSA
ECH
LA-C
*04:
01 id
entifi
ed a
s pr
edic
tive
mar
ker
of n
evira
pine
-indu
ced
Stev
ens–
John
son
synd
rom
e [14]
Fluc
loxa
cilli
nA
ntim
icro
bial
DIL
IC
auca
sian
DIL
IGEN
/iSA
ECA
s pa
rt o
f th
e D
ILIG
EN c
onso
rtiu
m, H
LA-B
*570
1 w
as id
entifi
ed a
s a
pred
ictiv
e m
arke
r of
fluc
loxa
cilli
n-in
duce
d he
pato
toxi
city
NSA
IDs
Ana
lges
ia/in
flam
mat
ion
Gas
troi
ntes
tinal
bl
eedi
ngM
ixed
NH
S C
hair
in
Phar
mac
ogen
etic
sM
ultic
ente
r tr
ial c
oord
inat
ed b
y th
e W
CPM
rec
ruiti
ng a
ppro
xim
atel
y 15
00
patie
nts
Inha
led
cort
icos
tero
idA
sthm
aA
dren
al s
uppr
essi
on:
(dim
inis
hed
cort
isol
pr
oduc
tion)
Mix
ed
pedi
atric
NH
S C
hair
in
Phar
mac
ogen
etic
sSt
udy
coor
dina
ted
from
Liv
erpo
ol A
lder
Hey
Chi
ldre
n’s
Hos
pita
l in
colla
bora
tion
with
the
NIH
R M
edic
ines
for
Chi
ldre
n Re
sear
ch
Net
wor
kSt
atin
sH
yper
chol
este
role
mia
Myo
path
yC
auca
sian
MRC
Clin
ical
res
earc
h pr
actic
e da
talin
k el
ectr
onic
med
ical
rec
ords
use
d to
id
entif
y st
atin
-indu
ced
myo
path
y fr
om a
UK
dat
abas
e of
>5
mill
ion
patie
nts
Dru
g e
ffica
cy
War
farin
Ant
icoa
gula
tion
Thro
mbo
embo
lism
Mix
ed (
UK
)EU
FP7
(EU
-PA
CT)
Dem
onst
ratio
n of
clin
ical
util
ity
of V
KORC
1 an
d C
YP2
C9
geno
type
-ba
sed
dosi
ng a
lgor
ithm
usi
ng p
oint
-of-
care
gen
etic
tes
ting
Clo
pido
grel
/asp
irin
Acu
te c
oron
ary
synd
rom
eA
ntip
late
let
resp
onse
Mix
ed (
UK
)N
HS
Cha
ir in
Ph
arm
acog
enet
ics
Mul
ticen
ter
obse
rvat
iona
l tria
l coo
rdin
ated
by
the
WC
PM
stud
y in
corp
orat
es u
se o
f su
rrog
ate
phen
otyp
e m
easu
res
of d
rug
resp
onse
suc
h as
pla
tele
t ag
greg
omet
ryA
ntie
pile
ptic
sEp
ileps
yRe
frac
tory
epi
leps
yC
auca
sian
EU F
P7 (
EURI
PID
ES)
Ex v
ivo
stud
ies
to id
entif
y m
echa
nism
s of
cel
lula
r m
ultid
rug
tran
spor
ter
func
tion
and
iden
tifica
tion
of c
ompo
unds
inhi
bitin
g dr
ug
tran
spor
t at
the
blo
od–b
rain
bar
rier
Ant
idep
ress
ants
Dep
ress
ion
Mod
erat
e-to
-sev
ere
depr
essi
onM
ixed
NIH
R-H
TAFo
lATE
D is
a r
ando
miz
ed c
ontr
olle
d tr
ial l
ooki
ng a
t th
e po
tent
ial
bene
fit o
f fo
lic a
cid
supp
lem
enta
tion
to a
ntid
epre
ssan
t th
erap
y.
WC
PM is
con
trib
utin
g to
the
stu
dy w
ith g
enet
ic a
na ly
sis
DIL
I: D
rug-
indu
ced
liver
inju
ry; D
oH: D
epar
tmen
t of
Hea
lth; H
TA: H
ealth
Tec
hnol
ogy
Ass
essm
ent;
iSA
EC: I
nter
natio
nal S
erio
us A
dver
se E
vent
Con
sort
ium
; MRC
: Med
ical
Res
earc
h C
ounc
il; N
HS:
Nat
iona
l Hea
lth S
ervi
ce;
WC
PM: W
olfs
on C
entr
e fo
r Pe
rson
alis
ed M
edic
ine.
Pharmacogenomics (2013) 14(8)864 future science group
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design, statistical genetics, bioinformatics and computational biology to ensure the most appropriate and up-to-date methods are applied to the design and ana lysis of studies. For computationally intensive work the department utilizes high-per-formance and high-throughput comput-ing facilities in which the WCPM and the wider UoL have made significant invest-ment. Access is also possible through the Northwest Grid Cluster, which has systems hosted in Daresbury, Lancaster, Liverpool and Manchester. In addition, the UoL also offers a high-throughput computing ser-vice in the form of a Condor pool, making widespead use of PCs across the university campus (up to 1400 cores).
�� Drug efficacyThe WCPM conducts a number of efficacy studies aimed at identifying genetic predic-tors of patient drug response (Table 1). Sev-eral independent and collaborative studies undertaken on the pharmacogenetics of the anticoagulant drug warfarin demon-strated the clinical utility of CYP2C9 and VKORC1 genotyping-based dosing algo-rithms [7] leading to the development of clinical guidelines.
The WCPM has played a key role in the NIHR Health Technology Assess-ment-funded FolATED study. This is a randomized controlled trial (RCT), where moderate to severely depressed patients
received 5 mg folic acid or placebo as adju-vant to their prescribed antidepressant. In a total of 440 patients, we are investigat-ing whether genetic polymorphisms in genes in the one-carbon folate metabolism and methionine synthesis pathways could be predictive markers for the efficacy of folic acid.
Drug treatment resistance is an impor-tant hurdle in many disease therapies including cardiovascular and CNS disease treatments. Our focus is on identification of factors leading to clinical resistance to drugs such as aspirin in acute coronary syndrome patients or in pregnant women at risk for preeclampsia. Additionally, refractory epilepsy has been investigated in the European Commission Seventh Framework Programme (EU FP7)-funded collaborative European project (EURIP-IDES) [106]. In collaboration with academ-ics from Australia and the USA we are also investigating genetic factors in methadone response variability in individuals treated for heroin addiction.
�� Use of emerging technologies for biomarker discoveryWith the cost of massively parallel sequenc-ing continuing to fall rapidly, we have uti-lized next-generation sequencing capabili-ties to identify rare genetic variants asso-ciated with drug toxicity and efficacy. In collaboration with the Centre for Genomic
Figure 1. Research network and academic collaborations: Wolfson Centre for Personalised Medicine.
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Research, University of Liverpool and the US FDA National Center for Toxicological Research [107], we are undertaking whole-exome and whole-genome sequencing of ADR patients. Through this work we are testing the hypotheses that rare variants and noncoding variants contribute to com-plex phenotypes with a large effect size, beyond the contribution of nongenetic factors and common genetic variants.
Clinical validation of biomarkers & therapeutic interventionsTranslation of research from bench-to-bedside is integral to the approach employed by the WCPM. In order to do this, appropriate validation of evidence collected (biomarkers, interventions, dos-ing algorithms and so on) and ascertain-ment of clinical utility are essential. The hierarchy of evidence required for clini-cal validation and utility [8] range from expert opinions and observational studies to RCTs and meta-analyses; the WCPM is involved in all levels of evidence synthesis as this process invariably depends on the clinical context [9].
RCTs are considered to be the gold stan-dard for demonstrating the clinical valid-ity and utility of a particular biomarker or intervention. However, for personal-ized medicine, novel design RCTs may be necessary. For example, TAILoR [108] is a novel Phase IIb adaptive design clinical trial undertaken by the WCPM translating findings from an in vitro adipocyte model of antiretroviral-induced cardiometabolic toxicity. The trial has been designed in collaboration with the MRC North West Hub for Trials Methodology Research (NWHTMR) [109]. Clinical trials are time consuming and expensive, and thus novel designs such as this, as noted in the FDA draft guidance [110], are required to reduce trial cost and duration, and allow for decision making on whether to move to a Phase III trial or to discontinue at the stage of interim ana lysis.
Another trial being conducted as part of an EU Consortium is the EU-PACT trial. This focuses specifically on warfa-rin, in collaboration with Sweden – the trial utilizes a biomarker strategy design [10] to evaluate whether genotype-guided dosing improves the safety and efficacy of anticoagulation therapy over conventional
dosing. In the trial we are also testing the feasibility of a point-of-care device, which provides genotype information for three alleles in CYP2C9 and VKORC1 in approximately 2 h. The trial will be reported in late 2013.
Besides RCTs, the WCPM also under-takes case–control and prospective cohort studies. Outcome measures vary and include categorical, continuous and sur-vival outcomes, often adjusted for clinical and environmental factors. The studies are designed in collaboration with the Department of Biostatistics. The design of a study really does depend on the area being studied – thus, for example, for most serious adverse reactions a case–control design is the most efficient, which we have utilized in identifying HLA bio-markers associated with hypersensitivity reactions to abacavir and carbamazepine. Additionally, we undertake systematic reviews and meta-analyses with a particu-lar interest is the methodological quality of pharmacogenetic studies [11].
An important aspect of developing the evidence base for determining valid-ity and utility is the cost–effectiveness of the intervention. As part of studies per-formed in WCPM, we routinely collect data on healthcare utilization. A typical example is our work on abacavir hyper-sensitivity, where the demonstration of the cost–effectiveness of HLA-B*5701 geno-typing prior to prescription was key in facilitating clinical uptake in the UK.
Clinical implementationIt is well known that the process from dis-covery to implementation is long and ardu-ous – the figure of 17 years is often quoted. There are many barriers to implementation of novel biomarkers into clinical practice, which vary across different healthcare sys-tems. Common issues include consistency in evidence utilization, training and educa-tion, and public engagement.
We have recently argued that the evi-dence required for implementing genetic tests is higher than nongenetic tests [12]. An important issue here may be the lack of familiarity with genetic testing, which could be addressed through better edu-cation and training. For this reason, we are involved in both undergraduate and postgraduate training of scientists and
Pharmacogenomics (2013) 14(8)866 future science group
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clinicians. An important initiative is the FP7-sponsored Marie Curie Initial Train-ing Network in Pharmacogenomics [111] providing training and research experi-ence to early stage PhD and postdoctoral researchers across several European coun-tries including Germany, UK, Russia and Slovenia. We are also actively involved in training of clinical scientists – we run the MRC Clinical Pharmacology Training Scheme [112], training clinicians to PhD level with personalized (or stratif ied) medicine as a cross-cutting theme.
Clinical implementation of pharma-cogenomic biomarkers will not only require the active engagement of clini-cians but also patients and the public. Without acceptance of these approaches by patients, the process of implementation will be almost impossible. The WCPM fronts a university-wide initiative promot-ing interdisciplinary research in personal-ized approaches, which has allowed us to actively engage with researchers in differ-ent disciplines including arts and humani-ties, providing us with novel insights into barriers to implementation.
The WCPM recognizes the value of public engagement – we have been involved in a range of activities from speaking at schools and public events, such as science festivals; providing short-term placements for high school pupils; and actively engaging in patient–public involvement groups, particularly involv-ing those patients who have developed severe ADRs. A notable activity over the last 2 years has been the Y-touring theatre company, which led to the development of a play on pharmacogenetics and personal-ized medicine at the Royal Albert Hall (London, UK) [113] that was broadcast to
schoolchildren, medical students and at science festivals.
Public healthAs we move forward with implementa-tion of pharmacogenetic tests, it will be important to ensure that this has a positive impact on public health. This is an area that has been poorly researched. Our strat-egy is to use electronic healthcare records allowing the follow-up and assessment of patient outcomes in real-world clinical set-tings. To this end, we have been working with the UK CPRD, as well as secondary care informatics systems.
ConclusionThe WCPM is dedicated to the develop-ment of the science of pharmacogenomics and personalized medicine. It is staffed by a multidisciplinary team, which is important given the complexities of implementing any findings into clinical practice. We continue to develop new clinical areas utilizing the latest advances in genomics and other omic technolo-gies collaborating globally with the aim of moving medicine from our current empirical approach to one that is more precise and predictable.
Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the sub-ject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
No writing assistance was utilized in the production of this manuscript.
Highlights
� The Wolfson Centre for Personalised Medicine houses a multidisciplinary research group with the aim of improving the translation of pharmacogenetic biomarkers into the clinic.
� A comprehensive approach from bench-to-bedside to application and implementation is utilized in the areas of both drug safety and drug efficacy.
� We apply state-of-the-art genomic analytical platforms to personalized medicine, which is combined with the most relevant clinical study designs and analytic (statistical and bioinformatic) platforms.
� Numerous national and international collaborations have been established to facilitate high-quality research.
� There is training and education of scientists and clinicians at all levels, and patient and public engagement activities to promote personalized medicine.
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13 McCormack M, Alfirevic A, Bourgeois S et al. HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans. N. Engl. J. Med. 364(12), 1134–1143 (2011).
14 Carr DF, Chaponda M, Jorgensen AL et al. Association of human leukocyte antigen alleles and nevirapine hypersensitivity in a Malawian HIV-infected population. Clin. Infect. Dis. 56(9), 1330–1339 (2013).
�� Websites101 The Wolfson Centre for Personalised
Medicine. www.liv.ac.uk/pharmacogenetics/centre_for_personalised_medicine
102 MRC Centre for Drug Safety Science. www.liv.ac.uk/drug-safety/research
103 International Serious Adverse Events Consortium. www.saeconsortium.org
104 Mechanism Based Integrated Approaches to Drug Induced Liver Injury. www.mip-dili.eu
105 Clinical Practice Research Datalink. www.crpd.com
106 European Research initiative to develop Imaging Probes for early In-vivo Diagnosis and Evaluation of response to therapeutic Substances. www.euripides-europe.com/en/joint-research-project.php
107 US FDA National Center for Toxicological Research. www.fda.gov/AboutFDA/CentersOffices/OC/OfficeofScientificandMedicalPrograms/NCTR/default.htm
108 TAILoR trial website. https://mcrnctu.org.uk/Staging/Tailor/Home/Login
109 MRC North West Hub for Trials Methodology Research (NWHTMR). www.liv.ac.uk/nwhtmr
110 Guidance for Industry: investigational new drug applications (INDs) – determining whether human research studies can be conducted without an IND. www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM229175.pdf
111 Marie Curie Initial training Network. www.ikp-stuttgart.de/content/language1/html/13119.asp
112 MRC Clinical Pharmacology Training Scheme. www.liv.ac.uk/north-west-england-mrc-fellowship-cpt
113 Y Touring Theatre Company. http://ytouring.myresourcecloud.net/component/tortags/tag/pharmacogenetics.html?Itemid=157