Diagnostics : EU-supported research in genomics and biotechnology for health : Sixth Framework Programme (2002-2006).
Date: 2008-08-19
Institutions: Directorate-General for Research and Innovation
Subjects: biology, biotechnology, medical diagnosis, medical research, new technology, research programme, small and medium-sized enterprises

Diagnostics
Diagnostics  refers  to  the  tools  and  technologies  used  in  early  diagnosis  of  disease, 
monitoring of disease progression and response to therapy. Use of diagnostic methods 
can greatly increase the effectiveness of therapy. Research into new diagnostics formed 
part  of  the  EU’s  Sixth  Framework  Programme  (2002-2006)  and  the  purpose  of  this 
catalogue is to demonstrate the activities started over the duration of the programme 
and the initial results obtained. Diagnostics research involves many disciplines, including 
molecular  biology,  physiology,  biomedical  engineering  and  information  technology, 
where new research is opening up exciting opportunities, and is a particularly active area 
for industry, especially SMEs.

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Diagnostics

EUR 23347

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Interested in European research? 
Research*eu is our quarterly magazine keeping you in touch with main developments (results, 
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European Commission

Genomics and Biotechnologies for Health — DIAGNOSTICS

Luxembourg: Office for Official Publications of the European Communities

2008 — 168 pp. — 17.6 x 25.0 cm

ISBN 978-92-79-08527-7

This publication is also available online at: 
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EUROPEAN COMMISSION

Directorate F – Health

Unit F5 – Health Biotechnology

Contacts 

Philippe Jehenson  

Jean-Luc Sanne

Office CDMA 2/123 

Office CDMA 2/115

Tel (32-2) 29 86454 

Tel (32-2) 29 92589

Fax (32-2) 29 94693 

Fax (32-2) 29 94693

Directorate F – Health

Unit F5 – Health Biotechnology

Head of Unit 

Arnd HOEVELER (arnd.hoeveler@ec.europa.eu)

 Secretary: Andrea JAEGER (andrea.jaeger@ec.europa.eu)

Diagnostics 

Jean-Luc SANNE (jean-luc.sanne@ec.europa.eu) 

Torbjoern INGEMANSSON (torbjoern.ingemansson@ec.europa.eu) 

Philippe JEHENSON (philippe.jehenson@ec.europa.eu)

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EUROPEAN COMMISSION

DIAGNOSTICS

EU-supported research in Genomics and Biotechnology for Health
Sixth Framework Programme (2002-2006)

Edited by
Charles Kessler

2008

Life Sciences, Genomics and Biotechnology for Health

EUR 23347

Directorate-General for Research

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DIAGNOSTICS
NEW THERAPIES

TABLE OF CONTENTS

INTRODUCTION  

7

GENETIC TESTING AND 
BIOMARKERS 

 11

EuroGentest
Genetic  testing  in  Europe  –  network  for  test 
development,  harmonisation,  validation  and 
13
standardisation of services 

EUROGENGUIDE
Patient  led  education  and  development  for 
19
genetic testing in research and medicine 

GLYFDIS
Glycans  in  body  fluids  –  potential  for  disease 
44
diagnostics 

MolDiag-Paca
Novel  molecular  diagnostic 
the 
prevention  and  diagnosis  of  pancreatic  cancer
47

tools 

for 

SAFE
Special  non-invasive  advances  in  foetal  and 
22
neonatal evaluation  

COBRED
Colon and breast cancer diagnostics 

51

QuAGSIC
Quantitative analysis of genes in single cells  28

IBDchip
Usefulness of a new DNA array (IBDchip) to predict 
clinical  course,  development  of  complications 
in  patients  with 
and  response  to  therapy 
30
inflammatory bowel disease (IBD) 

AntePrion
Development of a preclinical blood test for prion 
33
diseases 

integrated 

TSEUR
An 
immunological  and  cellular 
strategy  for  sensitive  TSE  diagnosis  and  strain 
37
discrimination 

ADDNET
Paradigm shift from kidney biopsies to advanced 
41
molecular diagnostics from patient urine 

EuroFlow
Flow  cytometry  for  fast  and  sensitive  diagnosis 
and follow-up of haematological malignancies 

DRoP-ToP
Integration of DNA, RNA and protein markers in 
a tool for the prognosis and diagnosis of human 
57
disease 

54

TB-trDNA
Evaluation  of 
diagnose tuberculosis 

transrenal-DNA  detection 

to 
62

GENEPARK
Genomic biomarkers for Parkinson’s disease  64

PREGENESYS
Development  of  early  non-invasive  biomarkers 
and  means  for  the  diagnosis  and  progression 
tailoring 
monitoring  of  preeclampsia  and 
67
putative therapies 

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Diagnostics - Table of Contents

3

 
 
 
TABLE OF CONTENTS

EDAR
Beta amyloid oligomers in the early diagnosis of 
69
AD and as marker for treatment response 

NeuroScreen
Sensitive and differential blood and cerebrospinal 
for  neurodegenerative  dementia 
fluid 
test 
71
diagnostics 

IMAGING, 
NANOPARTICLES AND 
BIOSENSORS 

 75

DiMI
Diagnostic Molecular Imaging (DiMI): a European 
network  of  excellence  for  the  development  of 
new  molecular  imaging  strategies  aiming  to 
improve  the  diagnostic  and  therapy  of  human 
77
diseases 

DASIM
Diagnostic  Applications  of  Synchroton  Infrared 
84
Microspectroscopy 

NeuroTAS
Microfluidic  total  analysis  system  for  the  early 
88
diagnostic of neurodegenerative disorders 

POC4life
Multiparametric quantum dot bioassay for point 
91
of care diagnosis 

DIAGNOSIS
Development of new and cost-effective methods 
for non-invasive diagnosis of human pathogens  
94

USDEP
Capture and enrichment of emerging pathogens 
97
for multiple and ultra-sensitive diagnostic 

NEMO
Nano  based  capsule-endoscopy  with  molecular 
100
imaging and optical biopsy 

FLUOROMAG
Multiparameter  sensing 
for  high  sensitivity 
diagnostics  using  fluorescent  and  magnetic 
103
nanoparticles 

BONSAI
Bio-imaging with smart functional nanoparticles 
106

NanoSense
Moving  sensitive  immunoassays  from  slow  and 
expensive  to  fast  and  affordable  nanoparticle-
110
based methods 

DiaNa
Predictive  diagnostics  for  diabetic  nephropathy 
— novel nanotechnology based test platforms 

112

NANOMYC
Multiparametric  detection  of  bio-molecule 
conjugated  nanoparticles  for  the  diagnostic 
infections  of 
investigation  of  mycobacterial 
114
humans and animals 

DETECTHIV
Sensitive nanoparticle assay for the detection of 
117
HIV 

NACARDIO
Nanoparticle-based  electronic  biosensor 
diagnostics of cardiovascular disease 

for 
120

4

Diagnostics - Table of Contents

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DIAGNOSTICS

SLIC
in  molecular  diagnostics: 
SLIC-Biosensors 
nanotechnology  for  the  analysis  of  species 
124
specific microbial transcripts 

eBIOSENSE
Electrical biosensor arrays for analyses of harmful 
125
micro-organisms and microbial toxins 

FP7 PROjECTS -
Biomedical imaging 

129

CARS Explorer
Innovative contrast imaging by non-linear optics 
(NLO) for the observation of biological tissues in 
vivo  and  in  real  time,  at  cellular  and  molecular 
130
levels 

resolution 

FLUODIAMON
Ultra-high 
ultra-sensitive 
fluorescence methods for objective sub-cellular 
diagnosis of early disease and disease progression 
132
in breast and prostate cancer 

and 

SKINSPECTION
Multimodal skin inspection with hybrid acoustic 
145
and optical spectroscopic imaging  

EURIPIDES
European Research initiative to develop Imaging 
Probes for early In vivo Diagnosis and Evaluation 
147
response to therapeutic substances 

ENCITE
European Network for Cell Imaging and Tracking 
150
Expertise 

FUN OCT
Functional Optical Coherence Tomography  135

nEUROPT
Non-invasive  imaging  of  brain  function  and 
137
disease by pulsed near infrared light 

FMT-XCT
Hybrid  Fluorescence  Molecular  Tomography 
–  X-ray  Computed  Tomography  method  and 
139
system 

HYPERImage
Hybrid  PET-MR  system  for  concurrent  ultra-
141
sensitive imaging 

MEGMRI
Hybrid MEG-MRI Imaging System 

143

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Diagnostics - Table of Contents

5

FP7 PROjECTS - 
Molecular testing 

 153

SPIDIA

Standardisation  and  improvement  of  generic 
pre-analytical  tools  and  procedures  for  in  vitro 
154
diagnostics 

EURO-GENE-SCAN
European Genetic Disease Diagnostics 

157

NMD-Chip
Development  of  targeted  DNA-Chips  for  High 
Throughput  Diagnosis  of  NeuroMuscular 
159
Disorders 

throughput  molecular  diagnostics 

TECHGENE
in 
High 
individual  patients  for  genetic  diseases  with 
163
heterogeneous clinical presentation 

INDEX OF PROjECTS 

 166

INDEX OF 
COORDINATORS 

 167

6

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INTRODUCTION

DIAGNOSTICS

Diagnostics  refers  to  techniques  for  deter-

mining  the  nature  and  cause  of  disease. 
As part of its Sixth Framework Programme 
for Research (2002-2006, FP6) , the EU supported 
diagnostics  research  notably  under  the  heading 
“Applications  of  knowledge  and  technologies 
in  the  field  of  genomics  and  biotechnology  for 
health”  in  the “Life  sciences,  genomics  and  bio-
technology for health” thematic priority. Details of 
this research have been compiled in the present 
volume, whose objectives are to demonstrate the 
range  of  activities  undertaken  and  initial  results 
obtained. Diagnostics research is continued in the 
EU’s Seventh Framework Programme (2007-2013, 
FP7), and brief details of research projects started 
in 2007 and 2008 are also included.

The overall objective of the diagnostics research 
described  here  is  to  develop  new  tools  and 
techniques  for  early  diagnosis  of  disease,  for 
monitoring disease progression and for guiding 
therapeutic  interventions.  A  particular  feature 
of the techniques is that they should be non- or 
minimally-invasive  towards  the  patient.  Since 
the  projects  are  essentially  technology-driven 
they have been ordered on the basis of similar-
ity  in  approach  and  have  been  grouped  into 
two  chapters  reflecting  the  major  technologies 
employed. These  are  followed  by  summaries  of 
work proposed in FP7 projects.

GENETIC TESTING aNd BIOMaRKERS. Genetic 
testing refers to determining the susceptibility to 
inherited disease. It is an area that has advanced 
rapidly as a result of recent developments in ge-
nomics, a major thrust of the FP6. Genetic testing 
is also linked to the use of biochemical tests for 
the  possible  presence  of  genetic  disease.  More 

generally,  a  biomarker  refers  to  a  substance 
whose  detection  indicates  a  particular  disease 
state. The  aim  of  projects  described  in  this  sec-
tion  is  the  development  of  genetic  testing  and 
biomarker  technology  in  a  general  way.  Some 
projects  deal  with  specific  disease  applications 
chosen by scientists as a way of developing tech-
nology  rather  than  necessarily  targeting  a  spe-
cific disease objective. Since genetic testing may 
open  up  ethical  questions,  this  aspect  has  also 
been included in projects.

IMaGING,  NaNOPaRTICLES  aNd  BIOSEN-
SORS. Diagnostics tools are also expanding rap-
idly  as  a  result  of  progress  in  non-medical  disci-
plines and the tool development described in this 
section  derives  particularly  from  nanotechnolo-
gies,  physics,  electronics,  molecular  biology  and 
computer  science.  Imaging  work  described  here 
aims at the visualisation of biological processes at 
the cellular and molecular level. Bioimaging and 
molecular tests can also be used in combination 
and  share  the  need  for  specific  biomarkers  and 
probes. Recent developments in nanotechnology 
have led to design of very powerful probes, allow-
ing detection in vivo through bioimaging and in 
vitro through “lab-on-a-chip” designs. Biosensors 
combine a biological component, such as an an-
tibody  or  nucleic  acid,  with  a  physico-chemical 
detector  and  an  electronic  processor  to  display 
the  results.  As  in  the  previous  section,  projects 
aim at technology development in a general way 
but often with application to prototype stage in a 
particular disease situation.

FP7 – Biomedical imaging. Advances in imaging 
techniques have had a major impact in everyday 
medical  practice.  Following  earlier  work  in  FP6, 

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Diagnostics – Introduction

7

INTRODUCTION

biomedical imaging research was a major thrust 
in the first calls for proposals in FP7. Bioimaging 
allows  the  visualisation  and  characterisation  of 
both structure and function, and combining im-
aging technologies can lead to even more pow-
erful tools to diagnose, track and treat a variety 
of  diseases.  The  projects  described  here  cover 
novel  optical  methodologies,  hybrid  imaging 
systems, the development of imaging probes to 
evaluate response to therapy, and tracking cells 
used in cell therapy.

FP7  –  Molecular  testing.  In  vitro  diagnostics 
have allowed a great deal of progress in medicine 
but are limited by lack of guidelines in collection, 
handling, stabilisation and storage of biosamples. 
The first project described in this section aims to 
develop standard guidelines for molecular in vit-
ro diagnostics and to develop pre-analytical tools 
to use with free biomolecules from samples. The 
second  area  of  work  concerns  high-throughput 
molecular diagnostics for genetic diseases.

The  following  table  shows  the  number  of 
projects  supported  in  diagnostics  research  and 
the  EC  financial  contribution  to  them.  It  shows 
that during FP6 34 projects were supported with 
an EC contribution of around EUR 105.7 million, 

and that in the first 2 years of operation of FP7, 
14 projects are planned to be supported with an 
EC contribution of around EUR 73.7 million.

In order to achieve their objectives, FP6 projects 
were built around five different funding schemes:

Integrated  Projects.  These  are  the  larg-
est size projects and integrate a range of 
different activities, such as research, dem-
onstration and training. They also permit 
projects  to  take  a  multidisciplinary  ap-
proach,  to  link  underlying  biology  and 
tool  development  and  enable  scientists, 
clinicians and other stakeholders to work 
together to achieve their deliverables.

Networks of Excellence, whose objective 
is to reduce fragmentation in EU research, 
structure  the  way  it  is  carried  out  and 
strengthen its excellence. 

Specific  Targeted  Research  Projects. 
These are smaller projects which focus on 
specific  research  issues.  They  may  have 
an applied focus but are less multi-disci-
plinary  and  wide-ranging  than  the  Inte-
grated Projects.

Area

FP6

Genetic testing and Biomarkers

Imaging, nanoparticles and biosensors

Total

FP7*

Biomedical imaging

Molecular testing

Total

* 2007 and 2008 only

8

Diagnostics – Introduction

Number of projects

EC financial 
contribution (million €)

18

16

34

10

4

14

61.7

44.0

105.7

55.9

17.8

73.7

Number of projects supported and EC financial contribution to diagnostics research 

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DIAGNOSTICS
DIAGNOSTICS

Targeted 

SME-Specific 
Research 
Projects. Targeted  Research  Projects  de-
signed  to  encourage  research  and  inno-
vation efforts of small and medium-sized 
enterprises  (SMEs)  and  where  research-
led SMEs play a leading role.

Specific  Support  actions  for  training, 
conferences or prospective studies in sup-
port of the programme.

FP7  projects  described  here  are  all  categorized 
as Collaborative Projects and receive EU financial 
contributions of between around EUR 3 million 
and  EUR  12  million.  The  smaller  ones  approxi-
mate  to  the  format  of  the  specific  targeted  re-
search  projects  described  above  and  the  larger 
ones to the integrated projects.

The number of projects supported by the differ-
ent funding schemes and the EC financial contri-
bution to them is shown in the table below. This 
was distributed in FP6 among over 400 research 
teams,  around  80  of  which  are  SMEs,  including 
some as coordinators. 

FP7 has included in its first 2 years of operation 
around 150 teams, including about 25 SMEs.

European  research  projects  are  encouraged  to 
be  open  towards  the  general  public  and  to  en-
gage with stakeholders and interest groups. This 
is  particularly  important  in  the  field  of  genetic 
testing  which  is  of  considerable  public  inter-
est.  Accordingly  many  projects  organise  public 
meetings  and  dialogue  and  set  up  websites  on 
the consortium, the research and results. Website 
addresses are given in the details of each project 
and provide more detailed and more up-to-date 
information than this publication.

This compilation shows that diagnostics is an ex-
tremely active area of research for European sci-
entists both from the public and private sectors. 
These efforts in the health programme are com-
plemented by related research undertaken by the 
EU’s nanosciences, nanotechnologies, materials & 
new production technologies programme. EU di-
agnostics research is an especially attractive area 
for health-related SMEs since there are many op-
portunities for placing of products on the market.

Funding scheme

Number of projects

EC financial contribution  
(million €)

FP6

Integrated project

Network of excellence

Specific Targeted Research Project

SME-Specific Targeted Research Project

Specific Support Action

Total

FP7*

Collaborative project

* 2007 and 2008 only

1

3

16

12

2

34

14

8.5

32.7

36.4

27.3

0.8

105.7

73.7

Funding schemes used in diagnostics research and EC financial contribution

The  EU  will  continue  to  support  diagnostics  research  as  FP7  develops.  Further  information  can  be 
found at: http://cordis.europa.eu/fp7/health/home_en.html 

Diagnostics – Introduction

9

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Genetic Testing and Biomarkers

10

Diagnostics

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Genetic Testing and Biomarkers

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12

Diagnostics - Genetic Testing and Biomarkers

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DIAGNOSTICS

EuroGentest

Genetic testing in Europe – network for test development, harmonisation, 
validation and standardisation of services

LSHB-CT-2004-512148
Contract No 
Project type  Network of Excellence

EC contribution  e 10 000 000

Starting date   1 January 2005
duration  60 months

Website  www.eurogentest.org

Background and objectives: 

The  EuroGentest  NoE  (Network  of  Excellence) 
is  a  five-year  EU-funded  programme  aiming 
to  develop  the  necessary  infrastructure,  tools, 
resources,  guidelines  and  procedures  that  will 
lead to the establishment of harmonised, quality 
genetic testing services in Europe. 

This will be achieved by bringing together, in a real 
long-term partnership, experts and expert centres 
in  Europe  that  are  active  in  different  aspects  of 
testing. The Network includes researchers, small 
and  medium-sized  enterprises  (SMEs),  testing 
laboratories,  quality  management  and  public 
health  experts,  ethicists,  lawyers,  sociologists, 
educational authorities and consumers. 

The  management  group,  together  with  the 
Steering Committee that is composed of the unit 
leaders,  is  responsible  for  the  coordination  and 
financial management of the NoE, as well as for 
the  smooth  implementation  of  the  horizontal 
activities,  which 
the  provision  of 
include 
fellowships and communication about the NoE.

In the figure (next page), the different units and 
the  interacting  networks  and  projects  are  indi-
cated.  In  the  centre,  the  management  and  the 
coordination  are  shown  to  interact  with  an  ad-
visory board composed of representatives of dif-
ferent international organisations.

Expected outcome:

EuroGentest  is  focusing  on  the  following  four 
major areas of activities: 
•	
•	

quality	of	the	laboratories;
quality	 of	 the	 clinical	 aspects	 of	 the	
s	ervices;
translation	 of	 technologies	 into	 routine	
diagnostic	practice;
education	aspects.

•	

•	

For operational reasons, the NoE was structured 
into six different units, each with a specific focus 
on  one  of  the  activities  of  the  Network,  as  well 
as  with  a  unit  board  which  coordinates  the 
different  Work  Packages  (WPs)  of  the  unit  and 
the interactions between them. 

•	

•	

the	 quality	 assurance	

Quality management
Evaluation	 of	
•	
information database.
Training	 session	 on	 the	 use	 of	 LIMS	 and	
quality management of informatic systems. 
Final	
and	
report	 with	 guidelines	
requirements for quality management of 
genetic testing labs.
Organisation	 and	 coordination	 of	 follow-
up workshops and training for accredited 
labs and internal auditors.
Final	 conclusion,	 and	 if	 necessary,	 ISO	
draft  guidelines  for  genetic  testing  labs 
submitted to the ISO / TC212 committee. 
Model	 for	 sustainability	 of	 the	 quality	
management services.

•	

•	

•	

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Diagnostics - Genetic Testing and Biomarkers

13

 
 
 
 
 
 
EuroGentest

•	

•	

•	

•	

•	

•	

Report	 on	 the	
impact	 of	 measures	
to  coordinate,  harmonise  and  make 
sustainable  molecular  genetics  External 
Quality Assessments (EQAs) across Europe 
within  a  recognised  governance  and 
standards framework.
Endpoint	 evaluation	 of	 the	 measures	
taken to expand molecular genetics EQA 
participation, and to meet the developing 
needs  of  diagnostic  service  laboratories 
across Europe.
Report	 on	 the	 impact	 and	 future	 of	 best	
practice guidelines for molecular genetics 
in Europe.
Proposal	
of	
cytogenetics  EQA  schemes  and  for  the 
certification for cytogenetics EQA schemes 
has been approved. 
Cytogenetics	EQA	schemes	flexibility	and	
responsiveness to changing technologies 
has been successfully tested.
A	 pan-European	

cytogenetics	

governance	

EQA	

the	

for	

available 
to  all  Europe  cytogenetics 
registration  and 
laboratories,  online 
management  of  electronic  cytogenetics 
EQA scheme has been established.
Steps	 for	 certification	 of	 biochemical	
genetics  EQA  schemes  in  harmonisation 
with cytogenetics and molecular genetic 
schemes have been initiated.
A	 European	 directory	 of	 biochemical	
genetic  service  providers  linked  to  EQA 
participation has been established.
Prepare	sustained	activities	of	the	Network	
for Validation and Technology Testing.
A	 number	 of	 technologies	 has	 been	
validated  and  generic  SOPs  are  now 
available.
New	
developed and the field has been tested.

control	 materials	 have	 been	

•	

•	

•	

•	

•	

Information
•	

information	 on	 all	 testing	 activities	 in	
Belgium,  Bulgaria,  the  Czech  Republic, 

ECA

EMQN

ORPHANET

2
Database

CANGENETEST
EUROCARE-CF
CAPABILITY
PHGEN
RELAGH

3
Clinic

Unit 1
Quality Issues

ERNDIM

OECD
CDC
ACMG
WHO
EFB
ESHG
EUROPABIO

ESHG

6
Education

5
Technology

4
Ethics, Legal

INDUSTRY
SAFE NoE

GeneBanC

14

Diagnostics - Genetic Testing and Biomarkers

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DIAGNOSTICS

•	

•	

•	

with existing facilities will be available.
A	 syllabus	 for	 each	 genetic	 course,	 with	
a  minimal  common  basis  among  the 
partner countries for the education of the 
different  categories  of  professionals,  will 
be available.
A	collection	with	the	existing	regulations	
controlling  the  licence  to  practise  as 
a  designated  genetic  professional  to 
facilitate  harmonisation  within  the  MS, 
will be available.
New	 flyers	 with	 information	 for	 patients	
are available in several languages.

Main findings: 

•	

In  general,  the  different WPs  and  units  achieved 
their milestones and deliverables in the first two 
years of the programme, and their achievements 
are already clearly visible, including the following.
A	European	central	database	of	laboratories	
•	
with  quality  criteria  is  being  developed 
in  collaboration  with  Orphanet  and  will 
be  online  soon.  Very  successful  training 
sessions  about  quality  management  and 
accreditation have been organised.
EQAs	 for	 molecular,	 cytogenetic,	 bio-
chemical  tests  (electronic  EQA  for  cy-
togenetics)  have  been  organised  and 
have been extended.
Control	 materials	 for	 different	 genetic	
tests  are  available  and  more  are  under 
development.
Generic	SOPs	for	DNA	extraction	–	MLPA	
are being finalised.
Expert	groups	have	been	set	up	for	quality	
aspects,  counselling,  clinical  validation, 
ethical issues and educational aspects.
Surveys	 of	 stakeholders	 and	 literature	
surveys were held on different aspects of 
counselling,  quality  issues,  educational 
materials and ethical aspects.
Newsletters	were	published,	a	website	was	
developed, press releases were drafted and 
scientific publications were submitted.

•	

•	

•	

•	

•	

Denmark,  Germany,  Estonia, 
Ireland, 
Greece, Spain, France, Italy, Cyprus, Latvia, 
Lithuania,  Hungary, 
the  Netherlands, 
Austria,  Poland,  Portugal,  Romania, 
Sweden, the UK and Norway.
A	unique	European	portal	for	information	
on genetic testing activities and diseases 
has  been  established  and  contains  infor-
mation on all testing activities in Europe. 
The data are updated once per year.

•	

Clinical genetics and public health
•	

Major	needs	for	professional	education	in	
the field have been identified.
Endorsed	 recommendations	 for	 counsel-
ling will be published in the NoE website 
and elsewhere.
Tools	for	assessing	the	quality	of	genetic	
counseling have been tested.
Agreement	 on	 and	 establishment	 of	 a	
formal basis for widely accepted guidelines 
in relation to accreditation/certification of 
clinical genetic services.

Ethical legal social issues
•	

development	 of	 European	 guidelines	 for	
genetic testing (in close collaboration with 
patient	organisations	and	geneticists);
evaluation	 of	 the	 convergences	 and	
divergences  in  the  protection  of  rights 
of  patients  between  the  different  EU 
members  in  the  light  of  the  common 
European 
framework  offered  by  the 
European Convention.

Research and emerging technologies
•	

description	 and	 analysis	 of	 the	 current	
European and International IP framework 
for	diagnostic	patents;
technological	 platform	
for	 beta-site	
testing  of  new  diagnostic  technologies 
will be available.

Education
•	

Training	 programmes	

in	 collaboration	

•	

•	

•	

•	

•	

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EuroGentest

•	

•	

•	

in	 different	

EuroGentest	 participated	
expert meetings (EU, OECD, ISO, etc.).
EuroGentest	 gave	 a	 whole	 series	 of	
presentations at international congresses.
Plans	
the	
for	 communication	 with	
stakeholders,  for  sustainability  and  for 
gender issue analysis were drafted. 

Training activities
In addition to the training sessions detailed in the 
WP reports, the NoE has provided six fellowships 
for  training. These  fellowships  have  allowed  sci-
entists either to be trained in a laboratory of one 
of the participants of the NoE, or to attend a train-
ing course relevant to the activities of the NoE.

dissemination of knowledge
In  addition  to  a  very  active  website,  www.
eurogentest.org,  and  the  production  of  regular 
newsletters  and  flyers,  the  participants  of  the 
NoE  are  regularly  solicited  to  participate  in 
international  expert  meetings,  and  are  invited 
to  present  the  achievements  of  the  network  at 
international  congresses  and  symposia  (more 
than 40 in 2006).

In  conclusion,  international  awareness  of  the 
existing  problems  has  been  improved.  The  will 
to make the necessary improvements is present 
within the NoE, and the tools necessary to make 
these improvements are becoming available.

Major publications: 

Chedraui, P., Landivar, X., ‘Eurogentest’, DS News, 
Vol. 13, No 2, 2006, pp. 27.

Chedraui,  P., ‘CLP  in  Ecuador’,  DS News, Vol.  12, 
No 2, 2005.

Chedraui, P., ‘Standardization of molecular biology 
techniques  for  Down’s  syndrome  diagnosis  in 
amniotic fluid in Guayaquil-Ecuador: The intiation 
of a new era’, DS News, 2004, Vol 11, No 2.

Van  Overwalle,  G.,  van  Zimmeren,  E.,  Verbeure, 
B.,  Matthijs,  G., ‘Models  for  facilitating  access  to 
patents  on  genetic  inventions’,  Nature  Reviews 
Genetics, doi:10.1038/nrg1765 

‘EuroGentest  —  a  European 
Cassiman,  J.J., 
Network  of  Excellence  aimed  at  harmonizing 
genetic 
testing  services’,  European  Journal 
of  Human  Genetics,  2005,  13,  1103–1105. 
doi:10.1038/sj.ejhg.5201484;	 published	 online	
10 August 2005. 

Verbeure  B.,  Matthijs,  G.,  Van  Overwalle,  G., 
relation  with 
‘Analysing  DNA  patents 
diagnostic  genetic  testing’,  European  Journal  of 
Human Genetics,  advance  online  publication  12 
October 2005, doi:10.1038/sj.ejhg.5201503. 

in 

Borry,  P.,  Fryns,  J.P.,  Schotsmans,  P.,  Dierickx,  K., 
‘Carrier testing in minors: a systematic review of 
guidelines and position papers’, European Journal 
of  Human  Genetics  advance  online  publication, 
2005,	Nov	2;	doi:10.1038/sj.ejhg.5201509.	

Coordinator

Jean-Jacques Cassiman
Center Human Genetics/
Centrum Menselijke Erfelijkheid
Campus gasthuisberg
Herestraat 49, Box 602
B 3000 Leuven
E-mail: jean-jacques.cassiman@med.kuleuven.be

Partners 

antoon Vyverman
Ascent Consultancy
Leuven, Belgium

Michael Morris
Geneva University Hospitals
Geneva, Switzerland

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Helena Kääriäinen
University of Turku
Turku, Finland

Ulf Kristoffersson
Lunds Universitet
Lund, Sweden

Jörg Schmidtke
Medizinische Hochschule Hannover
Hannover, Germany

Jorge Sequeiros
Instituto de Biologia Molecular e Celular
Porto, Portugal

Bert Bakker
Leiden University Medical Center
Leiden, Netherlands

Guillermo antiñolo
Hospitales Universitarios Virgen del Rocîo-Servicio 
Andaluz de Salud
Sevilla, Spain

Maj Hutten
The University of Warwick
Coventry, UK

alastair Kent
Genetic Interest Group
London, UK

Beverly Searle
The Rare Chromosome Disorder Support Group
Surrey, UK

dada Radojkovic
Institute of Molecular Genetics
Belgrade, Serbia

Peter Chedraui
Universidad Cató de Santiago de Guayaquil
Guayaquil, Ecuador

Robert George Elles
The University of Manchester
Manchester, UK

Clemens Reible-Müller
Bayerische Julius-Maximilians Universität Würzburg
Wuerzburg, Germany

György Fekete
Semmelweis University
Budapest, Hungary

Michal Witt
International Institute of Molecular and Cell Biology
Warsaw, Poland

Milan Macek Jr
Charles University Prague
Prague 5, Czech Republic

david Barton
National University of Ireland, Dublin
Dublin, Ireland

Philippe Corbisier
European Commission, Joint Research Centre
Geel, Belgium

Rosalind Janice Hastings
Oxford Radcliffe Hospital
Oxford, UK

Brian Fowler
University Children’s Hospital Basel
Basel, Switzerland

Ségolène aymé
Institut National de la Santé et de la Recherche Médicale
Paris, France

Bruno dallapiccola
Istituto Casa Sollievo Della Sofferenza, 
San Giovanni Rotondo
Rome, Italy

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EuroGentest

Jan Schouten
MRC-Holland
Amsterdam, Netherlands

david Bishop
Waypoint Systems Ltd
Shewsbury, Shropshire, UK

Peter Rosseel
Management Consulting and Research
Hevertee, Belgium

Orfeu Flores
Stab Vida investigação e serviços 
em ciências biológicas lda
Oeiras, Portugal

david atlan
Phenosystems SA
Brussels, Belgium

Juergen Oster
Chemagen Biopolymer – Technologie AG
Baesweiler, Germany

Irmgard Nippert
Westfälische Wilhelms-Universität Münster, 
Universitätsklinikum Münster
Muenster, Germany

domenico Coviello
Ospedale Maggiore Policlinico,
Mangiagalli e Regina Elena
Milan, Italy

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EUROGENGUIDE

Patient led education and development for genetic testing in research  
and medicine

Contract No 
Project type 

LSHB-CT-2006-518156
Specific Support action 

EC contribution  e 499 476

Starting date   1 January 2007
duration  36 months

Website  www.gig.org.uk/teammember_ 
  projectofficereuro1.htm

Background and objectives:

Health  professionals  are  often  unaware  of  the 
ethical,  legal  and  psychosocial  implications 
genetic  tests  may  have.  What  is  more,  these 
tests  are  often  not  in  compliance  with  ethical 
and  clinical  guidelines  especially  regarding  in-
formed consent and indications for testing.

Health  professionals  who  are  poorly  informed 
and ill-prepared for engaging patients in an ap-
propriate informed consent process can have a 
detrimental effect on the welfare of clients and 
their families. Shared practices in the informed 
consent  process  are  urgently  needed  to  help 
both professionals and the public.

The key objectives of EuroGenGuide are to create 
tools, a manual for patients and consumers, and 
educational materials for health professionals, to:
empower	 the	 European	 public	 to	 make	
•	
informed  choices  about  participation  in 
genetic  research  and  genetic  testing  , 
which  will  be  understandable,  culturally 
competent	and	widely	available;
educate	
health	
and	
professionals to engage patients/clients in 
an appropriate informed consent process.

researchers	

•	

The  tools  EuroGenGuide  proposes  to  develop 
will  reflect  a  clear,  consumer/patient-focused 
perspective  on  issues  common  to  all  genetic 
human  subject  research  and  clinical  testing 
situations,  such  as  informed  consent,  storage 

of  genetic  information,  confidentiality,  risks 
and  benefits,  communication  of  results,  etc. 
EuroGenGuide  will  advance  these  objectives 
through  a  patient-led  collaborative  approach 
involving  stakeholders  from  patient  support 
groups  representing  a  wide  range  of  genetic 
(as 
conditions, 
partners  and  advisors)  in  the  field  of  genetics, 
biotechnology,  science  communication,  social 
sciences, bioethics and law. 

academic 

experts 

and 

Approach and methodology:

EuroGenGuide  will  create  a  multidisciplinary 
European  stakeholder  task  force  that  will  de-
velop the following:
1. 

The first European consensus based con-
sumer  manual  for  use  by  patients,  fam-
ily members of patients and the general 
public  who  are  recruited,  elected  or  co-
opted 
into  genetic/genome  research 
projects and clinical trials and/or will have 
to decide whether or not to undergo ge-
netic  testing. The  consumer  manual  will 
help  them  to  better  understand  the  im-
plications of informed consent in genetic 
research	and	testing;	it	will	inform	them	
about  issues  that  may  be  important  for 
them  to  consider  before  a  decision  is 
made and will provide sets of questions 
people may want to ask researchers/doc-
tors before they decide 

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EUROGENGUIDE

2. 

Educational  materials  to  prepare  re-
searchers and health professionals about 
how  best  to  enable  potential  research 
participants  and  patients  to  make  in-
formed  decisions,  and  to  raise  profes-
sionals’ awareness for patients/consumer 
concerns and needs. These materials will 
help to structure, harmonise and improve 
the  quality  of  professional  training,  and 
will fill the current gap in this field.

The  process  leading  to  the  compilation  of  the 
consumer  manual  and  the  creation  of  corre-
sponding  training  materials  for  professionals 
will  be  based  upon  an  extensive  dialogue  be-
tween  different  stakeholders  and  an  emphasis 
on  collaborative  partnership  and  open  discus-
sion.  By  developing  the  manual  and  training 
materials  in  this  way,  EuroGenGuide  will  em-
bark  upon  a  set  of  measurable  and  verifiable 
activities including:
•	

stakeholders 
of 

establishment	of	a	working	collaboration	
of  different 
including 
a 
European  patient 
network 
organisations  and  academic  experts  in 
the field of genetics, including bioethics, 
law	and	social	sciences;
issues	 pertinent	 to	
identification	 of	
in  genetic 
informed  decision-making 
the 
testing 
research  and 
consumer manual and training materials 
by	a	multidisciplinary	task	force;
the	 drafting	 of	 a	 culturally	 competent	
and  easily  understandable  consumer 
manual,  as  well  as  training  materials  for 
professionals  by  providing  a  structured 
internal  and  external  review  process  to 
ensure	consensus	and	validity;
effective	
dissemination.

for  both 

EU-wide	

delivery	

and	

•	

•	

•	

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Coordinator

alastair Kent
Genetic Interest Group Ltd
436 Essex Road
London, N1 3QP, UK
E-mail: mail@gig.org.uk

Partners 

domenico Coviello
University Hospital Milan
Milan, Italy

Robert Gerard
Rare Disorders Belgium
Jambes-Namur, Belgium

Ysbrand Poortman
World Alliance of Neuromuscular 
Disorder Associations-Europe
Baarn, Netherlands

Selena Freisens
Central and Eastern European Genetic Network
Konstanz, Germany

david Bennett
Cambridge Biomedical Consultants Ltd
Delft, Netherlands

Irmgard Nippert
Frauengesundheits-forschung
Muenster, Germany

Cor Osterwijk
Vereniging Samenwerkende 
Ouder- en Patiëntenorgani-saties
Soestdijk, Netherlands

Michael Livingston
Heart Europe
Hoofddorp, Netherlands

Rodney Elgie
Global Alliance for Mental Illness 
Advocacy Networks-Europe
Brussels, Belgium

Jean Georges
Alzheimer Europe
Luxemburg, Luxembourg

avril daly
Fighting Blindness
Dublin, Ireland

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SAFE

Special non-invasive advances in foetal and neonatal evaluation 

LSHB-CT-2004-503243
Contract No 
Project type  Network of Excellence 

EC contribution  e 12 000 000
Starting date   1 March 2004
duration  60 months

Website  www.safenoe.org

Background and objectives:

SAFE, a Network of Excellence (NoE), has drawn 
together European expertise in the area of non-
invasive prenatal diagnosis (NIPD) to provide sig-
nificant impetus to the objective of replacing the 
potentially  risky  procedures  of  amniocentesis 
and chorionic villus sampling. These techniques, 
which are currently the norm for prenatal diag-
nosis  of  common  chromosomal  disorders  (e.g. 
aneuploidies), impart a small but significant risk 
of  miscarriage  during  the  procedure.  SAFE  has 
drawn on a rich background of research on the 
presence and isolation of foetal cells in the ma-
ternal  circulation  that  has  existed  in  Europe  for 
decades, and a host of new research activity fol-
lowing the discovery of free foetal DNA in mater-
nal plasma in 1997. 

SAFE  has  served  to  centralise  and  unify  a  com-
mon  technical  approach  and  programme  of 
activities for a relatively new area of medical di-
agnostics, which has the potential to become a 
multibillion Euro market within the next decade. 
NIPD,  if  technically  proven,  would  completely 
replace invasive prenatal diagnosis, as the NIPD 
procedures impart no risk to the foetus and are 
of	 negligible	 cost	 difference	 per	 assay;	 further-
more, they would also reduce clinicians’ time in 
performing a surgical procedure to procure foe-
tal material for diagnosis. 

Some aspects of NIPD can be applied on a mass 
scale.  For  example,  prenatal  diagnosis  of  the 

foetal RhD blood group can reduce the level of 
usage  of  human-derived  blood  products  (pro-
phylactic  anti-D)  administered  during  preg-
nancy, to prevent immunisation of the mother 
to  a  paternally-inherited  blood  group  antigen 
on  foetal  red  blood  cells.  This  new  mass-scale 
diagnosis  requires  careful  cost-evaluation  of 
the impact on the different health economies in 
Europe, and one of SAFE’s areas of activity is the 
socioeconomic  evaluation  of  new  NIPD  tech-
nology and implementation. 

Mass-scale  adoption  of  NIPD  will  have  signifi-
cant  psychological  and  ethical  implications. 
Their impact on decision-making and policy de-
cisions that need to be considered are also core 
areas  of  activity  within  the  project.  In  particu-
lar, sex-selection was a specific focal point, the 
subject  of  detailed  evaluation  during  the  first 
half  of  the  project.  In  common  with  all  NoEs, 
SAFE hopes to create long-term partnerships of 
research groups in Europe that are performing 
and developing NIPD. 

Approach and methodology:

The project is divided into eight Work Packages 
(WPs),  five  of  which  explore  the  new  technol-
ogy necessary to develop a diverse range of new 
tests that will be applied to a range of disorders 
of the foetus and pregnancy, including Aneuploi-
dy  (Down’s  Syndrome),  foetal  sex,  blood  group, 
cystic  fibrosis,  β-thalassemia,  preeclampsia  and 
preterm labour. This involves the analysis of foe-

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DIAGNOSTICS

SAFE has been a key driver in the assembly of a 
critical  mass  of  European  researchers  that  will 
play a key role in its eventual introduction in the 
not too distant future. The NoE will also provide 
the infrastructure for new diagnostic laboratories 
wishing to implement NIPD, to adopt a standard-
ised approach. 

Main findings:

Since its launch, SAFE has held three large stand-
ardisation workshops for foetal sexing and RhD 
blood group genotyping using maternal plasma 
as  the  source  of  foetal  DNA.  These  workshops 
have  focused  on  a  standardised  approach  to 
DNA  extraction  and  standard  PCR  protocols  for 
foetal  sexing  and  RhD  blood  group  determina-
tion. SAFE has effectively delivered a set of pro-
tocols  within  the  public  domain  which  are  the 
consortium’s  recommendations  for  the  imple-
mentation of RhD and foetal sexing in diagnos-
tic laboratories worldwide. A workshop has also 
been held, in which state-of-the-art approaches 
for the automated detection of rare foetal cells in 
maternal blood were presented.

SAFE  is  also  focusing  on  the  implementation  of 
maternal  plasma-based  typing  for  single  gene 
disorders, in particular for β-thalassemia, and has 
organised  a  series  of  workshops  specifically  in-
tended to assess the implementation of NIPD for 
this disorder, which is widespread in southern Eu-
rope. Coupled with all maternal plasma research 

tal cells, free foetal DNA and foetally-derived pro-
teins that are present in maternal blood and offer 
diagnostic potential.

In some cases, such as foetal sex and RhD blood 
group,  the  technology  is  far  advanced,  and  is 
currently in routine diagnostic use. SAFE labora-
tories were amongst the first to implement such 
tests,  and  are  leading  a  series  of  workshops  to 
spread this standard of good practice within and 
outside the consortium. Research projects have a 
priority to aid the development of a new genera-
tion of diagnostic tests for chromosomal abnor-
mality,  which  may  involve  the  analysis  of  foetal 
cells  isolated  from  the  maternal  circulation,  the 
analysis of foetally-derived biomarkers in mater-
nal blood, or epigenetic markers present or ab-
sent on fetal DNA found in maternal plasma. 

The three socioeconomic WPs focus on the cur-
rent  and  potential  impact  of  NIPD  on  health 
economics, parental choice and ethics. NIPD will 
have a significant impact on all aspects of prena-
tal care, and it is critical that any controversial is-
sues are considered and debated openly, within 
and outside the consortium. A particular area of 
focus  has  been  the  potential  mass-scale  appli-
cation of foetal sexing, and the impact this may 
have in different cultures.

Expected outcome:

SAFE is currently driving the introduction of NIPD 
within the EC. SAFE workshops are attended by 
both SAFE and non-SAFE partners, with the sole 
objective of spreading the excellence generated 
within the project to the wider medical commu-
nity. Whilst the application of NIPD to the most 
common  request  for  prenatal  diagnosis  —  for 
foetal  chromosomal  disorders  —  is  technically 
challenging, SAFE hopes to generate internation-
ally competitive researchers in this field. Realisti-
cally, NIPD for Down’s syndrome and other chro-
mosomal disorders may not be widely available 
by the end of SAFE EC funding in 2009. However, 

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23

SAFE

programmes, is the production of a microfluidic-
based device for enrichment and/or purification 
of foetal DNA from this rich source of foetal mate-
rial. This technology exploits the known physical 
characteristic of foetal DNA in being significantly 
smaller than fragmented maternal DNA.

SAFE  has  a  large  laboratory  programme  for  the 
identification of protein biomarkers and chromo-
somal markers which are hyper or hypomethyl-
ated  in  foetuses.  Novel  protein  biomarkers  for 
Down’s syndrome, trisomy 18, foetal sex, preec-
lampsia and preterm labour have all been iden-
tified  and  are  currently  undergoing  validation 
using a large biobank of clinical samples that is 
being assembled by SAFE partners. This biobank 
will be of critical importance to prove the effec-
tiveness of any candidate biomarkers identified. 

Overall,  SAFE  has  implemented  a  framework  of 
health technology evaluation which can be test-
ed against any of the emerging technologies un-
der  investigation  by  the  consortium.  Psychoso-
cial and ethical evaluation of parental decisions 
have  revealed  significant  variation  between 
Western and Eastern cultures, which warrant fur-
ther investigation, especially as NIPD may bring 
diagnostic tools to the free market. 

Major publications:

Avent, N.D., Chitty, L.S., ‘Non-invasive diagnosis of 
fetal	sex;	utilisation	of	free	fetal	DNA	in	maternal	
plasma and ultrasound’, Prenatal Diagnosis, 2006, 
26(7):598-603.

Hall,  S.,  Chitty,  L.,  Dormandy,  E.,  et  al., ‘Undergoing 
prenatal 
syndrome: 
presentation  of  choice  and  information  in  Europe 
and Asia’, European Journal of Human Genetics, 2007.

for  Down’s 

screening 

Li,  Y.,  Zimmermann,  B.,  Rusterholz  ,C.,  et  al., 
‘Size  separation  of  circulatory  DNA  in  maternal 
plasma  permits  ready  detection  of  fetal  DNA 
2004, 
polymorphisms’, 

Chemistry, 

Clincal 

50(6):1002-11.

Li, Y.,  Di  Naro,  E., Vitucci,  A.,  et  al., ‘Detection  of 
paternally  inherited  fetal  point  mutations  for 
beta-thalassemia using size-fractionated cell-free 
DNA in maternal plasma’, Journal of the American 
Medical Association, 2005, 293(7):843-9.

Bianchi,  D.W.,  Avent,  N.D.,  Costa,  J.M.,  van  der 
Schoot,  C.E., ‘Noninvasive  Prenatal  Diagnosis  of 
Fetal  Rhesus  D:  Ready  for  Prime(r) Time’,  Obstet 
Gynecol, 2005, 106(4):841-4.

‘Direct 
Zhong,  X.Y.,  Holzgreve,  W.,  Hahn,  S., 
quantification  of  fetal  cells  in  maternal  blood 
by  real-time  PCR’,  Prenatal  Diagnosis,  2006,  26: 
850-854. 

Huang,  D.,  Nelson,  M.R.,  Zimmermann,  B., 
Dudarewicz,  L.,  Wenzel,  F.,  Spiegel,  R.,  Nagy,  B., 
Holzgreve,  W.,  Hahn,  S.,  ‘Reliable  detection  of 
trisomy 21 using MALDI_TOF mass spectrometry’, 
Genetics in Medicine, 2006, 8: 728-735.

Special  edition  of  Prenatal  Diagnosis,  2006, 
26(7):587-647.

Coordinator

Kate Hughes
University of Warwick
Research Support Services
University House
CV4 7AL Coventry, UK
E-mail: kate.hughes@warwick.ac.uk

Scientific coordinator

Sinuhe Hahn
Universität Basel
Department of Research laboratory 
for Prenatal Medicine
Spitalstrasse 21
4031 Basel, Switzerland
E-mail: shahn@uhbs.ch

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Peter Sedlmayr
Medizinische Universitaet Graz
Institute of Cell Biology, Histology and Embryology
Graz, Austria

Ellen van der Schoot
Stichting Sanquin Bloedvoorziening
Department of Experimental Immunohematology
Amsterdam, Netherlands

Ilona Hromadnikova
Charles University
2nd Medical Faculty
Prague, Czech Republic

andreas Plesch
Metasystems GmbH
Altlussheim, Germany

Françoise Soussaline
IMSTAR SA
Paris, France

Jim Schröder
University of Helsinki
Department of Biosciences 
Helsinki, Finland

andres Metspalu
Estonian Biocentre
Tartu, Estonia

Stan Urbaniak
University of Aberdeen
Academic Transfusion Medicine Unit
Aberdeen, UK

Laura Cremonesi
Fondazione Centro San Raffaele Del Monte Tabor
Unit of Genomics for Diagnosis of Human Pathologies
Milan, Italy

Partners

Maj Hulten
University of Warwick
Department of Biological Sciences
Coventry, UK

ala Szczepura
University of Warwick
Warwick Medical School
Coventry, UK

Neil avent
University of the West of England
Faculty of Applied Sciences
Bristol, UK

William Clocksin
Oxford Brookes University
Department of Computing
Oxford, UK

Theresa Marteau
King’s College London
Psychology and Genetics Research Group
London, UK

Lucia Savadori
Dipartimento di Scienze della Cognizione 
e della Formazione
Università degli Studi di Trento
Rovereto, Italy

Ciara O’Sullivan
Department of Chemical Engineering
Universitat Rovira i Virgili
Tarragona, Spain

Barbara Pertl
Medizinische Universitaet Graz
Department of Obstetrics and Gynaecology 
Graz, Austria

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25

SAFE

dorine Swinkels
University Nijmegen Medical Centre
Nijmegen, Netherlands

Jean-Marc Costa
American Hospital of Paris
Paris, France

ariadni Mavrou
National and Kapodistrian University of Athens
Department of Medical Genetics
Athens, Greece

Esther Guetta
Chaim Sheba Medical Center
Danek Gertner Institute of Human Genetics
Tel-Hashomer, Israel

Francisco alvarez
Hospital Universitario Central de Asturias
Laboratory of Biochemistry
Oviedo, Spain

Nicholas Fisk 
Imperial College
Paediatrics, Obstetrics and Gynaecology
London, UK 

Marina Kleanthous
Cyprus Institute of Neurology and Genetics
Thalassaemia Department
Nicosia, Cyprus

Philippos Patsalis
Cyprus Institute of Neurology and Genetics
Department of Cytogenetics
Nicosia, Cyprus

Peter Soothill
University of Bristol
Obstetrics and Gynaecology
Bristol, UK

andres López Bernal
University of Bristol
Dorothy Hodgkin Building
Bristol, UK

Michael Siegrist
Universität Zürich
Division of Psychology
Zurich, Switzerland

Gian Carlo di Renzo
Universitá Degli Studi di Perugia
Department of Medical-Surgical Specialties and Public 
Health
Perugia, Italy

Tobias Legler
Georg-August-Universität Göttingen
Transfusionsmedizin
Göttingen, Germany

Patrizia Paterlini-Bréchot and
 Jean-Jacques Toulmé
Institut National de la Santé et
 de la Recherche Médicale (INSERM)
Paris and Bordeaux, France

Mauro Buser
Statistik Buser
Riehen, Switzerland

Maurizio d’Esposito
Institute of Genetics and Biophysics
Naples, Italy

alastair Kent
Genetics Interest Group
London, UK

Janet Grant
Open University
Open University Centre for Education in Medicine
Milton Keynes, UK

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DIAGNOSTICS

Yiming Wang
Sun Yat-Sen University
Department of Medical Genetics
Guangxhou, People’s Republic of China

Madhulika Kabra
All India Institute of Medical Sciences
Pediatrics Genetics Subdivision
New Delhi, India

Geoff daniels
National Blood Authority
International Blood Group Reference Laboratory
Bristol, UK

Martin Olsson
Lund University Hospital
Lund, Sweden

Charles Rodeck
University College London
Obstetrics and Gynaecology
London, UK

Lyn Chitty
University College London
Institute of Child Health
London, UK

Lars Larsen 
Københavns Universitet
Department of Medical Genetics
Copenhagen, Denmark

Tadeusz Tyszka
Wyższa Szkoła Przedsiębiorczości i Zarządzania im. 
Leona Koźmińskigo (LKAEM)
Warsaw, Poland

Etienne Mullet
Ecole Pratique des Hautes Etudes
Toulouse, France

Renate Burgemeister
P.A.L.M. Microlaser Technologies GmbH
Bernreid, Germany

Giovanni Romeo
Universitá degli Studi di Bologna
Bologna, Italy

Elisabeth Blennow and The-Hung Bui
Karolinska Institutet
Department of Molecular Medicine
Stockholm, Sweden

Jan Schouten
Microbiology Research Centre-Holland
Amsterdam, Netherlands

Beverly Searle
Rare Chromosome Disorder Support Group (Unique)
Caterham, UK

Michael Christiansen and Paal Skytt andersen
Statens Serum Institut
Copenhagen, Denmark

Ray O’Connor
Genomed Ltd
Paisley, UK

Vincenzo Cirigliano
General Lab
Department of Molecular Genetics
Barcelona, Spain

Cees Oudejans
VU Medical Centre
Amsterdam, Netherlands

Olivia Willcocks
Waypoint Systems Ltd
Shrewsbury, UK

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QuAGSIC

Quantitative analysis of genes in single cells

Contract No 
Project type 

LSHB-CT-2006-037293
SME_Specific Targeted 

EC contribution  e 1 433 600

  Research Project 

Starting date   1 September 2006

duration  24 months

Website  www.uni-ulm.de/quagsic/index.php

Background and objectives:

The partners of the QuAGSIC project will develop 
methods  and  instruments  to  analyse  the  copy 
number  of  nucleic  acid  sequences  down  to  the 
single  cell  /  single  molecule  level,  with  the  goal 
of  developing  an  early  diagnosis  system  for  the 
children’s  disease  hemophagocytic  lymphohis-
tiocytosis  (HLH).  The  underlying  technique  is 
amplification-based counting (ABC), enabling the 
quantification of the copy number of genetic se-
quences with a resolution of about 100 base pairs 
in single cells. The method provides a resolution, 
i.e. orders of magnitudes higher than for fluores-
cence in situ hybridisation (FISH), and works quan-
titatively with much lower sample amounts than 
quantitative polymerase chain reaction (PCR). 

To  prove  ABC’s  effectiveness  in  clinical  applica-
tions, the partners will develop a single cell ma-
nipulation  unit  that  picks  cells  from  a  solution 
and transfers them onto an integrated PCR and 

Picture of a semi-automatic 3D cellector

hybridisation  slide  (AmpliGrid).  The  AmpliGrid 
contains  dried-on  PCR  reagents,  as  well  as  hy-
bridisation  probes  to  detect  the  presence  and 
specificity  of  the  PCR  products. The  single  cells 
on  the  AmpliGrid  will  then  be  processed  auto-
matically in an integrated PCR and hybridisation 
machine  (AmpliHyb).  Clinical  samples  will  be 
investigated,  in  which  copy  number  deviations 
are pathologic as in genetic diseases. As a model 
system,  QuAGSiC  chose  HLH  which  is  hard  to 
diagnose  and  fatal  without  specific  therapeutic 
measures, as well as trisomy 21 which is relevant 
in prenatal and postnatal diagnostics. 

Many  basic  questions  in  biology  and  medicine 
demand  methods  for  the  analysis  of  the  basic 
unit of life: the single cell. The QuAGSIC partners 
will  thus  develop  methods  and  instruments  to 
analyse  the  genetic  content  of  single  cells  with 
regard to the quantitative variation of sequences 
(copy number variations), as well as the qualita-
tive  variation  of  sequences  (single  nucleotide 
polymorphisms).

Once the project is finalised, QuAGSIC will put on 
the  market  machines  and  consumables  that  al-
low gene measurements down to the single cell 
level with high precision, in a parallel format (an 
Ampligrid can accommodate 48 cells), with high 
amount of automation.

Role of SMEs

The three SMEs in QuAGSIC have central roles:

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DIAGNOSTICS

Without doubt, the single cell is the basic entity 
of a living organism (or it is even the whole or-
ganism). Therefore, applying the methods men-
tioned above to single cells is not only a techno-
logical challenge but it is also the critical task in 
system  biology  for  the  coming  years,  especially 
for addressing medical diagnostics in the regime 
of single cells. Single cell analysis becomes more 
and more attractive because of limited cell popu-
lation  of  interest,  cell  heterogeneity  of  samples 
or when cells are isolated automatically as early 
dissemination  of  tumour  cells.  Hopefully,  the 
QuAGSIC effort will bring breakthrough analytic 
tools  and  systems  for  prevention,  diagnosis,  or 
monitoring of a broad range of diseases.

Coordinator 

Claude Weisbuch
Genewave SAS
XTEC - Bâtiment 404
Ecole Polytechnique
91128 Palaiseau, France
E-mail: claude.weisbuch@polytechnique.fr

Partners 

Wolfgang Mann
Advalytix AG
Munich, Germany

Stefan Niehren
Molecular Machines & Industries AG (MMI)
Glattbrugg, Switzerland

andres Metspalu
Estonian Biocentre
Tartu, Estonia

Marion Schneider
Clinical Center University of Ulm
Ulm, Germany

Diagnostics - Genetic Testing and Biomarkers

29

•	

•	

•	

Imaging of an Ampligrid

MMI	(Molecular	Machines	&	Industries)	is	
developing an automated cell picker from 
its  semi-automatic,  two  dimensional  cell 
selection  tool,  capillary-based  cell  han-
dling system, to a fully automated three-
dimensional  cell  finding  and  sorting  sys-
tem (cellector 3D).
Adavlytix	is	using	its	photolithographically	
structured microscope slide AmpliGridTM 
suitable  for  performing  48  different  1µl 
PCR reactions on the same substrate. The 
special  AmpliGridTM  surface  chemistry 
will be used to define a physical platform 
for  the  integrated  PCR  and  hybridisation 
at the single cell level.
Genewave	 is	 developing	 an	 integrated	
system which will allow the performance 
of both the PCR and optical detection of 
hybridisation  in  an  unsupervised  single 
machine. 

Expected outcome:

By the end of the project, the partners will be in 
a position to quickly market systems that allow 
gene analysis at the single cell level at low cost, 
with high speed, reliability and throughput.

Potential applications:

The technologies developed in QuAGSIC demand 
a minimum amount of material to be  analysed. 

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IBDchip

Usefulness of a new dNa array (IBdchip) to predict clinical course, development of 
complications and response to therapy in patients with inflammatory bowel disease (IBd)

Contract No 
Project type 

LSHB-CT-2006-37319
SME-Specific Targeted

EC contribution  e 2 467 314

  Research Project 

Starting date   1 december 2006

duration  36 months

Website  http://ibdchipproject.eu

Background and objectives:

resulting  in  better  clinical  outcomes  and  im-
proved cost-effectiveness of treatment.

The IBDchip project targets the development of 
an easy-to-use DNA array and accompanying in-
novative chip reading device. The IBDchip will be 
a non-invasive tool with the capacity to simulta-
neously analyse around 100 relevant mutations 
to predict the following:
clinical	evolution;
•	
risk	 of	 developing	 IBD-related	 complica-
•	
tions;
likelihood	of	responding	to	certain	drugs	
for  each  IBD  (inflammatory  bowel  dis-
ease) patient.

•	

IBD  includes  Crohn’s  disease  (CD)  and  ulcera-
tive  colitis  (UC).  Both  are  increasingly  common 
chronic illnesses, and are currently impacting the 
lives  of  nearly  1  million  patients  in  Europe.  CD 
and UC affect patients early in life, seriously im-
pairing their quality of life, and resulting in enor-
mous personal, social and economic costs.

There  is  evidence  suggesting  that  genetic  fac-
tors play a key role in IBD pathogenesis, pointing 
towards a polygenic mode of inheritance for CD 
and UC. To date, however, studies have only ad-
dressed the influence of single mutations on IBD, 
resulting in a poor prediction of clinical course or 
response to therapy in individual patients. 

Role of SMEs

Progenika  Biopharma  SA,  one  of  the  two  SMEs 
involved in the project, has been the main driver 
of IBDchip, having originated the idea, and iden-
tified and engaged the partners. It will perform 
tasks  that  use  a  major  part  of  the  EC  contribu-
tion  to  the  budget.  Building  on  development 
work done for their existing products, Progenika 
will use this project to validate new technology 
and knowledge, as well as to create a prototype 
IBDchip  that  has  been  clinically  tested,  and  is 
therefore  close  to  final  commercialisation.  The 
innovative  prototype  chip  will  give  Progenika 
a  clear  advantage  over  competitors,  since  they 
will be the first to bring to the market their new 
knowledge-intensive product. 

Innopsys, the second SME involved in the project, 
will develop a slide reader to be commercialised 
alongside  the  IBDchip. This  slide  reader  will  be 
smaller  and  much  cheaper  than  existing  ma-
chines  and  will  take  the  company  into  a  new 
market  (the  reading  of  DNA  arrays)  while  rein-
forcing  its  scientific  and  technological  capacity 
for future innovations. 

Expected outcome:

The main aim of this project is to provide doctors, 
for the first time, with a non-invasive, predictive 
tool to optimise treatment in IBD patients, thus 

IBDchip anticipates the following results:
•	

a	fully	validated	innovative	prototype	IBD-

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DIAGNOSTICS

(i.e. in 2011). These illnesses are increasing, and 
the  project  team  expects  that  the  IBDchip  and 
new reader will be embedded as a routine part 
of treatment over the coming decade.

It is also probable that the IBDchip project R&D 
processes and the resulting technologies can be 
adapted  to  address  problems  in  the  prediction 
and treatment of other polygenic inflammatory 
conditions,  such  as  rheumatoid  arthritis.  Over 
the duration of the project, the team will use the 
consortium and its work as the foundation for fu-
ture projects, to explore other potential applica-
tions of the technology. 

Ccoordinator

Miquel Sans
Hospital Clínic / IDIBAPS
Department of Gastroenterology 
Barcelona, Spain
E-mail: msans@clinic.ub.es

Partners

Marta artieda
Progenika Biopharma SA
Parque Tecnológico de Zamudio
Derio, Spain

Stéphane Le Brun
Innopsys SA
Carbonne, France

derek Jewell
University of Oxford
Nuffield Department of Medicine and Oxford GKP
Oxford, UK

Severine Vermeire
The University Hospital in Leuven
Leuven, Belgium

Diagnostics - Genetic Testing and Biomarkers

31

Analysing the results

chip that will give doctors vastly improved 
capacities to make more accurate individ-
ualised predictions of clinical outcomes of 
IBD and to choose the optimum and most 
cost-effective	therapy	for	each	patient;
a	new	DNA	array	reader	that	will	be	faster	
and one fifth of the price of existing ma-
chines, to optimise the reading of the IBD-
chip	and	help	make	it	ubiquitous;
a	clear	understanding	of	the	pathways	to	
clinical  service,  ethical  and  legal  issues, 
and  cost-effectiveness  of  the  IBDchip, 
which will result in a maximum uptake of 
the	IBDchip	in	routine	clinical	practice;
results	 for	 the	 academic	 partners	 will	 be	
new knowledge derived from the research 
undertaken in the project and published 
in various leading academic publications.

•	

•	

•	

Potential applications:

The IBDchip will have very wide application across 
the  EU  and  beyond. The  team  has  the  working 
objective of using the IDBchip for 15% of both UC 
and CD patients (a total of approximately 320 000 
people) within 3 years of the end of the project 

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IBDchip

Salvador Peña
VU University Medical Center
The Laboratory of Immunogenics
Department of Pathology
Amsterdam, Netherlands

Stefan Schrei
University Hospital Schleswig-Holstein
The Institute for Clinical Molecular Biology (ICMB)
Keil, Germany

Milan Lukas
The University Hospital in Prague
Prague 2, Czech Republic

Silvio danese
Istituto Clinico Humanitas
Milan, Italy

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DIAGNOSTICS

AntePrion

development of a preclinical blood test for prion diseases

Contract No 
Project type 

LSHB-CT-2006-019090
Specific Targeted 
  Research Project

EC contribution  e 2 450 000
Starting date   1 June 2006

duration  36 months

Website  www.antePrion.eu

Background and objectives:

There are currently no tests for early prion diag-
nosis. Such tests would help to prevent transmis-
sion  through  blood,  biologicals,  the  food  chain 
and  medical  procedures,  as  well  as  to  identify 
candidates  for  emerging  anti-prion  therapies 
and  prophylactic  procedures,  especially  among 
silent carriers of pathogenic PrP mutations. Cur-
rent tests are based on the identification of PrPSc 
or of characteristic pathologies in brain samples 
collected  post-mortem.  Recent  advances  have 
shown  that  minute  amounts  of  PrPSc  exist  in 
body fluids, such as blood. Although these PrPSc 
levels are too low to be detected reliably by exist-
ing methods, they point to the feasibility of using 
these fluids with improved methods. 

Backed  by  a  powerful  consortium  that  is  com-
prised  of  partners  with  proven  clinical,  experi-
mental  and  industrial  achievements,  AntePrion 
is  seeking  to  develop  methods  for  the  preclini-
cal detection of prions in body fluids, based on 
PrPSc and novel surrogate (non-PrP) markers of 
prion diseases. PrPSc detection in body fluids will 
be  achieved  by  systematically  improving  every 
step in the process:
•	

sample	fractionation:	fluids	will	be	separat-
ed	to	identify	fractions	enriched	in	PrPSc;	
PrPSc	concentration;
PrPSc	amplification;
PrPSc	detection.	

•	
•	
•	

Surrogate  markers  and  molecular ‘signatures’  of 
prion diseases will be identified using novel sen-
sitive proteomic and genomic approaches, such 
as  SELDI,  MALDI  and  DNA  microarrays.  Proprie-
tary software will be developed to analyse these 
emerging signatures.

Prions are infectious proteins. There is currently no 
effective  therapy  for  prion  diseases,  collectively 
called transmissible spongiform encephalopathies 
(TSEs), and the disease is lethal. There is no sensi-
tive and reliable preclinical or even ante-mortem 
diagnostic test for detection of prions in blood or 
other  body  fluids.  Post-mortem  diagnosis  relies 
on pathological findings in the CNS and especially 
on the detection of PrPSc. Due to the difficulty of 
detecting low levels of prion infectivity and PrPSc, 
little is known about prion infectivity and PrPSc in 
peripheral tissues. The sensitivity of existing PrPSc 
detection methods is insufficient for the identifica-
tion of PrPSc in body fluids (blood, CSF, milk) or in 
non-neural tissues. The use of 14-3-3 and S-100 as 
surrogate markers to PrPSc has been proposed as 
the basis for diagnostic TSE tests, but such mark-
ers are not very specific. 

AntePrion is therefore striving to find novel TSE-
specific markers using novel mass spectrometric 
and  genomic  approaches,  as  well  as  immuno-
logical  methods.  Thus,  the  search  for  non-PrP 
markers,  in  parallel  with  improved  procedures 
for detecting both the protease-sensitive (s) and 
-resistant (r) PrPSc, may give rise to a reliable pre-
clinical test.

Diagnostics - Genetic Testing and Biomarkers

33

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AntePrion

Approach and methodology: 

AntePrion’s  goal  is  to  use  a  combination  of  re-
search and engineering approaches to attain the 
following goals: 
•	

improve	 PrPSc	 detection	 in	 blood	 and	
fluids;	
discover	 novel	 proteomic,	 genomic,	 and	
immunologic	surrogate	markers	of	TSE;
integrate	these	advances	into	a	preclinical	
test for TSEs. 

•	

•	

To  achieve  these  goals,  experts  in  the  field  of 
prions, cell biology, antibody discovery and pro-
duction, and diagnosis are present in the consor-
tium, as are end-users, a national blood bank, a 
national biosafety regulatory agency and a cen-
tre for neurodegenerative diseases. 
Four  types  of  activities  can  be  discerned  in  An-
tePrion: 
1. 

 collection and preparation of human and 
animal	samples;
analysis of samples (finding enriched frac-
tions,	discovering	surrogate	markers);
development of novel detection systems 
(e.g. cultured cells), reagents (such as anti-
bodies)	and	novel	software;
integration and assessment of the devel-
oping technologies. 

2.  

3. 

4.  

The principal aim is to devise a preclinical blood 
test to do the following:
•	

identify	human	TSE	cases	early	enough	so	
that emerging therapies can be adminis-
tered in time (i.e. prior to extensive neuro-
degeneration);	
prevent	 transfusion	 of	 tainted	 human	
blood;	
remove	 TSE-tainted	 meat	 and	 animal	
products from the food chain.

•	

•	

Expected outcome:

With  fluorescence-activated  cell  sorting  (FACS), 
subpopulations of white blood cells (WBCs) from 

34

Diagnostics - Genetic Testing and Biomarkers

humans and animals will be isolated, and PrPSc in 
fractionated populations of cells will be measured 
using  conformation-dependent 
immunoassay 
(CDI). Localisation of PrPSc will be studied by im-
munoelectron  microscopy.  The  AntePrion  part-
ners  expect  to  reveal  the  blood  cell  type(s)  with 
a high PrPSc content. Enrichment gained by FACS 
may  yield  a  blood  test  for  PrPSc  detection  at  a 
phase before any clinical symptoms appear. Mass 
spectrometry  will  be  used  to  obtain  profiles  of 
molecules from body fluids, as well as brain and 
muscle from prion-infected animals which bind to 
different chromatographic surfaces. 

The aim is to identify prion-infection specific bi-
omarkers, most likely proteins. Measurements of 
such a biomarker might provide a target for de-
velopment of a non-PrP based ante-mortem test. 
Alternatively, specific patterns of protein expres-
sion or ‘signatures’ detected by mass spectrom-
etry might be used as the basis of such a test. 

European countries aim for high consumer pro-
tection standards and target high standards con-
cerning the safety of blood and blood products. 
The presence of prion infections in cattle (sheep 
and goats) and the transmission of the disease to 
human  beings  seriously  threaten  public  health. 
Low levels of PrPSc have been detected in WBCs 
in the blood circulation of prion-infected animals. 
Moreover, recent data suggest that vCJD can be 
transmitted  from  humans  to  humans  via  blood 
or blood products. 

AntePrion’s initiative will help to establish mark-
ers  and  methods  for  the  early,  preclinical  diag-
nosis  of  prion  infections  in  animals  and  human 
beings,  and  will  lead  to  the  development  of  a 
new  and  sensitive  ante-mortem  diagnostic  test 
for prion diseases. Since several partners are in-
volved  in  national  and  international  research 
activities through networks and control/surveil-
lance programmes on other infectious or trans-
missible diseases, AntePrion will have a large im-
pact on public health.

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DIAGNOSTICS

Coordinator 

Peter J. Peters
Nederlands Kanker Instituut
Department of Tumor Biology 
Plesmanlaan 121 – H4
1066 CX Amsterdam, Netherlands
E-mail: p.peters@nki.nl

Partners 

albert Taraboulos
Department of Molecular Biology
Hebrew University Hadassah Medical School
Jerusalem, Israel

Krister Kristensson
Karolinska Institutet
Department of Neuroscience
Stockholm, Sweden

Jesus Requena
Universidade de Santiago de Compostela
Prion Research Unit
Santiago, Spain

R. G. Will
University of Edinburgh
National CJD Surveillance Unit
Edinburgh, UK

Markus Otto
University of Ulm
Medical Faculty
Department of Neurology
Ulm, Germany

Eva Mitrova
Slovenska Zdravotnicka Univerzita
Department of Prion diseases and
National Reference Centre for prion diseases
Institute of Preventive and Clinical Medicine
Bratislava, Slovakia

Major publications:

Dollinger, S., Löber, S., Klingenstein, R., Korth, C., 
Gmeiner,  P., ‘A  Chimeric  Ligand  Approach  Lead-
ing to Potent Anti-Prion Active Acridine Deriva-
tives:  Design,  Synthesis  and  Biological  Inves-
tigations’,  Journal  of  Medicinal  Chemistry,  2006, 
49:6591-659.

Klingenstein,  R.,  Melnyk,  P.,  Leliveld,  S.R.,  Ryke-
busch, A., Korth, C., ‘Similar structure activity rela-
tionships in the antiprion and antimalarial activ-
ity  of  quinoline  derivatives’,  Journal of  Medicinal 
Chemistry, 2006, 49:5300-8.

Collins, S.J., Sanchez-Juan, P., Masters, C.L., Klug, 
G.M.,  van  Duijn,  C.M.,  Poleggi,  A.,  Pocchiari,  M., 
Almoti, S., Cuadrado-Corrales, N., de Pedro Cues-
ta,  J.,  Budka,  H.,  Gelpi,  E.,  Glatzel,  M., Tolnay,  M., 
Hewer, E., Zerr, I., Heinemann, U., Kretszchmar, H., 
Jansen,  G.H.,  Olsen,  E.,  Mitrova,  E.,  Alperovitch, 
A.,  Brandel,  J.P.,  Mackenzie,  J.,  Murray,  K.,  Will, 
R.G.,  ‘Determinants  of  diagnostic  investigation 
sensitivities across the clinical spectrum of spo-
radic Creutzfeldt-Jakob disease’, Brain, 2006, 129: 
2278-2287.

Cepek,  L.,  Brechlin,  P.,  Steinacker,  P.,  Mollenhau-
er,  B.,  Klingebiel,  E.,  Bibl,  M.,  Kretzschmar,  H.A., 
Wiltfang,  J.,  Otto,  M., ‘Proteomic  Analysis  of  the 
Cerebrospinal Fluid of Patients with Creutzfeldt-
Jakob  Disease’,  Dementia  and  geriatric  cognitive 
disorders, 2007, 23:22-8

Campana, V., Caputo, A., Sarnataro, D., Paladino, 
S.,  Tivodar,  S.,  Zurzolo,  C.,  ‘Characterization  of 
the  properties  and  trafficking  of  an  anchorless 
form  of  the  prion  protein’,  J  Biol  Chem,  2007, 
282:22747-56.

Fasano, C., Campana, V., Schiavo, G, and Zurzolo, 
C,. ‘Gene expression profiles of quinacrine-cured 
prion-infected  mouse  neuronal  cells’,  J.  Neuro-
chemistry, 2008, epub Jan 8.

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AntePrion

Chiara Zurzolo
Institute Pasteur
Department of Cell Biology and Infection/
Unité Trafic Membranaire et Pathogenèse
Paris, France

Carsten Korth
Heinrich Heine Universität Düsseldorf
Department of Neuropathology
Düsseldorf, Germany

Michael Baier and Georg Pauli
Robert-Koch-Institut
Berlin, Germany

Lothar Stiz
Friedrich-Loeffler-Institut –
 Federal Institute for Animal
Health
Greifswald - Insel Riems, Germany

Martin Wiesenfeldt
Matrix Advanced Solutions Germany GmbH
Göttingen, Germany

H. Schuitemaker
Stichting Sanquin Bloedvoorziening
Amsterdam, Netherlands

36

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DIAGNOSTICS

TSEUR

an integrated immunological and cellular strategy for sensitive  
TSE diagnosis and strain discrimination

Contract No 
Project type 

LSHB-CT-2006-018805
Specific Targeted 
  Research Project

EC contribution  e 1 750 000 
Starting date   1 June 2006

duration  36 months

Website  www.pathol.uzh.ch/tseur

Background and objectives:

Prion  infections,  or  Transmissible  Spongiform 
Encephalopathies  (TSEs),  result  in  progressive, 
fatal  neurodegeneration.  No  effective  therapies 
are available, and medical interventions, possibly 
including  blood  transfusions,  have  resulted  in 
human-to-human  transmission  of  prions.  How-
ever, no biomarkers are available for the preclini-
cal diagnosis of prion infection in body fluids. All 
approved methods of diagnosis rely exclusively 
on  the  detection  of  pathological  prion  protein 
(PrPSc), which may not be present in all TSEs. The 
TSEUR  consortium  proposed  to  develop,  vali-
date, and exploit innovative reagents and tech-
nologies that will address the above challenges, 
within the following three areas:
•	
•	
•	

enhanced	detection	of	PrPSc;	
direct	measurement	of	prion	infectivity;
validation	of	new	TSE	biomarkers	in	body	
fluids. 

Each partner brings to the TSEUR project a signif-
icant	body	of	existing	knowledge	and	data;	this	
includes a potent new panel of picomolar-affin-
ity  anti-PrP  monoclonal  antibodies  for  a  variety 
of PrP domains. Their work will enable the highly 
sensitive detection of PrPSc and discrimination of 
prion strains (‘epitope coding’). The project part-
ners  will  field-test  the  validity  of  their  recently 
identified secreted surrogate markers — whose 
levels are significantly higher in preclinical prion 
infections  ¬—  for  identifying  potentially  con-
taminated body fluids. Immuno-PCR technology 

will be explored as a means to enhance the sen-
sitivity threshold of each assay. 

Finally, the partners will extend the use of scrapie 
cell  assays  to  the  rapid  and  sensitive  detection 
of  actual  prion  infectivity  under  different  sets  of 
conditions. Ongoing work indicates that all Work 
Packages  are  highly  feasible. TSEUR  will  develop 
innovative diagnostic technologies to address the 
current gaps in prion detection. The project’s goals 
are to enhance the safety of the blood supply, to 
provide  minimally  invasive  techniques  for  diag-
nosing  human  and  animal  TSEs,  and  to  develop 
highly sensitive tools for identifying prion strains.

The current need for sensitive tests to detect pri-
ons or the surrogate markers of prion diseases in 
affected  individuals  before  the  clinical  onset  of 
disease, has intensified the search for new tech-
nologies  and  tools.  Currently,  diagnosis  relies 
exclusively on the detection of PrPSc which may 
not be present in all TSEs. Significantly, even by 
using  detection  methods  specifically  for  PrPSc, 
no sensitive tests are available to detect prions in 
the blood or urine of affected individuals, such as 
human  CJD  patients  or  scrapie-infected  sheep. 
Therefore, not only are new tools required for de-
tecting PrPSc in various body fluids or organs at 
different stages of the disease, but also new sur-
rogate  markers  are  needed  that  can ‘sense’  the 
presence of prions.

Therefore, in order to detect affected individuals 
at  the  subclinical  stage,  it  is  crucial  to  find  sur-

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37

 
 
 
 
 
 
 
 
TSEUR

rogate markers other than PrPSc. Moreover, the 
appearance of new prion strains that do not dif-
fer in their primary amino acid sequence but are 
believed to vary in their three-dimensional struc-
ture, shows that there is a big demand for tools 
that  enable  scientists  to  differentiate  among 
prion strains. Prions strains possess different or-
gan tropisms, can be replicated in different hosts 
with different efficiency, and can induce diseases 
with  varying  incubation  times,  lesion  profiles, 
etc. Therefore,  it  will  be  of  great  importance  to 
generate tools that can differentiate between a 
range of prion strains. 

The TSEUR consortium proposes to develop, vali-
date, and exploit innovative reagents and tech-
nologies that will address the current challenges 
faced by prion diagnostics in three areas: 
•	

developing	 innovative	 diagnostic	 tech-
nologies  addressing  the  current  gaps  in 
prion	detection;	
providing	 minimally	 invasive	 diagnostic	
techniques  for  human  and  animal  TSEs 
(e.g.  detection  of  prions  in  blood  and 
urine	 of	 affected	 individuals;	 surrogate	
markers found in urine or blood that can 
be used to identify subclinically infected 
individuals);	
producing	highly	sensitive	tools	for	iden-
tifying prion strains.

•	

•	

Approach and methodology: 

Work Package (WP) 1 investigates whether other 
inflammatory conditions will give rise to ectopic 
prion replication (e.g. granulomas). For this rea-
son, the partners have established a granuloma 
mouse model, in which granulomas are induced 
subcutaneously,  and  prions  are  peripherally 
administered  to  mice  with  granulomatous  in-
flammation. They also set up in vitro-based cell 
systems  (e.g.  stable  transformation  of  various 
neuronal  and  non-neuronal  cell  lines  with  or 
without  PrP  expression)  to  investigate  prion 
replication competence of various cell lines (e.g. 

38

Diagnostics - Genetic Testing and Biomarkers

for sheep scrapie). This is expected to lead to in 
vitro assays for monitoring infectivity in various 
organs,  infectious  properties  of  various  prion 
strains  (e.g.  ovine  prions)  and  other  species,  in-
cluding  elk  and  deer  with  Chronic Wasting  Dis-
ease or sheep scrapie).

In WP2, the partners are attempting to map re-
gions  that  could  be  of  importantance  to  prion 
conversion  and  replication.  To  this  end,  they 
have  generated  various  PrP  mutants  with  addi-
tional  disulphide  bridges  which  induce  folding 
and  different  three-dimensional  structures  at 
the  particular  sites  investigated. The  disulphide 
mutants will be expressed in vitro, purified and 
analysed by mass spectrometry and by NMR. Af-
ter  transfection  into  cell  lines,  prion  replication 
competence  of  the  respective  mutants  will  be 
analysed in a scrapie cell assay-like set-up. 

WP3  and  WP4  are  producing  highly  sensitive 
monoclonal  antibodies  for  human  Cystatin  F,  a 
surrogate  marker  of  transmissible  spongiform 
encephalopathy found in body fluids of infected 
individuals,  including  cerebral  spinal  fluid  and 
urine.  The  antibody  will  be  used  to  establish  a 
diagnostic test. In addition, the partners will de-
liver a technological platform in which low levels 
of the antigen are amplified by a PCR technology 
(quantitative  immuno-PCR).  Tools  will  be  pro-
duced  for  the  benefit  of  the  whole  consortium 
(POM antibodies). 

The  extraneuronal  prion  distribution  in  scrapie 
infected sheep is being investigated in WP5. Sev-
eral different methods are being followed that in-
clude the analysis of organs and body fluids from 
both healthy sheep and those infected by scrapie 
by natural means. The partners are also analysing 
prion distribution and body fluids including milk, 
blood and urine in sheep artificially infected with 
scrapie. PrPSc deposition is monitored by NaPTA 
precipitation  followed  by  conventional Western 
blot analysis and PMCA. 

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DIAGNOSTICS

Furthermore,  inoculation  studies  with  urinary 
proteins  or  other  tissue  homogenates  (e.g.  kid-
ney, mammary gland) are being performed. In or-
der to investigate whether inflammation induces 
prion deposition in previously prion-free organs, 
mammary glands derived from scrapie-infected 
sheep with mastitis were isolated. Homogenates 
of these organs are transmitted into bank voles. 
Similarly, inflamed lungs are monitored, analysed 
and  transmitted  into  susceptible  ruminants  to 
examine infectivity. In addition, milk proteins are 
transmitted  into  New  Zealand  lambs,  believed 
to be devoid of scrapie. Moreover, urine will be 
carefully analysed for prion infectivity and PrPSc. 

1. 

2. 

Generation  of  retroviral  vectors/superna-
tants for: 
•	 Myc	tagged	mouse	PrP	(92,	95,	97,	190, 
	 195,	202,	230);	
•	 Flash	tagged	mouse	PrP	(97,	202,	230);	
•	 ovine	PrP	(VRQ,	ARQ,	ARR);	
•	 3F4	antibody	epitope	tagged	ovine	
  PrP (VRQ, ARQ, ARR). 
Generation of cell lines stably expressing: 
•	

tagged	mouse	PrP	
(HpL3-4	MoPrP-Myc	and	-Flash);	

•	 ovine	PrP	(HpL3-4	and	RK13	
	 ovPrP-VRQ,	-ARQ,	-ARR);	
•	

tagged	ovine	PrP
(HpL3-4 ov3F4-VRQ, -ARQ, -ARR). 

By using TaqMAN analysis, a sensitive and quali-
tative assay will be established in WP6, that can 
differentiate among the various Maedi Visna vi-
ruses responsible for inflammatory disorders, in 
sheep,  for  example.  Furthermore  nanotechnol-
ogy  will  be  specifically  used  as  a  detection  sys-
tem for prions. In addition, WP6 provides various 
tissues  and  body  fluids  of  naturally  scrapie-in-
fected and healthy sheep used for the investiga-
tion of peripheral prion pathogenesis, as well as 
for  establishing  various  systems  (immuno-PCR) 
to detect prions within organs or body fluids of 
scrapie-infected ruminants. 

Main findings:

WP 1 has established a mouse model with long-
lasting, subcutaneous granulomas. The partners 
can  show  that  after  peripheral  prion  adminis-
tration  these  granulomas  have  gained  prion 
replication  competence.  Furthermore,  they  can 
demonstrate  that  the  stromal  compartment  in 
the granuloma is responsible for expressing the 
cellular  prion  protein.  Additionally,  histoblot 
analysis  has  localised  PrPSc  to  the  granuloma-
tous nodules which are composed of epitheloid 
macrophages, fibroblasts and dendritic cells. 

In WP2, cells expressing various forms of the pri-
on protein were established and analysed: 

Confirmation of cell surface expression of all con-
structs,  as  depicted  above,  except  202PrPFlash, 
as  well  as  subcloning  of  RK13  cells  expressing 
ovPrP was performed.

In WP3 and WP4, multiple human Cystatin F-spe-
cific antibodies were isolated and the strongest 
binders have been identified by ELISA. Sequence 
analysis  of  the  antibodies  shows  that  most  are 
related to one another. The 3 strongest binders 
are being expressed in 293T cells and have been 
purified as single chain FC fusion proteins while 
12 high binders from the last sort experiment are 
being  further  investigated.  These  antibodies  or 
single  chain  fusion  proteins  are  currently  being 
evaluated in an ELISA-like set-up.

The  first  batches  of  POM  antibodies  were  pro-
duced as a basis for providing Abs to the whole 
TSEUR consortium (POM1, POM2, POM3). In ad-
dition, the Abs are used for the establishment of 
immuno PCR and other techniques for detecting 
PrPSc or PrPC .

As part of WP5, PrPSc was identified in the lungs, 
kidneys  and  urine  of  sheep  naturally  infected 
with	 scrapie;	 a	 paper	 is	 now	 being	 prepared.	
Further  transmission  experiments  were  begun, 
using milk from sheep infected with scrapie and 

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39

	
 
 
TSEUR

suffering from mastitis. Milk proteins were orally 
transmitted into lambs from New Zealand sheep. 
Urinary proteins from sheep with PrPSc deposits 
in kidney as well as all control samples were also 
transmitted into bank voles, and into transgenic 
mice  expressing  the  bank  vole  protein.  In  addi-
tion  to  test  prion  infectivity  in  renal  homoge-
nates,  transmission  experiments  in  bank  voles 
were also performed. So far, prion infectivity has 
been detected in the kidneys of scrapie-infected 
sheep, as well as PrPSc by PMCA in the urine of 
sheep infected with scrapie, but not in controls. 

In  WP6,  various  tissues  and  body  fluids  from 
healthy sheep and sheep naturally infected with 
scrapie were provided to the whole consortium. 
In  addition  a  multicolour  TaqMAN  analysis  was 
established  as  a  sensitive  and  qualitative  assay 
for different Maedi visna viruses. 

Coordinator

adriano aguzzi 
Institute of Neuropathology 
University Hospital Zurich
Schmelzbergstrasse 12
8091 Zurich, Switzerland
E-mail: adriano.aguzzi@usz.ch

Partners 

Ina Vorberg
Institute of Virology
Technical University of Munich
Munich, Germany

Roman Jerala
National Institute of Chemistry
Ljubljana, Slovenia

Ciriaco Ligios
Istituto Zooprofilattico 
Sperimentale della Sardegna
Sassari, Italy

Martin Bachmann
Cytos Biotechnology AG
Schlieren, Switzerland

Ingolf Lachmann
AJ Roboscreen GmbH
Leipzig, Germany

Max Basagni
Prion Diagnostica Srl
Rho (MI), Italy

40

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DIAGNOSTICS

ADDNET

Paradigm shift from kidney biopsies to advanced molecular diagnostics  
from patient urine

Contract No 
Project type 

LSHB-CT-2003-503364
Specific Targeted 
  Research Project

EC contribution  e 2 000 000

Starting date   1 January 2004
duration  36 months

Background and objectives:

Proteinuria is a common medical symptom often 
found in association with infectious, inflammatory 
or  immunological  diseases.  However,  the  most 
important  cause  of  proteinuria  is  progressive 
level 
kidney  damage  due  to  diabetes.  The 
of  proteinuria  correlates  with  the  severity  of 
glomerular  damage,  and  persistent  proteinuria 
leads  to  scarring  and  end-stage  renal  disease 
(ESRD) requiring dialysis treatment or ultimately 
renal 
treatments  are 
severely  and  chronically  debilitating  for  the 
patient  and  increase  the  risk  for  cardiovascular 
complications. 

transplantation.  Both 

In Europe, the need for these treatments is pro-
jected to clearly exceed their availability during 
the next few years. At present, the diagnostics 
of  proteinuric  kidney  diseases  consists  of  se-
lected serum markers and urine analysis. How-
ever, mainly due to their limited sensitivity and 
specificity,  the  diagnostic  method  of  choice  is 
still  direct  kidney  biopsy.  Although  inherently 
accurate,  this  is  invasive  and  carries  a  notable 
risk for severe complications. There is therefore 
a recognised need for a more accurate, predic-
tive,  non-invasive  and  modern  diagnostics  re-
flecting  the  precise  molecular  pathogenesis  of 
proteinuric diseases.

The  main  objective  of  the  ADDNET  project  was 
to  identify  and  evaluate  kidney  damage  associ-
ated molecules in the urine to develop, establish 

and validate new diagnostics directly from urine, 
an  easily  accessible  source.  Furthermore,  the 
project aimed at gaining information about the 
structure and interactions of the podocyte pro-
teins, as well as identifying novel pathways in the 
development of proteinuria.

Approach and methodology: 

The  consortium  produced  the  first  knowledge 
of  new  and  previously  unknown  molecules  in-
volved  in  determining  the  kidney  glomerular 
filtration  barrier  in  health  and  disease.  For  this 
purpose, identification of candidate genes/pro-
teins  for  proteinuric  diseases  as  derived  from 
various activities in Work Packages (WP) 1-5 was 
performed.  The  first  level  of  verification  came 
from using in vitro methods, further extending 
to  established  experimental  models  of  disease 
and, finally, to the use of unique database col-
lections of human sample material and associ-
ated clinical information. 

The  project  combined  state-of-the-art  tools  to 
understand  the  mechanisms  of  proteinuric  kid-
ney  disease.  An  expanding  set  of  crucial  podo-
cyte molecules and their role in proteinuric dam-
age was achieved. Specific objectives included:
•	

exploitation	of	data	from	gene	expression	
analysis  of  the  human  single  gene  dis-
ease CNF as well as its transgenic animal 
model  (nephrin  deficient  “TRAP”)  and, 
particularly,  clustering  of  the  Affyme-
trix®  derived  expression  data  to  achieve 

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ADDNET

•	

•	

•	

•	

a	comparative	genomics	approach;
sophisticated	 bioinformatics	 tools,	 such	
as gene promoter analyses, were used to 
identify  new  molecules  involved  in  pro-
teinuric  damage  as  based  on  identifica-
tion  of  transcription  factor  patterns  of 
differentially expressed genes in specific 
tissues;
equipment	 including	 the	 SELDI-tof	 (Ci-
phergen®)  to  search  for  molecular  differ-
ences between urines of healthy individu-
als and diabetic patients with nephropathy 
to identify potential molecules involved in 
diabetic	nephropathy	was	used;	
establishment	 of	 the	 role	 of	 novel	 key	
molecules,  their  regulation  and  protein 
partners in the pathogenesis of early kid-
ney disease was initiated using appropri-
ate	experimental	models;
information	 generated	 to	 establish	 sim-
ple and non-invasive test methods from 
urine  for  diagnostics,  prognostics  and 
follow-up  of  kidney  patients  was  gath-
ered. For this, conventional immunologic 
methods  including  Western  blot,  and 
ELISA techniques were used.

Main findings: 

Based  on  microarray  analyses  of  nephrin-defi-
cient mouse embryonal kidneys, a ranking list of 
proteinuria associated genes was generated and 
analysed further. The expression of selected can-
didate genes as teased out from the bioinformat-
ics  platforms  was  replicated  using  classical  bio-
chemical  and  immunochemical  methods  in  an 
independent set of samples of wildtype, as well 
as gene-deficient kidneys using quantitative RT-
PCR to confirm the results of microarray analysis. 

Methods to analyse nephrin-binding proteins in 
silico were used with novel candidate interacting 
proteins  identified.  Dual  immunofluorescence 
staining  was  used  to  verify  the  appropriate  co-
localisation within the kidney. 

The collection of urine and kidney samples from 
two  experimental  models  of  nephropathy  was 
completed, and the urine samples were analysed 
by SELDI-tof technology. The expression of novel 
target hits were shown within distinct structures 
of  the  normal  and  diseased  kidney  and  regula-
tion  also  by  RT-PCR  and  Western  blot  verified 
in  kidney  injury.  Immunohistochemistry  was 
used  to  show  semiquantitatively  the  regulation 
of novel target antigens within the tubular and 
glomerular compartments. 

Type 1 diabetic patients and healthy control sub-
jects were phenotyped for multiple parameters, 
which were correlated with findings in the urine 
biomarker profiling by SELDI-technology. Several 
potentially interesting markers were identified.

A  wide  range  of  antibodies  against  candidate 
molecules  were  acquired  from  commercial  as 
well as collaborative sources, and then tested and 
used with human and animal kidney samples to 
gain  biological  information  and  validation  with 
respect to diseases on these molecules. Work on 
these potential markers is continuing.

Major publications:

Ihalmo,  P.,  Schmid,  H.,  Rastaldi,  M.P.,  Mattinzoli, 
D.,  Langham,  R.G.,  Luimula,  P.,  Kilpikari,  R.,  Las-
sila,  M.,  Gilbert,  R.E.,  Kerjaschki,  D.,  Kretzler,  M., 
Holthofer,  H,.  ‘Expression  of  filtrin  in  human 
glomerular  diseases’,  Nephrol  Dial  Transplant, 
2007,	Jul;22(7):1903-9.

Heikkila, E., Ristola, M., Endlich, K., Lehtonen, S., 
Lassila, M., Havana, M., Endlich, N., Holthofer, H. 
(on  behalf  of  the  Addnet  consortium), ‘Densin 
and beta-catenin form a complex and co-local-
ize in cultured podocyte cell junctions’, Mol Cell 
Biochem,	 2007.	 Nov;305(1-2):9-18.	 Epub	 2007	
Jun 21.

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DIAGNOSTICS

Coordinator

Harry Holthöfer 
University of Helsinki
POB 21 (Haartmaninkatu 3)
00014 Helsinki, Finland
E-mail: harry.holthofer@helsinki.fi

Partners

Klaus-Robert Müller
Fraunhofer Institute
Berlin, Germany

Per-Henrik Groop
Samfundet Folkhälsan i Svenska Finland r.f.
Helsinki, Finland

Jesus Egido
Fundación Jimenez Diaz 
Autónoma University
Madrid, Spain

Kimmo Kaski
Helsinki University of Technology
Espoo, Finland

Peter N. Iversen
Ciphergen Biosystems A/S
Copenhagen, Denmark

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43

 
GLYFDIS

Glycans in body fluids – potential for disease diagnostics

Contract No 
Project type 

LSHB-CT-2006-037661
SME-Specific Targeted

EC contribution  e 2 793 722

  Research Project 

Starting date   1 November 2006

duration  36 months

Website  www.glyfdis.org

Background and objectives:

Developing effective tools to screen for cancer is 
an important endeavor, where there is much re-
search taking place. The GLYFDIS project’s objec-
tive is to develop methods for earlier diagnostic 
and  effective  disease  screening  of  prostate  and 
pancreatic  cancer  that  will  lead  to  better  treat-
ment  outcomes.  Early  diagnosis  of  cancer  is  of 
far greater prognostic impor¬tance than any at-
tempts to treat the disease in its late stages. Even 
in cases where the eventual outcome cannot be 
changed, treatment is simpler and quality of life 
improved for those cases where early diagnosis 
is achieved. For this purpose, GLYFDIS proposed 
a method of a simple noninvasive blood testing. 
Accurate  monitoring  of  a  cancerous  state  fol-
lowing diagnosis can contribute significantly to 
prognosis  determination  and  online  evaluation 
of therapeutic regimens.

The  most  widespread  and  diverse  post-transla-
tional modification is glycosylation. The location 
and variation of glycans place them in a position 
to  mediate  cellular  and  intracellular  signalling 
events, as well as participate in different biologi-
cal processes including pathology states such as 
cancer.  Therefore,  the  project  proposes  to  use 
analyses of glycans for identifying novel biomar-
kers  that  can  be  used  for  the  diagnostics  and 
monitoring of cancer.

Cancer  is  a  significant  burden  on  individuals, 
families  and  society.  The  economic  impact  of 

44

Diagnostics - Genetic Testing and Biomarkers

cancer  is  substantial.  In  2002,  the  overall  cost 
of  cancer,  as  published  by  the  National  Cancer 
Institute, was USD 172 billion. This does not ac-
count  for  the  psychological  toll  that  it  takes  on 
individuals and families.

Early detection and diagnosis of cancer is based 
on  the  observation  that  treatment  is  more  ef-
fective  when  the  disease  is  detected  earlier  in 
its  natural  history,  prior  to  the  development  of 
symptoms,  than  in  an  advanced  stage.  Diagno-
sis  of  cancer  in  the  early  stages  of  the  disease 
influences  many  aspects  of  life.  It  can  signifi-
cantly decrease cancer-associated morbidity and 
mortality and to relieve the burden on patients, 
their  families  and  society.  Accurate  monitoring 
of a cancerous state following diagnosis can sig-
nificantly contribute to prognosis determination 

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DIAGNOSTICS

and  online  evaluation  of  therapeutic  regimens. 
Developing  effective  tools  to  screen  for  cancer 
is an important endeavour and there is much re-
search  taking  place  to  develop  these  tools. The 
goal is to detect the cancer when it is localised to 
the organ of origin without invasion of surround-
ing tissues or distant organs.

cer. The company operates a dedicated biobank 
of biological samples selected from patients that 
have  undergone  surgery  for  the  removal  of  di-
gestive tract solid tumour.

RNTech’s role in GLYFDIS has three facets:

Approach and methodology:

The  GLYFDIS  project  will  make  use  of  glycans. 
Their  diversity,  compared  to  genome  or  pro-
teome, makes the glycans ideal for diagnosis and 
monitoring of cancer. Cancer-associated chang-
es in the glycome of the tumoural tissue are very 
frequent. Currently, one of the main obstacles is 
the lack of sufficient technology. Glycome-anal-
ysis  technologies  today  fall  behind  the  rapidly 
developing  genome-  and  proteome-analysing 
technologies.

The  consortium  hopes  to  identify  biomark-
ers  that  can  be  used  to  develop  a  non-invasive 
method  for  the  early  diagnosis  of  prostate  and 
pancreatic cancer based on glycan analysis.

GLYFDIS’ main objectives are:
•	

optimising	 high-throughput	 methods	 of	
glycan analysis for the diagnosis of pros-
tate and pancreatic cancer by the analysis 
of	glycans	in	blood;
identifying	cancer	associated	glyco-mark-
ers in serum samples of prostate and pan-
creatic	cancer	patients;
developing	 and	 validating	 protocols	 for	
lectin-based  microarrays 
for 
large scale screening of cancer associated 
glyco-markers in serum samples.

intended 

•	

•	

Role of SMEs

RNTech Diagnostics
RNTech Diagnostics is an SME specialising in ear-
ly stage diagnosis of digestive tract cancers with 
special  focus  on  colorectal  and  pancreatic  can-

1. 

2. 

3. 

To  provide  biological  samples  collected 
from  pancreatic  and  prostate  cancer  pa-
tients and healthy control subjects for the 
discovery  and  validation  phases  of  the 
project. 
To  contribute  to  the  project  database  by 
providing  genomics  data  on  pancreatic 
cancer patients, as well as clinical data on 
all selected patients and healthy subjects 
and  by  participating  in  the  bio-statistical 
and  bio-informatics  treatment  of  such 
data and research results. 
To  contribute  to  the  validation  of  identi-
fied potential biomarkers with its network 
of clinical oncologists and cancer biology 
specialists.

Procognia
Procognia  has  developed  a  lectin-array  based 
technology  for  rapid  analysis  of  glycosylation 
profiles  of  intact  glycoproteins.  The  array  con-
tains  25–30  well-characterised  lectins  (carbohy-
drate binding proteins) with overlapping specifi-
cities. The binding of a glycoprotein to the array 
results in a characteristic fingerprint that is highly 
sensitive to changes in the protein’s glycan com-
position. The large number of lectins, each with 
its  specific  recognition  pattern,  ensures  high 
sensitivity  to  changes  in  the  glycosylation  pat-
tern. Automatic algorithms were constructed for 
deconvoluting these signals into a glycan profile 
output. The major advantages of this technology, 
in comparison to traditional methods of glycoa-
nalysis, are its short analysis times, the relatively 
low  protein  amount  needed  for  analysis,  the 
possibility to analyse multiple samples in paral-
lel, and the relatively low costs compared to the 
classical analysis methods (HPLC/MS).

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GLYFDIS

A  highly  sophisticated,  automated  platform 
(GlycoScope)  was  first  developed  for  use  in  the 
biopharmaceutical industry for the analysis of re-
combinant glycoprotein drugs. By tailoring algo-
rithms  for  various  protein  families,  this  product 
provides accurate, quantitative glycoanalysis for 
single proteins. 

•	

come  bio-bank  integrating  GLYFDIS  re-
sults and serving as a basis for a continu-
ously	growing	public	glycome	databank;
the	 dissemination	 of	 the	 information	 to	
the scientific community and community 
at large.

Potential applications:

The project will generate knowledge relevant for 
non-invasive diagnosis of cancerous states with 
the effort in developing a standard protocol for 
diagnosis of serum samples.

Coordinator 

angel Porgador
Ben-Gurion University of the Negev
Beer-Sheva, Israel
E-mail: angel@bgu.ac.il

Partners

Rakefet Rosenfeld
Procognia Ltd
Ashdod, Israel

Pauline Rudd
The National Institute for 
Bioprocessing Research and Training (NIBRT)
Dublin, Ireland

Jasna Peter-Katalinic
Muenster University
Muenster, Germany

Julien Taieb
RNTech Diagnostics
Charleroi-Gosselies, Belgium

In  addition,  Procognia  is  developing  a  line  of 
products  for  the  life  science  and  academic  re-
search market. The products are a line of off-the-
shelf  kits  for  glycoanalysis,  distributed  by  QIA-
GEN. The first product, QproteomeTM GlycoArray, 
launched  in  2006,  provides  a  rapid  and  simple 
tool  for  glycoanalysis  of  glycoproteins.  This  kit 
can  be  used  without  sophisticated  equipment, 
and  generic  interpretation  algorithms  provide 
semi-quantitative glycoanalysis for purified glyc-
oproteins. The second product was launched in 
2007 for analysis of global glycosylation patterns 
of membrane protein extracts. The kit is intend-
ed for analysing global changes in glycosylation 
patterns in extracts of cell membrane proteins of 
cultured mammalian cells, with the aim of ena-
bling  characterisation  of  glycosylation-related 
biological effects.

As a partner in GLYFDIS, Procognia will optimise 
the  existing  technology  for  analysis  of  global 
glycosylation patterns to allow the characterisa-
tion of complex protein mixtures in serum from 
healthy  donors  and  donors  with  pancreatic  or 
prostate cancer.

Expected outcome: 

The project partners expect:

•	

•	

•	

the	identification	of	biomarkers	using	gly-
comic  and  proteomic  methods  together 
with	computer-based	algorithms;
the	development	of	a	non-invasive,	mod-
est, diagnostic kit that will identify specific 
markers	for	cancer	in	the	blood;
the	 construction	 of	 a	 website	 and	 a	 gly-

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DIAGNOSTICS

MolDiag-Paca

Novel molecular diagnostic tools for the prevention and diagnosis  
of pancreatic cancer

Contract No 
Project type 

LSHB-CT-2006-018771
Integrated Project 

EC contribution  e 8 495 490

Starting date   1 august 2006
duration  36 months

Website  www.moldiagpaca.eu

and advanced tumours, as well as prognostic and 
therapeutic  tumour  subgroups.  At  this  level,  es-
sential resources and datasets are created for the 
successful completion of all other WPs.

Level  2  comprises  WPs3  through  WP6.  They 
generate  novel  molecular  diagnostic  tools 
based on the profiles of genetic alterations de-
fined in Level 1. Diagnostic tools on the level of 
the  proteome  and  transcriptome  are  also  be-
ing produced, and they make use of epigenetic 
changes in tumours, so as to develop diagnostic 
tools. The WPs specifically focus on developing 
molecular imaging approaches to be tested ini-
tially in animal models of preneoplastic lesions 
and pancreatic cancer, and later intended as in 
vivo diagnostic imaging tools. 

First, the ideal targets or signatures are selected 
for  the  proposed  molecular  diagnostic  tools. 

Examples of comet assays (left) and micronuclei 
assays (right) to uncover DNA repair defects.

Background and objectives:

Malignant  tumours  of  the  pancreas,  known  as 
pancreatic carcinomas, remain among the most 
serious challenges in modern medicine. Although 
they are not among the most common tumours, 
they are among the most frequent causes of can-
cer-related  deaths,  with  approximately  28  000 
deaths per year in the USA and 40 000 per year in 
Europe. There are currently no means for reliable 
diagnosis  of  early  stages  and  for  curative  treat-
ment of late stages of the tumour.

The overall aim of the MolDiag-Paca project is to 
make use of genetic profiles of pancreatic cancer 
and precursor lesions to improve the outcome of 
pancreatic  cancer  patients,  by  providing  novel 
and  highly  efficient  molecular  diagnostic  tools. 
In  order  to  achieve  this  ambitious  aim,  an  inte-
grated multidisciplinary research approach is re-
quired, as it calls for a strong interaction between 
technology,  biology  and  medicine  to  translate 
genome data into practical, clinical applications.

Approach and methodology:

The basic structure of the Work Programme com-
prises 3 levels and 7 Work Packages (WPs):

Level 1 comprises WP1 and WP2. They provide the 
patient resources required to develop and validate 
molecular  diagnostic  tools.  They  also  generate 
and  collect  data  on  genome,  transcriptome  and 
proteome  profiles  of  preneoplastic  lesions,  early 

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Diagnostics - Genetic Testing and Biomarkers

47

 
 
 
 
 
 
MolDiag-Paca

Expected outcome:

The  MolDiag-Paca  partners  expect  that  global 
differential genetic analyses on the genome and 
transcriptome and proteome level of PanINs, as 
well as on early and advanced tumours, may help 
to identify complex genetic patterns associated 
with the individual progression steps. Combined 
with  innovative  diagnostic  approaches,  such  as 
molecular  imaging  technology  or  detection  of 
minimal amounts of marker genes in secretions, 
these analyses will create the necessary tools to 
devise early diagnostic strategies for patients at 
risk.  Equally  important  is  that  the  collection  of 
aberrantly expressed genes and proteins gener-
ated by such analyses may prove instrumental in 
the  identification  of  targets  for  innovative  che-
moprevention  strategies,  which  may  in  future 
replace  or  augment  the  only  existing  curative 
treatment  option  (radical  surgery)  with  a  phar-
macological approach.

Main results:

During the first reporting period (months 1-12), 
the  consortium  laid  the  fundamental  prerequi-
sites for the final project goals (development of 
molecular tools for early diagnosis of pancreatic 
cancer).  In  summary,  that  means  that  material 
(i.e.  tissue,  serum,  plasma,  DNA,  RNA,  tissue  ar-
rays)  was  collected,  databases  and  gene  lists 
were generated, and protocols optimised. At the 
same time a number of assays were established.

The WPs  initially  design  preclinical  prototypes, 
and  then  validate  them  using  animal  models 
and  patient  samples  archived  in  Level  1. Then, 
together  with  the  participating  small  and  me-
dium-sized enterprises (SMEs) and the pharma-
ceutical industry, the prototype molecular diag-
nostic tools will be prepared and standardised 
for use in clinical trials. 

Molecular diagnostic tools developed in Level 2 
aim at improving the diagnosis and prognosis for 
pancreatic cancer patients or patients at risk, in 
the following major areas:
•	

diagnosis	 of	 preneoplastic	 lesions	 in	 pa-
tients	at	risk	for	pancreatic	cancer;
diagnosis	 of	 early	 stage	 tumours	 in	 pa-
tients at risk and sporadic pancreatic can-
cer	patients;
diagnosis	of	different	types	and	origins	of	
pancreas	tumours;
prognostic	and	therapeutic	risk	stratifica-
tion of pancreatic cancer patients.

Level 3 contains WP7, which represents the final 
stage of the development of novel molecular di-
agnostic tools. Experienced clinical oncologists 
focused  on  clinical  trials  of  pancreatic  cancer 
patients  and  populations  at  risk  for  pancreatic 
cancer,  work  together  to  jointly  organise  pro-
spective clinical trials for the newly developed 
tools. The first clinical trials will involve studies 
on the following:
•	

pancreatic	juice	of	populations	at	risk	for	
pancreatic cancer to detect preneoplastic 
lesions	or	early	tumours;
resected	pancreatic	tumours	to	predict	the	
responsiveness	to	an	adjuvant	therapy;
fine	 needle	 aspirates	 of	 primary	 pancre-
atic tumours or liver metastases to differ-
entiate	distinct	pancreatic	tumours;
fine	needle	aspirates	of	primary	tumours	
or  liver  metastases  of  pancreatic  adeno-
carcinomas to obtain prognostic and ther-
apeutic signatures.

•	

•	

•	

•	

•	

•	

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DIAGNOSTICS

aldo Scarpa, Patrick Moore, Claudio Sorio
University of Verona
Department of Pathology
Verona, Italy

Claudio Basso
University of Verona
Department of Surgery
Verona, Italy

Stephan Hahn, Irmgard Schwarte-Waldhoff
University of Bochum 
Molecular GI-Oncology
Department of Internal Medicine
Bochum, Germany

Hans-dieter Pohlenz and annette Sommer
Bayer Schering Pharma AG
Berlin, Germany

Helmut Friess and Jörg Kleeff 
University of Heidelberg
Department of General Surgery
Heidelberg, Germany

Ian Fleming and Simon Green
Cyclacel Ltd
Dundee, UK

Günther Klöppel and Bence Sipos
University of Schleswig-Holstein
Department of Pathology
Kiel, Germany

Martin Highett
Tepnel Life Sciences
Manchester, UK

Christoph Bremer
University of Münster
Department of Clinical Radiology
Muenster, Germany

Coordinator 

Thomas M. Gress 
Universitätsklinikum Gießen und Marburg GmbH
Standort Marburg
Klinik für Innere Medizin
SP Gastroenterologie und Endokrinologie
Baldingerstrasse
35043 Marburg, Germany
E-mail: gress@med.uni-marburg.de

Scientific coordinator

Björg V. Pauling
BMFZ-Building
Hans-Meerwein-Str. 2
35043 Marburg, Germany
E-mail: pauling@staff.uni-marburg.de

Partners

Sven N. Reske
University of Ulm
Nuclear Medicine Clinic
Ulm, Germany

John Neoptolemos, Bill Greenhalf, Eithne Costello
University of Liverpool
School of Cancer Studies
Division of Surgery and Oncology
Liverpool, UK

Nick Lemoine and Tatjana Crnogorac-Jurcevic
Institute of Cancer
Molecular Oncology Unit
London, UK

Jörg Hoheisel and andrea Bauer
German Cancer Research Centre (DKFZ)
Division of Functional Genome Analysis
Heidelberg, Germany

Francisco Real (Paco) and Núria Malats
Institut Municipal d’Investigacio Medica, IMIM
Barcelona, Spain

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49

MolDiag-Paca

Matthias Wassermeier and Zeno von Guttenberg
Advalytix AG
Brunnthal, Germany

Katrin Sak
Asper Biotech
Tartu, Estonia

Johan Permert and Magnus Nilsson
Karolinska Institute
Department of Surgical Gastroenterology
Stockholm, Sweden

Jutta Lütges
Karolinska Institute
Department of Pathology
Stockholm, Sweden

Jörg Rademann and Jens Peter von Kries
Leipniz Institute for Molecular Pharmacology (FMP)
Berlin, Germany

50

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DIAGNOSTICS

COBRED

Colon and breast cancer diagnostics

Contract No 
Project type 

LSHB-CT-2007-037730
SME-Specific Targeted

EC contribution  e 2 985 102

  Research Project 

Starting date   1 March 2007
duration  36 months

Website  www.cobred.eu

Background and objectives:

COBRED seeks to discover colon cancer or color-
ectal cancer (CRC) and breast cancer (BC) biomar-
kers  for  patient  follow-up  (monitoring  markers) 
by exploiting the capacity of three state-of-the-
art high-throughput technologies in an integrat-
ed  systems  biology  approach. The  specific  RTD 
objectives are: 
•	

clinical  CRC 

the	 design	 of	 a	 clinical	 protocol	 for	
and  BC 
prospective 
collections that fit the needs of the three 
high-throughput 
‘-omics’  technologies 
used  (i.e.  transcriptomics,  proteomics, 
metabolomics);	
the	 identification	 of	 biomarker	 candi-
dates  (metabolites,  proteins,  peripheral 
blood  Leucocytes  (PBL)-derived  mRNAs) 
capable  of  detecting  and  assessing  the 
status  of  minimal  residual  disease,  me-
tastases and recurrence after surgery and 
chemotherapy;	
the	 development	 of	 a	 centralised	 data-
base  to  integrate  the  data  generated  by 
the  three  technology  platforms  with  the 
clinical  and  pathological  information  of 
the	collections;	
the	 discovery	 of	 biomarkers	 with	 better	
specificity and sensitivity using cross-plat-
form  advanced  data  mining  techniques 
on  the  combined  data  from  the  consoli-
dated	database;	
the	validation	of	the	biological	relevance	
and diagnostic potential of the identified 

•	

•	

•	

•	

biomarkers by testing their specificity on 
tissue  arrays  and  in  relevant  preclinical 
models. 

COBRED gathers the expertise and RTD resourc-
es of three biotech small and medium-sized en-
terprises (SMEs), leading academic partners and 
two leading cancer treatment centres renowned 
for their expertise in BC and CRC treatment. 

An apparent paradox of current cancer epidemi-
ology is that while new therapies and diagnostics 
improve  survival  rates  in  common  cancers,  e.g. 
colon and breast cancer, the incidence rates are 
also increasing, and thus the net effect is nega-
tive.  CRC  is  the  third  commonest  cancer  type 
worldwide;	in	the	year	2000	the	global	incidence	
was about 1 million, close to 10% of all cancers, 
and it resulted in about 0.5 million deaths, equal-
ling some 8% of all cancer mortality (Midgley R. 
et	al,	Nat	Clin	Pract	Oncol.	2005	Jul;	2(7):364-9).	
Lifetime risk of colorectal adenocarcinoma is one 
of the highest of all cancers, approximately 6%, 
and  of  colorectal  adenoma  —  the  benign  but 
precancerous lesion — it is approximately 50%. 
The  risk  of  CRC  rises  with  age,  especially  in  pa-
tients over the age of 60. 

BC is the most common cancer in women from 
western  countries.  In  these  patients,  it  is  not 
the  primary  tumour,  but  its  distant  metastases 
that are the main cause of mortality. The yearly 
incidence  rate  is  over  0.5  million  (630  000  new 
breast  cancer  cases)  that  results  in  about  0.2 

Diagnostics - Genetic Testing and Biomarkers

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COBRED

million deaths. Recently, the rates of metastasis 
and  mortality  in  BC  patients  have  decreased  as 
a  result  of  early  diagnosis  by  mammographic 
screening  and  the  implementation  of  systemic 
adjuvant  therapy  similarly  to  CRC.  However,  as 
the  population  ages,  the  incidence  of  breast 
cancer increases (Parkin D.M. et. al., Int J Cancer 
1999;	80:	827-841.	(1999),	Elmore	J.G.	et	al.,	JAMA;	
293:1245-1256 (2005)).

Continuous  improvements  in  the  treatment  of 
another major life terminating illness, namely
cardiovascular  disease,  has  lead  to  an  increase 
in  the  overall  life  expectancy.  This  contributes 
to the increase of the incidence rate in CRC and 
BC, among others, due to population ageing. The 
speed of population ageing is higher than the de-
creased mortality, due to the accumulated treat-
ment benefits from new cancer diagnostics (Shen 
Y.	 J.	 et	 al.,	 Natl	 Cancer	 Inst.	 17;97(16):1195-203	
(2005)] and therapies (Nygren P. et al., Acta On-
col. 44(3):203-17. (2005)) thus leading, paradoxi-
cally, to a negative net effect.

There  is  ample,  but  ‘only’  circumstantial  evi-
dence  derived  from  survival  data  of  patients 
with  early  stages  of  cancer,  suggesting  that 
earlier diagnosis would allow a 10% to 20% sur-
vival  rate  improvement.  In  fact,  the  potential 
benefits  of  early  CRC  and  BC  diagnosis  are  so 
high that an extensive range of community and 
governmental  efforts  have  been  implemented 
for population-wide screening.

Biomarkers  are  substances  found  in  the  blood, 
other body fluids (e.g. urine) or tissues that alone 
or  in  combination  may  signal  the  presence  of 
cancer  or  the  risk  for  cancer.  Diagnostics  based 
on biomarkers have the potential to significantly 
improve  current  cancer  diagnostic  means,  thus 
providing a higher sensitivity (i.e. much smaller 
tumours  can  be  detected),  easier,  faster  and  at 
a  much  lower  cost  (Baker  M.,  Nat  Biotechnol. 
23(3):297-304. (2005)).

Biomarker  discovery  and  validation,  similarly  to 
drug discovery and validation, is a long process 
with  a  high  rate  (60-80%)  of  attrition  of  candi-
date biomarkers along the major steps of quali-
fication, that ultimately ends in the approval by 
the US Food and Drug Administration (FDA) and 
the European Agency for the Evaluation of Me-
dicinal Products (EMEA) in the EU. 

Often,  seemingly  good  candidates  that  have 
been identified and found valuable in one study 
do  not  show  the  expected  predictive  values  in 
another study. In fact, the number of new diag-
nostics approved per year is decreasing in sharp 
contrast to the intensifying biomarker discovery 
efforts. Thus, despite having the highest poten-
tial value in numbers, COBRED chose not to pur-
sue the discovery of screening markers because 
of  the  economic  and  logistic  impracticalities  of 
a  large-scale  screening-marker  validation  in  BC 
and CRC. Instead, the partners will focus on the 
second largest clinical need — the improvement 
of patient follow-up — by the discovery of moni-
toring markers, which are expected to report re-
lapse, metastasis and minimal residual disease at 
earlier stages. They are more amenable to surgi-
cal and chemotherapy treatment, and are more 
likely to improve cancer patient survival.

Role of SMEs

The  three  SMEs  involved  (BioSystems  Interna-
tional,  Biocrates  Life  sciences  and  Ipsogen)  are 
actually  research-intensive  SMEs  and  they  play 
leading roles, since their expertise in ‘-omics’ (ge-
nomics, proteomics and metabolomics) technol-
ogies is at the heart of the COBRED project and 
forms the technology basis for the achievement 
of  the  project  objectives.  The  targeted  project 
results are clearly of interest and potential ben-
efit to SMEs, since those create business oppor-
tunities for them in the field of diagnostic tools 
and  methods  (and  related  intellectual  property 
rights  (IPR)). The  SME  ARTTIC  is  responsible  for 
the project management.

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Expected outcome: 

COBRED will deliver candidate protein, metabo-
lite  and  mRNA  biomarkers  tested  in  preclinical 
studies,  ready  for  large-scale  clinical  validation 
and  further  development  for  commercialisa-
tion  by  the  respective  SME  partners:  Ipsogen 
for  mRNA  derived  markers,  BioSystems  Interna-
tional for protein markers and Biocrates Life sci-
ences for metabolomics markers. Specific project 
results will include:
•	

sets	of	biomarkers	(gene	signatures,	pro-
teins,  metabolites  or  a  combination  of 
these)  that  will  be  considered  clinically 
relevant for early diagnosis of primary BC 
and	CRC	and	relapses;
a	 central	 repository	 system	 hosting	 the	
results  from  the  technological  platforms 
and	the	relevant	clinical	data;
prospective	 clinical	 collection	 of	 BC	 and	
CRC;
clinical	 validation	 for	 the	 diagnostic	 po-
tential of subsets of the identified biomar-
kers in comparison to existing biomarkers 
and for currently available imaging tech-
niques;
preclinical	models	for	the	biomarker	eval-
uation and biological studies.

•	

•	

•	

•	

Potential applications:

Diagnostic kits for BC and CRC patient follow-up.

DIAGNOSTICS

Coordinator

Laszlo Takacs
BioSystems International
4 rue Pierre Fontaine 
91058 Evry cedex, France
E-mail: laszlo.takacs@biosys-intl.com

Partners 

armin Graber
Biocrates Life sciences
Innsbruck, Austria

Fabienne Hermitte
Ipsogen
Luminy Biotech Entreprises, 
Marseille, France

Xavier Sastre-Garau
Institut Curie
Paris Cedex 05, France

david Malka
Institut Gustave Roussy
Villejuif, France

László Fésüs
University of Debrecen
Debrecen, Hungary

andras Guttman
Universität Innsbruck
Innsbruck, Austria

Jaak Vilo
University of Tartu
Tartu, Estonia

Bruno Cucinelli
ARTTIC
Paris, France

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53

EuroFlow

Flow cytometry for fast and sensitive diagnosis and follow-up  
of haematological malignancies

Contract No 
Project type 

LSHB-CT-2006-018708
Specific Targeted 
  Research Project

EC contribution  e 2 182 340
Starting date   1 april 2006

duration  36 months

Website  www.EuroFlow.org 

Background and objectives:

Laboratory diagnostics of haematological malig-
nancies  has  three  major  applications:  establish-
ment of the diagnosis, prognostic classification, 
and evaluation of treatment effectiveness. Over 
the  past  decade,  several  molecular  techniques 
have brought new insights into the classification 
and monitoring of treatment effectiveness. How-
ever,  they  have  several  major  disadvantages: 
they  are  time-consuming,  not  applicable  in  all 
categories of patients, and cannot focus on cel-
lular  subpopulations  without  purification  steps. 
These  limitations  can  be  overcome  by  innova-
tions in flow cytometry. 

Flow cytometric immunophenotyping is the sole 
technique  that  fulfils  the  requirements  of  high-
speed,  broad  applicability  at  diagnosis  and  fol-
low-up, and accurately focuses on the malignant 
cell population using membrane-bound and in-
tracellular proteins as targets. The required, inno-
vative  steps  concern  the  development  of  novel 
antibodies,  immunobead  technology,  flow  cy-
tometry software, and eight-color immunostain-
ing protocols. These are all key objectives of the 
EuroFlow consortium. 

A  multidisciplinary  translational  research  ap-
proach is needed, using cutting-edge technolo-
gies  and  biological  data  arising  from  genomic 
research, which can be addressed most success-
fully via a close collaboration between industry 
and academia. Consequently, the EuroFlow con-

54

Diagnostics - Genetic Testing and Biomarkers

sortium is comprised of two SMEs and eight di-
agnostic research groups, regarded as experts in 
the fields of flow cytometric and molecular diag-
nostics. Together, the 10 participants have suffi-
cient complementarity and congruence to cover 
all aspects of the development, standardisation, 
and validation of highly sensitive tests for diag-
nosis and follow-up. 

The  successful  implementation  of  the  proposal 
and the dissemination of the results to European 
haematological laboratories should result in im-
proved health care, through more precise diag-
nosis and individualised treatment, and stronger 
biotechnology enterprises across Europe.

Approach and methodology:

The  EuroFlow  project 
f ollowing:
•	

is  focusing  on  the 

design	of	new	antibodies,	particularly	for	
detection	of	intracellular	proteins;
development	of	an	immunobead	system	
for  the  detection  of  leukaemia-derived 
fusion proteins and other aberrant onco-
proteins;
development	of	new	software	for	fast	and	
easy  handling  of  large  data  sets  and  for 
the  integration  of  eight-color  stainings 
into	a	single	multicolor	data	file;
development	 of	 software	 for	 automated	
pattern  recognition  of  normal,  reactive, 
and aberrant (malignant) leukocyte popu-
lations in blood and bone marrow.

•	

•	

•	

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DIAGNOSTICS

Pedreira,  C.E.,  Costa,  E.S.,  Barrena,  S.,  Lecrevisse, 
Q.,  Almeida,  J.,  Van  Dongen,  J.J.M.,  Orfao,  A., ‘A 
new  automated  flow  cytometry  data  merging 
and  estimation  approach  for  the  generation  of 
‘n’-multi-dimensional  spaces:  comparison  be-
tween originally measured and estimated immu-
nophenotypic  data  on  a  series  of  B-cell  chronic 
lymphoproliferative disorders’, Submitted. 

Coordinator

Jacques J.M. van dongen 
Erasmus MC
Department of Immunology
Dr Molewaterplein 50
3015 GE Rotterdam, Netherlands
E-mail: b.vanbodegom@erasmusmc.nl 

Partners 

alberto Orfao
University of Salamanca
Salamanca, Spain

Frank J.T. Staal
DYNOMICS
Rotterdam, Netherlands

Marta Martin-ayuso
CYTOGNOS
Salamanca, Spain

antónio Parreira
Instituto Portugués de Oncologia
Lisbon, Portugal

Michel Kneba
University of Schleswig-Holstein
Kiel, Germany

Elisabeth Macintyre
Hôpital Necker-Enfants Malades
Paris, France

Diagnostics - Genetic Testing and Biomarkers

55

Expected outcome:

The consortium anticipates the following results 
by the end of the project:
•	

multiplex	 immunobead	 assay	 for	 detec-
tion of fusion proteins and oncoproteins 
per  disease  category  (particularly  ALL 
and	AML);
standardised	 8-color	
immunostaining	
protocols for fast and easy flow cytomet-
ric diagnosis and classification of haema-
tological	malignancies;
standardised	 8-color	
immunostaining	
protocols  for  highly  sensitive  monitoring 
of leukaemia and lymphoma patients for 
evaluation	of	treatment	effectiveness;
large	 database	 with	 hundreds	 of	 well-
defined  normal,  reactive  and  malignant 
cell  samples,  which  can  be  utilised  as  a 
ready-to-use  template  for  a  fully  auto-
mated  comparison  with  newly  analysed 
patient samples.

•	

•	

•	

Main findings:

In 2006/2007, the partners successfully designed 
the first immunobead assays for the detection of 
all three types of BCR-ABL fusion proteins (p190, 
p210, and p230) and for E2A-PBX1 fusion proteins. 
The first version of novel software for fast and easy 
integration of eight-color staining results was com-
pleted (INFINICYT) in 2007 as well. EuroFlow is se-
lecting the fluorochromes for the eight-color im-
munostainings  from  14  available  fluorochromes, 
and  new  antibodies  against  12  new  intracellular 
proteins/domains are being generated.

Major publications:

Orfao,  A.,  Lopez,  A.,  Flores,  J.,  Almeida,  J.,  Vid-
rialez,  B.,  Perez,  J.,  Kneba,  M.,  Macintyre,  E.,  Par-
reira, A., Richards, S., Szczepanski, T., Trka, T., Van 
der Velden, V.H.J., Van Dongen, J.J.M., ‘Diagnosis 
of hematological malignancies: new applications 
for flow cytometry’, Hematology, 2006, 2:6-13. 

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EuroFlow

Stephen Richards
University of Leeds
Leeds, UK

Jan Trka
Charles University
Prague, Czech Republic

Tomasz Szczepanski
Silesian Academy of Medicine
Zabrze, Poland

56

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DIAGNOSTICS

DRoP-ToP

Integration of dNa, RNa and protein markers in a tool for the prognosis  
and diagnosis of human disease

Contract No 
Project type 

LSHB-CT-2006-037739
SME-Specific Targeted 

EC contribution  e 1 834 331

  Research Project

Starting date   1 January 2007
duration  36 months

Website  www.drop-top.net

Background and objectives:

The  management  of  patients  with  superficial 
bladder  cancer  is  difficult.  No  reliable  means 
exists  to  determine  whether  a  tumour  will 
progress towards an infiltrative form, which re-
quires radical surgery (cystectomy), or whether 
it  will  remain  superficial,  which  requires  only 
conservative surgery (resection). In addition, no 
dependable  marker  exists  to  predict  whether 
a  primary  tumour  will  reappear  or  not  during 
the  years  following  surgical  resection,  forcing 
patients to undergo constant revisions that re-
duce their quality of life and overburden health-
care systems.

Numerous markers of various types (genes, tran-
scripts, proteins) have been analysed in bladder 
cancer studies. Some of them have been found to 
harbour potential for the prognosis (progression 
and recurrence) of superficial tumours. However, 
analyses have often been limited to a single type 
of marker or even to a single marker. To the best 
of the project partners’ knowledge, no study has 
attempted  to  integrate  different  types  of  mark-
ers for an increased predictive power.

The main scientific goal of DRoP-ToP is to iden-
tify a set of markers with high predictive power 
for tumour progression and recurrence. To this 
end,  the  project  proposes  to  collect  tumour 
and urine samples from bladder cancer patients 
with  a  detailed  clinical  record,  to  measure  in 
them markers of different types, to find statisti-

cally significant correlations between measure-
ments and clinical records, and to select a pre-
dictor set.

In  addition,  DRoP-ToP  pursues  an  ambitious 
technological  challenge:  the  development  of 
a  prognosis  microarray  for  the  detection  of 
the above-mentioned predictor set. In order to 
achieve this, the project proposes to measure all 
three types of marker biomolecules by means of 
a single type of probe: oligonucleotides. Specifi-
cally, it proposes to use short, long and aptamer 
oligonucleotides for the detection of gene, tran-
script and protein markers respectively.

Cancer  is  the  second  major  cause  of  death  in 
the western world and its incidence is increas-
ing due to the overall ageing of the population. 
Although advances in our understanding of the 
mechanisms  of  tumour  onset  and  progression 
have been enormous, major impact on survival 
has  been  restricted  to  haematopoietic  malig-
nancies,  some  paediatric  tumours,  and  very 
few solid tumours. Improvement in survival can 
be attributed not only to advances in standard 
chemo-  and  radio-therapy  and  to  the  recent 
implementation  of  targeted-drug  therapy,  but 
also to advances in the diagnosis and identifica-
tion of high-risk groups, which allow for earlier 
and better treatment selection.

In contrast, the overall prognosis of the most com-
mon cancers, such as lung, colon, prostate, breast 
and bladder, remains poor, particularly when the 

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57

 
 
 
 
 
 
 
DRoP-ToP

tumour cannot be cured by surgery. One limita-
tion is that the pathologist’s interpretation of the 
tumour’s  histological  features  remains  the “gold 
standard”. Recent advances in microarray technol-
ogy, together with information derived from the 
sequencing  of  the  human  genome,  have  raised 
hopes that this situation will change dramatically 
in the coming years. For these hopes to be real-
ised, it is essential to make appropriate use of in-
formation, technology and clinical resources. The 
project believes that resources are often wasted 
because  of  inappropriate  approaches  and  inad-
equate collaboration between clinical, academic 
and industrial partners.

Transcriptome  analysis  by  DNA  microarrays  has 
been  successfully  used  for  the  identification  of 
biomarkers of tumour progression. However, and 
due to the use of different microarray platforms 
and  patient  selection  strategies,  among  others, 
the biomarkers identified for a given clinical con-
dition vary from study to study. Therefore, their 
application to common clinical practice has not 
yet taken place, and requires prospective studies. 
The DRoP-ToP proposal intends to overcome the 
above limitations with a two-fold approach: 

•	

•	

•	

1)  Prospective  validation  of  the  information  ac-
quired through retrospective studies. For this, a 
collaborative multicentre effort is essential.

2) Integration of biomarkers from genome, tran-
scriptome and proteome analysis in a single pre-
dictor set. Even though each of these three anal-
yses by itself will likely contribute, it is expected 
that the combination of biomarker types will re-
sult in an enhanced predictive power. 

This type of strategy has rarely been used due to: 
•	
•	

the	high	cost	of	microarray	technology;	
the	need	to	have	access	to	different	plat-
forms  for  the  detection  of  different  bio-
molecules;	
the	 fragmentary	 nature	 of	 most	 of	 the	
published work (multiple DNA, mRNA and 
protein markers studied, but only individ-
ually and in most cases weakly associated 
to	disease	phenotype);
the	lack	of	bioinformatics	and	biostatistics	
tools	to	handle	heterogeneous	data;	
the	limited	amount	of	clinical	and	follow-
up information usually available. In addi-
tion, most of these studies are performed 

58

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DIAGNOSTICS

without taking into consideration poten-
tial  bias  in  the  patient  population  under 
study  (i.e.  large  tumour  cases  are  more 
likely  to  be  studied  than  small  tumour 
cases for sample availability reasons).

Approach and methodology:

DRoP-ToP has two major objectives: one techno-
logical and one scientific. Regarding the former, 
the project proposes to develop a tool for multi-
parametric analyses (mRNA levels, large genetic 
rearrangements, genetic mutations, genetic pol-
ymorphisms,  protein  levels,  post-translational 
modifications)  of  biological  samples,  to  better 
predict tumour progression and recurrence. The 
evaluation  of  such  heterogeneous  parameters 
will  be  performed  on  a  single  microarray:  the 
triple microarray, an oligonucleotide microarray 
for  simultaneous  DNA,  RNA  and  protein  assess-
ment). The triple microarray constitutes the test 
surface of a workstation that integrates technol-
ogy  for  the  hybridisation,  scanning  and  detec-
tion of biomarkers. Its simplicity should facilitate 
a wide implementation of this tool in the clinic.

As a scientific objective, the project proposes to 
identify a set of biomarkers with of the ability to 
predict the clinical behaviour of bladder cancer. 
The  selection  of  such  a  set  of  biomarkers  will 
be  the  end-point  of  a  five-phase  endeavour:  1) 
identification  of  candidate  biomarkers  for  blad-
der cancer progression and recurrence from the 
scientific  literature  and  from  existing  data  gen-
erated  by  two  DRoP-ToP  partners  specialised  in 
bladder	 cancer;	 2)	 pre-selection	 of	 biomarkers	
on the basis of the strength of their association 
to  tumour  behaviour  and  on  the  scientific  and 
technical	 quality	 of	 the	 study;	 3)	 measurement	
and  validation  of  said  candidate  biomarkers  in 
a  set  of  samples  from  patients  with  a  detailed 
clinical	 record	 and	 follow-up;	 4)	 application	 of	
bioinformatics  and  biostatistics  tools  for  the 
identification of a set of biomarkers with a strong 
association to tumour behaviour.

The  DroP-ToP  strategy  should  be  applicable  to 
the study of any tumour type, and more gener-
ally  to  any  disease  with  a  genetic  or  gene-ex-
pression component. However, and as a proof of 
concept, the project proposes to apply it to blad-
der carcinoma because it represents a paradigm 
of the need for useful biomarkers in the clinical 
setting: 1) it is one of the best models of tumour 
progression;	2)	its	incidence	ranks	fifth	among	all	
cancer types (the fourth most common in males 
and	the	ninth	in	females);	3)	despite	widely	vari-
able  outcomes,  the  diagnosis  and  prognosis 
tools used in the clinic are few and the same, and 
they are invasive even for asymptomatic patients 
(cystoscopy);	 4)	 it	 is	 the	 most	 expensive	 can-
cer  type,  as  it  can  recur  many  times  after  treat-
ment;	5)	its	evolution	is	very	difficult	to	predict,	
whereas  the  therapeutic  approach  for  its  two 
forms  is  completely  different:  when  invasive  at 
the time of diagnosis, it has a poor prognosis and 
requires	 aggressive	 surgery	 (cystectomy);	 when	
non-invasive, prognosis is favourable and it only 
requires	 conservative	 surgery	 (resection);	 6)	 its	
recurrence is also difficult to predict, which leads 
to unnecessary visits and cystoscopies for about 
50%	of	patients,	whose	tumours	will	never	recur;	
and 7) a number of highly promising biomarker 
candidates have already been identified and re-
ported in the literature.

Role of SMEs

The DRoP-ToP consortium is made of eight multi-
disciplinary partners coming from three Europe-
an Member States (Germany, Spain, France), two 
Associated  States  (Israel  and  Switzerland),  and 
one INCO country (the Former Yugoslav Republic 
of Macedonia). Among the partners, the partici-
pation  of  three  European  high-tech  SMEs  (Pro-
genika  Biopharma,  Genewave  and  NuAce Tech-
nologies)  must  be  noted.  Progenika  Biopharma 
is the coordinator of the DRoP-ToP consortium. 

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59

DRoP-ToP

Expected outcome: 

Cancer  is  the  second  leading  cause  of  death 
worldwide.  In  the  year  2002  there  were  10  mil-
lion new cases of cancer in the world, 6 million 
deaths and approximately 22 million people liv-
ing with cancer. It is estimated that by year 2020 
there will be 15 million new cases per year, and 
10  millions  deaths.  Bladder  cancer  is  a  highly 
common neoplasia, mainly among men, and its 
incidence is rising in several countries in Europe. 
Approximately 125 000 new cases with bladder 
cancer are diagnosed each year in the EU. 

Despite  continued  interest  in  the  development 
of  novel  tests  to  better  predict  bladder  cancer 
prognosis, there has been very limited progress. 
This is in part due to the fact that all tests devel-
oped  until  present  are  based  on  the  detection 
of  only  one  type  of  biomolecule  (i.e.  RNA,  DNA 
or  protein).  The  project’s  approach  is  radically 
different:  from  a  systematic  review  of  current 
knowledge on biomarkers of bladder cancer and 
existing research results of the participating aca-
demic partners, the partners propose to develop 
a  microarray  that  can  detect  the  three  major 
types of molecules in human biological samples. 
This should provide a much more solid basis to 
identify molecular predictors of the disease. 

The  DRoP-ToP  proposed  technology  will  bring 
about three main improvements:
•	

the	 number	 of	 invasive	 tests	 will	 be	
strongly  reduced,  leading  to  a  reduction 
in costs by decreasing hospital admissions 
and	the	number	of	working	hours	lost;
reduction	in	the	number	of	invasive	tests	
will also diminish morbidity and improve 
the	quality	of	life	of	patients;
a	 better	 prognosis	 will	 allow	 more	 ad-
equate  choice  of  treatment  i.e.  avoiding 
therapy  to  patients  who  do  not  need  it 
and applying more aggressive therapy to 
patients at risk.

•	

•	

While  most  patients  develop  bladder  tumours 
with  a  relatively  good  prognosis  in  terms  of 
survival,  their  management  is  very  expensive 
because  of  the  multiple  recurrences  that  most 
patients  suffer,  the  need  for  invasive  follow-up 
procedures,  and  the  frequent  hospitalisations. 
Overall,  bladder  cancer  patients  generate  the 
highest cost per patient and lifetime among pa-
tients with cancer. In conclusion, bladder cancer 
generates very high costs to society.

At the present time, there is no test recommended 
or approved to help establish the prognosis of pa-
tients with bladder cancer. Over the past 10 years 
several products have been approved by the FDA 
for  use  in  the  early  detection  of  bladder  cancer 
recurrence  (i.e.  nmp22,  BTA,  Diagnocure  Immu-
nocyt, Vysis). However, none of these tests is used 
routinely  in  the  clinical  setting  yet  because  they 
do  not  provide  a  substantial  benefit.  Therefore, 
there is a tremendous need for better tests. 

Patients  with  bladder  cancer  develop  multiple 
(up  to  30)  tumour  recurrences,  thus  requiring 
continued  follow-up  after  the  initial  diagnosis. 
For  this  reason,  most  patients  undergo  at  least 
two medical visits over the first few years after di-
agnosis. Subsequently, the frequency of medical 
examinations varies according to the evolution of 
the disease. Therefore, a test that would allow the 
early detection of recurrences and an improved 
establishment  of  prognosis  would  be  applied 
very  frequently  to  the  patients.  The  DRoP-ToP 
proposed  test  could  even  be  used  more  com-
monly  than  cystoscopies  are  performed  today, 
given that it would not be invasive. Its availability 
would allow demonstration of the concept that 
early  detection  of  tumour  recurrence  is  associ-
ated with improved overall outcome.

Potential applications: 

Diagnosis and prognosis for bladder cancer and 
other diseases.

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DIAGNOSTICS

Coordinator

Gorka Ochoa
Progenika Biopharma, SA
Parque Tecnológico de Bizkaia
Edificio 801 B
48160 Derio-Vizcaya, Spain
E-mail: gochoa@progenika.com

Partners

Francois Radvanyi
Institut Curie-CNRS 
Paris, France

Nuria Malats
Universitat Pompeu-Fabra
Institut Municipal d’Investigacio Medica
Barcelona, Spain

Gordana Cerovic
Genewave
Ecole Polytechnique 
Palaiseau Cedex, France

Melanie Hilanio 
University of Geneva
Geneva, Switzerland

Zivko Popov
University Cyril and Methodius-Faculty of Medicine
Skopje, Former Yugoslav Republic of Macedonia

Hader Kless
NuAce Tecnologies, Ltd
Rehovot, Israel

Joerg Hoheisel
Deutsches Krebsforschungszentrum
Heidelberg, Germany

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TB-trDNA

Evaluation of transrenal-dNa detection to diagnose tuberculosis

Contract No 
Project type 

LSHP-CT-2006-037785
SME-Specific Targeted

EC contribution  e 2 000 000

  Research Project

Starting date   1 January 2007
duration  36 months

Background and objectives:

Tuberculosis (TB) continues to be a global threat 
to public health. It is also of significant social and 
financial  concern  to  the  expanding  European 
Union  and  a  cause  of  enormous  morbidity  and 
mortality in much of the developing world. Time-
ly and accurate diagnosis is a critical obstacle to 
TB control, and the currently available diagnostic 
methods are marked by being insensitive, slow, 
and/or cumbersome to use. Nucleic acid ampli-
fication is the only rapid detection method with 
proven sensitivity and specificity, but it is difficult 
to  implement  in  its  current  format.  A  method 
that  avoided  complex  sputum  processing  and 
cell lysis steps that was applicable across multi-
ple amplification formats (e.g. in addition to PCR) 
would be a tremendous advantage. 

There is growing evidence that short DNA frag-
ments, arising from human or bacterial cells dy-
ing throughout the body, pass through the renal 
barrier and appear in urine as transrenal DNA (Tr-
DNA).  In  a  preliminary  study  conducted  at  the 
National Institute of Infectious Diseases in Rome, 
it has been shown that Tr-DNA from M. tubercu-
losis was detectable in the urine by polymerase 
chain  reaction  (PCR)  in  100%  of  patients  with 
pulmonary  tuberculosis,  and  that  these  DNA 
fragments  disappeared  following  anti-TB  drug 
therapy. The TB  tr-DNA  project  aims  to  validate 
the diagnostic potential of Tr-DNA detection for 
TB, to optimise and simplify the sample prepara-
tion methods, and to explore the feasibility of us-

ing a diagnostic approach based on this method 
in a developing world setting.

Tuberculosis remains among the most prevalent 
causes  of  death  from  an  infectious  disease  in 
the world. While global targets for rates of cure 
have been reached in many areas, case detection 
remains a significant bottleneck to effective dis-
ease  control.  Microscopy,  the  only  widely  avail-
able  laboratory  diagnostic  test  for  tuberculosis, 
is  both  difficult  to  implement  and  insensitive. 
Consequently, the availability of new diagnostic 
tools that are more accurate and accessible may 
greatly  benefit  individual  patients  and  signifi-
cantly contribute to the control of the disease.

TB tr-DNA aims to develop a new and highly in-
novative  platform  for  the  detection  of  poverty-
related  diseases  (TB  followed  by  HIV,  malaria). 
This platform is based on the principle that dying 
cells release cell-free DNA into the blood stream 
that  then  passes  through  the  renal  barrier  and 
can subsequently be detected in urine. 

Role of SMEs

The  small  and  medium-sized  enterprise  (SME) 
Innovative  New  Diagnostics 
Foundation  for 
(FIND)  is  an  independent,  not-for-profit,  foun-
dation  wholly  dedicated  to  the  development, 
evaluation  and  demonstration  of  diagnostics 
for infectious diseases relevant for the develop-
ing world. FIND has a minor role in most of the 
Work Packages of the project, but will coordinate 

62

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the  interface  between  test  development  and 
product evaluation, and conduct a project work-
shop in 2007 and project public health advisory 
meeting in 2009. FIND will provide documenta-
tion  and  technical  expertise  related  to  the  cus-
tomer  requirements  and  design  of  the  product 
version(s) to be tested. It will ensure that clinical 
protocols will yield data that will have the great-
est utility to determining the future of the tech-
nology for the public health sector.

Expected outcome: 

TB-trDNA  is  designed  to  develop  a  rapid  diag-
nostic  procedure  for  utilising  transrenal  DNA  as 
a target sample for the identification of Tubercu-
losis  patients. The  findings  of TB-trDNA  will  also 
contribute to policy development through knowl-
edge and awareness of the importance of TB di-
agnosis, with close association with the respective 
ministries  of  health  and  international  organisa-
tions, such as the World Health Organization. 

Potential applications:

Given  the  significant  challenges  of  Mtb  detec-
tion  and  monitoring  in  developing  countries, 
the application of the Tr-DNA test could provide 
a very useful new diagnostic tool. By simplifying 
the sampling procedure and combining this with 
improved  molecular  detection  methods  (which 
could  eventually  lead  to  simple  dip-stick  meth-
ods), the findings of TB tr-DNA could ensure that 
simple,  cheap,  efficacious TB  diagnosis  is  made 
available to the developing world to ensure tar-
geted use of the available therapy.

DIAGNOSTICS

Coordinator 

Jim Huggett
Centre for Infectious Diseases and International Health
Windeyer Institute, University College London
46 Cleveland St. 
London, W1T 4JF, UK
E-mail : j.huggett@ucl.ac.uk 

Partners 

david Tomei
Spaxen Italia, c/o National Institute 
of Infectious Diseases in Rome
Lazzaro Spallanzani – IRCCS
Rome, Italy

Peter Mwaba 
University Teaching Hospital D Block 
Department of Medicine
Lusaka, Zambia

Michael Hoelscher
University of Munich
Department of Infectious Diseases & Tropical Medicine
Munich, Germany 

Leonard Maboko
Mbeya Medical Research Programme
Mbeya, Tanzania

Enrico Girardi
Istituto Nazionale per le Malattie Infettive 
L. Spallanzani – IRCCS
Dipartimento di Epidemiologia
Rome, Italy

Giorgio Roscigno
Foundation for Innovative New Diagnostics (FIND)
Cointrin, Switzerland

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63

GENEPARK

Genomic biomarkers for Parkinson’s disease

Contract No 
Project type 

LSHB-CT-2006-037544
Specific Targeted 
  Research Project 

EC contribution  e 2 987 966

Starting date   1 January 2007
duration  36 months

Website  www.genepark.org

Background and objectives:

Parkinson’s  disease  (PD)  is  the  second  most 
prevalent  neurodegenerative  disease  after 
Alzheimer’s  disease. There  is  currently  no  spe-
cific clinical or laboratory diagnostic test avail-
able  for  PD.  The  diagnosis  of  PD,  which  relies 
on  expert  opinion,  is  only  about  75%  accurate 
when compared with brain autopsy, which is re-
garded as the gold standard..

The  most  important  differential  diagnosis  of  idi-
opathic  PD  remains  atypical  Parkinsonism,  such 
as multiple system atrophy (MSA), progressive su-
pranuclear palsy (PSP) and diffuse Lewy body dis-
ease (DLBD), These atypical forms of Parkinsonism 
may  initially  be  clinically  indistinguishable  from 
idiopathic  PD,  and  a  definite  diagnosis  can  cur-
rently only be established upon autopsy. In early 
stages of the disease and in patients with atypical 
presentations, the functional and structural neu-
roimaging can sometimes improve the diagnostic 
accuracy, as it provides objective markers for the 
patterns  of  dopaminergic  neurodegeneration  in 
the basal ganglia (SPECT, PET) and of regional at-
rophy (structural MRI, VBM). Despite these advanc-
es in neuroimaging, the need for better diagnos-
tic accuracy in PD and related disorders remains 
a great challenge for researchers and clinicians in 
the field of neurology and movement disorders.

In  addition  to  idiopathic  PD,  more  than  10  au-
tosomal  dominant  and  recessive  genes  or  gene 
loci  have  been  linked  to  PD.  Mutations  in  the 

three  most  common  genetic  forms  of  PD  (Par-
kin-,  PINK1-  and  LRRK2-associated  PD)  can  lead 
to  a  phenotype  indistinguishable  from  that  of 
idiopathic  PD.  The  similarities  between  genetic 
PD and idiopathic PD extend beyond the clinical 
picture.  For  example,  PET  findings  in  individuals 
with mutations in the Parkin gene resemble those 
obtained in idiopathic PD.

Since  genetic  PD  can  be  diagnosed  prior  to  the 
onset of clinical symptoms, it offers a unique op-
portunity to study PD in asymptomatic individu-
als.  Such  studies  could  prove  useful  for  the  un-
derstanding  of  disease  pathogenesis,  as  well  as 
for  providing  a  therapeutic  window  for  possible 
preventive  treatments.  In  order  to  develop  and 
monitor the effects of such preventive treatments, 
it would be important to develop surrogate mark-
ers of PD in asymptomatic individuals. Preliminary 
data suggest that such markers can be detected in 
blood by microarray technology.

The microarrays for gene expression profiling are 
rapidly becoming an important research tool for 
identifying  potential  biomarkers  and  for  novel 
classifications of the disease. The microarray-based 
biomarkers  have  been  described  for  numerous 
diseases, such as ovarian and prostate cancer, but 
the drawback of such studies still remains the ac-
cessibility of tissues in live patients. On the other 
hand, analysis of blood-derived mRNA by micro-
arrays may represent an important advancement 
for the development of biomarkers in neurologi-
cal and other diseases. 

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DLBD,  100  HD  and  50  doparesponsive  dystonia 
(DRD)  patients  are  involved,  along  with  the  im-
plementation of 300 healthy controls. In relation 
to  the  structural  and  functional  MRI  studies,  75 
PD mutation carriers, 200 patients with idiopath-
ic PD, 50 patients with MSA, 25 patients with PSP 
and 25 patients with DLBD are involved. RNA will 
be isolated from peripheral blood and prepared, 
as needed, for microarray analysis.

Using microarray data, a set of established com-
putational tools will be applied. Novel methods 
and new bioinformatic software tools for the se-
lection of genomic biomarkers will also be devel-
oped. Selected biomarkers will be validated with 
the real-time PCR method. Selected differentially 
expressed genes will be used for the design and 
production of a dedicated spotted microarray.

Expected outcome:

Three outcomes have been identified as a result 
of GENEPARK.
1. 

The  improvement  of  European  competi-
tiveness in the field of genomic approach-
es to the development of new diagnostic 
methods for nervous system disorders. To 
this  end,  a  unique  collection  of  patients 
(not  available  to  this  extent  in  countries 
outside of the EU), as well as expertise in 
microarray  profiling,  bioinformatic  analy-
sis  and  diagnostics  will  be  pooled  across 
research  groups  in  five  European  coun-
tries and Israel.
The  development  of  a  new  diagnostic 
test for PD based on the haemogenomic 
biomarkers.  To  date,  there  has  been  no 
such test for neurodegenerative disorders 
reported or in use. It has the advantage of 
being non-invasive and has the potential 
to provide early diagnosis of disease, esti-
mation of disease progression and evalu-
ation of treatment efficacy of the existing 
or newly-developed drugs. In addition, de-
velopment of new bioinformatic software 

In its preliminary work, the GENEPARK team used 
genome-wide  expression  profiling  of  human 
blood to identify biomarkers for Huntington’s dis-
ease (HD), a neurodegenerative disease that also 
affects basal ganglia. There are no reported studies 
on gene expression profiling from blood in PD pa-
tients;	however,	there	is	evidence	for	specific	gene	
expression  signatures  in  the  brain.  Preliminary 
studies have demonstrated that significant chang-
es in gene expression could be detected in blood 
from PD patients when compared with expression 
in samples from healthy individuals (Fig. 1). Moreo-
ver,  there  is  evidence  that  possible  pathogenetic 
mechanisms in PD, such as inflammation, apopto-
sis and oxidative stress, can be at least in part de-
tected in lymphocytes of PD patients.

In this STREP (Specific Targeted Research Project), 
the team is proposing to employ microarrays to 
identify  the  diagnostic  and  prognostic  tool  for 
the  diagnosis  of  PD.  In  addition,  they  are  plan-
ning  to  develop  new  sophisticated  analysis 
methods  and  user-friendly  bioinformatic  tools 
that  are  necessary  to  make  accurate  functional 
interpretation of these large-scale data sets. 

The genes were selected from 6 PD patients and 
6 healthy control subjects according to P value, 
fold change (>1.8 or <0.6) and expression maxi-
mum greater than 100. Each column represents 
a sample and each row a gene. Colorgram de-
picts  high  (red)  and  low  (green)  relative  levels 
of	gene	expression.	PD	denotes	patients;	PC	de-
notes controls.

Approach and methodology:

2. 

Key methodologies and techniques include clini-
cal  workup,  neuroimaging,  microarray  analysis, 
RT-PCR validation and bioinformatic analysis and 
development (Fig. 2). The researchers are aiming 
to include a total of 150 carriers of mutations in 
known PD genes and 400 idiopathic PD patients. 

In relation to disease controls, 50 MSA, 50 PSP, 50 

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65

GENEPARK

3. 

tools  for  microarray  analysis  is  planned, 
which is likely to improve genomic marker 
selection through disease modelling and 
existing knowledge integration.
Diagnosis  and  treatment  of  the  disease. 
As PD is one of the most common chronic 
neurodegenerative  diseases  in  Europe, 
improving public health is crucial. Due to 
the high costs associated with physicians, 
drugs,  and  hospitalisation  rates,  the  de-
creased  quality  of  life  in  PD  patients  ex-
tends to a decreased quality of life for the 
families of sufferers. Thus, PD causes con-
siderable strain on both patients and so-
ciety, as a whole. It is therefore of utmost 
importance  to  develop  new  diagnostic 
and  prognostic  tests  for  early  diagnosis 
of PD, as well as for the monitoring of the 
neuroprotective efficiency of existing and 
new candidate drugs for PD.

Major publications:

Binkofski,  F.,  Reetz,  K.,  Gaser,  C.,  Hilker,  R., 
Hagenah,  J.,  Hedrich,  K.,  v  Eimeren, T., Thiel,  A., 
Büchel,  C.,  Pramstaller,  P.P.,  Siebner,  H.R.,  Klein, 
C.,  ‘Morphometric  fingerprint  of  asymptomatic 
Parkin  and  PINK1  mutation  carriers  in  the  basal 
ganglia’, Neurology,	2007;69:842-850.

Cluster analysis of the 36 most differentially expressed 
genes on Affymetrix microarrays.

Coordinator 

Borut Peterlin
University Medical Centre
Division of Medical Genetics
Slajmerjeva 3
1000 Ljubljana, Slovenia
E-mail: borut.peterlin@guest.arnes.si

Partners

alexis Brice
Institut National de la Santé et 
de la Recherche Médicale (INSERM)
Paris, France

Christine Klein
University of Lüebeck and Neuroimage Nord
Department of Neurology 
Lüebeck, Germany

dimitri Krainc
Mediterranean Institute for Life Sciences 
Split, Croatia

Gorka Ochoa 
Progenika Biopharma SA 
Vizcaya, Spain

Olaf Riess
Eberhard-Karls-University Tüebingen 
Tüebingen, Germany

Ron Shamir
Tel Aviv University
Tel Aviv, Israel

Mojca Zajc
RR & CO. Business Consulting, d.o.o. 
Ljubljana, Slovenia

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DIAGNOSTICS

PREGENESYS

development of early non-invasive biomarkers and means for the diagnosis 
and progression monitoring of preeclampsia and tailoring putative therapies

Contract No 
Project type 

LHSB-CT-2005-037244
SME-Specific Targeted

EC contribution  e 2 326 567

  Research Project

Starting date   1 december 2006

duration  36 months

Website  http://pregenesys.net/main

Background and objectives:

Preeclampsia,  a  multi-system  disorder,  compli-
cates 5-7% of all pregnancies, and is responsible 
for  18%  of  maternal  deaths  during  pregnancy 
and for a third of prematurity. Major motor and 
cognitive  newborn  disabilities,  and  blindness 
and life-long complications place a heavy toll on 
obstetrics and paediatric expenditures. The com-
plex disorder, expressed as a newly onset hyper-
tension  developed  in  previously  normotensive 
women  after  20  weeks  of  gestation  along  with 
protein loss in the urine, is coupled to complica-
tions of the kidney, liver, blood system and brain. 
While  clinically  diagnosed  after  the  second  half 
of  pregnancy,  the  underlying  patho-physiology 
is  associated  with  deleterious  alterations  of  im-
plantation  and  placentation  already  starting  in 
the first trimester.

In the PREGENESYS project, the partners propose 
to  apply  an  inter-disciplinary  approach,  combin-
ing cell and molecular biology, tissue culture, mi-
croscopy and biochemistry in order to rigorously 
assess the effectiveness of first trimester non-inva-
sive markers, integrated with the power of sonog-
raphy, and leverage on their prediction power for 
drug  tailoring  thus  optimising  therapies  for  pre-
venting preeclampsia or reducing its severity.

The  consortium’s  working  hypothesis  is:  first 
trimester markers are the key for diagnosis and 
tailor putative medications for preventing preec-
lampsia.  The  group  has  an  unprecedented  rich 

repertoire	 of	 diversified	 candidates;	 each	 con-
tributes to preeclampsia prediction. The partners 
will apply multi-facet pathways for systematical-
ly identifying and characterising additional ones. 
Moreover, they have direct access to stored large 
specimen banks and to new patient enrolment. 
Their marker battery will be utilised for monitor-
ing  disease  progression.  Putative  medications 
will be tailored based on preassessment models 
thereby increasing their medical effectiveness.

Approach and methodology:

1. 

2. 

3. 

4. 

A  scientific  core  will  further  characterise 
markers and bring new ones based on ge-
nomics and proteomics and will develop 
in vitro and in vivo systems for detecting 
markers in human body specimens.
A clinical core will design and conduct nest-
ed case-control (Phase I) and a multi-centre 
(phase II) clinical trial for collecting medical 
records and human specimens along with 
randomised  patients  to  putative  medica-
tions  according  to  good  clinical  practice, 
correct definitions, ethics and logistics.
A  quantitative  core  will  apply  rigorous 
statistics  to  determine  the  effectiveness 
of markers and medications.
A  biotechnology  core  that  develops  kits 
and  assays  will  turn  the  research  results 
into  viable  commercial  products  and 
utilise  its  selling  power  to  generate  eco-
nomic  growth  ensuing  from  the  project, 
implementing  principles  of  good  manu-

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67

 
 
 
 
 
 
 
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5. 

facturing and laboratory practice.
Tailoring  drug  treatment  for  women  at 
risk  will  progress  individual  medicine 
suitable for such a multi-system disorder 
and the vision of deploying medicine be-
yond 2010.

Members of the PREGENESYS group have already 
led  the  development  of  first  trimester  prenatal 
screening  for  detecting  chromosomal  aberra-
tions,  and  will  lead  the  consortium  in  moving 
from the research and clinical study bench into 
education  and  training  programmes,  and  into 
successful implementation of prenatal screening 
of preeclampsia and drug tailoring to prevent it.

Immunohistochemistry for PP13 in placenta. A normal 
term placenta (left) and two cases of late-onset preeclamp-
sia cases (right) stained for PP13. Note the more intense 
staining for PP13 in the preeclamptic cases especially at 
the apical membrane of the syncytiotrophoblast. In the 
lower right image the frame in the middle right image has 
been enlarged to highlight the disturbed surface of the 
syncytiotrophoblast showing evidence for necrotic release 
of subcellular fragments only in preeclampsia (arrows).

Confocal microscopy of normal term placental villi. Placental 
villi from a normal term placenta stained for PP13 (red) and 
actin (green) are shown. Nuclei were counter stained with 
DAPI. Shown is an overlay of a stack of 20 single images.

Coordinator 

Hamutal Meiri
Diagnostic Technologies Ltd
2 Ha’Carmel St., Building B 4th Floor
20692 Yokneam, Israel
E-mail: Hamutal.meiri@pregenesys.com

Partners 

Kevin Spencer
Barking, Havering & Redbridge Hospitals NHS Trust
Romford, UK

Berthold Huppertz
Medical University Graz
Graz, Austria

Nandor Gabor Than
Semmelweis University Hospital
Budapest, Hungary

Pedro Seada
ImunoSTAR
Porto, Portugal

Yvonne Parker
Wallac
Turku, Finland

Kypros H. Nicolaides
Foetal Medicine Foundation
London, UK

Sinuhe Hahn
Basel University 
Basel, Switzerland

Irene Cetin
University of Milan
Milan, Italy

Michael T. Jones
Innomedica Oy Ltd
Turku, Finland

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EDAR

Beta amyloid oligomers in the early diagnosis of ad and as marker  
for treatment response

Contract No 
Project type 

LSHB-CT-2005-037670
Specific Targeted
  Research Project

EC contribution  e 621 002

Starting date   1 January 2007
duration  36 months

Website  www.edarstudy.eu/

Background and objectives:

Alzheimer’s disease (AD) is one of the most com-
mon neurodegenerative disorders, yet there are 
no accurate biomarkers for the early stage of the 
disease. The  goal  of  the  EDAR  project  is  to  de-
velop new diagnostic markers of AD that can be 
used for the early diagnosis and for the monitor-
ing of treatment response in drug trials. 

This STREP (Specific Targeted Research Project) fo-
cuses on beta amyloid oligomers and how these 
are  affected  by  genes  involved  in  beta  amyloid 
processing.  Oligomers  have  only  recently  been 
recognised as a key pathogen in AD. Due to their 
low concentration, they could not be measured 
with  regular  techniques.  In  the  present  study, 
ultra-sensitive assays are being used in order to 
measure oligomers in vivo. Thus, the project will 
transfer recent scientific discoveries in the early 
pathophysiology of AD to clinical application, us-
ing innovative technological methods.

The project has the following objectives.
•	

Develop	an	assay	for	the	detection	of	beta	
amyloid  oligomers  in  cerebrospinal  fluid 
(CSF)  and  plasma  using  ultra-sensitive 
multiplex  immuno-polymerase  chain  re-
action  (IPCR)  with  nano-structured  DNA-
protein	conjugates;	this	objective	has	five	
sub-objectives:
develop	 and	 characterise	 different	 oli-
gomer	isoforms;
develop	 antibodies	 against	 different	 oli-

•	

•	

gomer  isoforms  and  an  ELISA  based  on 
these	antibodies;
validate	the	pathological	relevance	of	oli-
gomers	in	AD;
experimentally	 validate	 the	 relevance	 of	
oligomers  as  early  biomarkers  in  body 
fluids and brain homogenates in a mouse 
model;
develop	an	IPCR	detection	method	using	
relevant antibodies.
Measure	oligomers	using	the	IPCR	and	im-
munoprecipitation assay in subjects with 
AD, other types of dementia, mild cogni-
tive impairment, and control subjects.
Investigate	 whether	 genes	 involved	 in	
beta  amyloid  processing  actually  modify 
the levels of beta amyloid oligomers.
Investigate	 the	 diagnostic	 value	 of	 beta	
amyloid  oligomers  in  CSF,  serum,  and 
plasma in subjects with AD across the dis-
ease  spectrum  from  MCI  (mild  cognitive 
impairment) to mild dementia.
Perform	a	cost-effectiveness	analysis	of	the	
oligomer assays for the diagnosis of AD.
Investigate	the	change	over	time	of	beta	
amyloid oligomers in CSF and plasma.

•	

•	

•	

•	

•	

•	

•	

•	

Approach and methodology:

The project consists of six Work Packages (WPs). 
WP1 aims to measure the oligomers in CSF and 
plasma  in  patients  with  AD,  other  types  of  de-
mentia, MCI (a prodromal state of AD), and con-
trol subjects. In WP2, a number of genes involved 

Diagnostics - Genetic Testing and Biomarkers

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EDAR

in beta amyloid processing will be genotyped. In 
WP3, clinical data, and CSF and blood samples of 
the patients and controls in the study will be col-
lected. In WP4, the data generated in WP1 to WP3 
will be analysed, and the diagnostic accuracy of 
the oligomer assay and the utility of the assay as 
a  marker  of  treatment  response  will  be  investi-
gated. The results from the study will be dissemi-
nated and exploited in WP5, and WP6 deals with 
project management.

Expected outcomes:

•	
•	

•	

•	

5	to	10	antibodies	against	oligomers;
1	 IPCR	 antibody-DNA	 probe	 and	 2	 to	 3	
multiplex  IPCR  probes  for  beta  amyloid 
oligomer	measurements;
data	 on	 oligomers	 levels	 and	 other	 bi-
omarkers	in	patients	and	controls;
guidelines	for	the	use	of	oligomer	assays	
in the diagnosis of AD and as a marker of 
treatment response.

Coordinator 

Pieter Jelle Visser
VU University 
Department of Neurology
Outpatient Clinic
PO Box 5075
1007 MB Amsterdam, Netherlands
E-mail: pj.visser@np.unimaas.nl

Partners 

Michael adler
Chimera Biotech
Dortmund, Germany

Wim Buurman
Hycult Biotechnology
Uden, Netherlands

Wiep Scheper
University of Amsterdam
Academic Medical Centre
Amsterdam, Netherlands

Lars-Olof Wahlund
Karolinska Institutet
Stockholm, Sweden

Magda Tsolaki
Aristotle University of Thessaloniki
Thessaloniki, Greece

Rik Vandenberghe
Katholieke Universiteit Leuven
Leuven, Belgium

Gunhild Waldemar
Rigshospitalet 
Copenhagen, Denmark

Harald Hampel
Ludwig Maximilian University of Munich
Munich, Germany

Frans Verhey
University of Maastricht
Maastricht, Netherlands

Heinz Hillen
Abbott GmbH & Co KG
Ludwigshafen, Germany

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DIAGNOSTICS

NeuroScreen

Sensitive and differential blood and cerebrospinal fluid test  
for neurodegenerative dementia diagnostics

Contract No 
Project type 

LSHB-CT-2006-037719
Specific Targeted
  Research Project

EC contribution  e 2 797 521

Starting date   1 January 2007
duration  36 months

Background and objectives: 

The  NeuroScreen  research  project  aims  to  de-
velop an integrated system allowing differential 
diagnosis of neurodegenerative diseases based 
on  several  patented,  unique,  sensitive  and  ro-
bust  technologies.  This  system  will  be  based 
on the detection of specific direct and indirect 
amyloid-related  markers  in  the  cerebrospinal 
fluid,  and  in  blood  with  new  derivative  prod-
ucts of nano- and/or micro-biosciences. Among 
those neurodegenerative diseases with amyloid 
deposits, NeuroScreen will focus on Alzheimer’s 
disease and Prion diseases, for which some am-
biguities still exist with respect to their differen-
tial diagnosis. 

At  present,  and  in  most  cases,  the  diagnosis 
of  these  diseases  must  be  confirmed  by  post-
mortem  cerebral  analysis.  Furthermore,  the  con-
sortium  will  determine  the  effectiveness  of  the 
technology developed within the project for the 
diagnosis  of  other  neurodegenerative  diseases, 
particularly those associated with the accumula-
tion of α-synuclein (e.g. Parkinson’s disease, Lewy 
body dementia and multiple system atrophy).

Sensitivity is needed for early diagnosis, as this will 
permit  more  cost-effective  therapeutic  interven-
tion, before the disease concerned has progressed 
to a stage where considerable damage to the brain 
has already occurred. In the case of prion diseases, 
and especially in the instances where there is a risk 
of transmission of prions, like blood transfusions, 

there are concerns not only for patient care, but 
for the wider community as well. 

Specificity  is  needed,  firstly  to  discriminate  the 
non-degenerative causes of dementia (alcoholic, 
psychiatric,  metabolic,  etc.)  from  degenerative 
dementia, and secondly to discriminate the dif-
ferent  molecular  aetiologies  in  order  to  choose 
an  appropriate  therapeutic  treatment.  For  ex-
ample,  anticholinesterase  drugs  show  certain 
efficacy  in  Alzheimer’s  disease,  whereas  frontal 
temporal dementia seems to be resistant to this 
kind of drug. In a similar manner, some compas-
sionate treatments can be proposed for patients 
with	 probable	 Creutzfeldt-Jakob	 disease	 (CJD);	
the  latest  treatment  proposed  in  the  UK  and 
France is highly invasive with an intraventricular 
delivery of the drug. A mistake in the diagnosis of 
CJD would be extremely unfortunate.

Approach and methodology:

The  work  is  being  carried  out  by  a  consortium 
comprised  of  12  partners  from  6  European 
Member States. A high-quality multidisciplinary 
partnership  with  complementary  expertise,  the 
NeuroScreen  network  includes  academics,  re-
search centres and a technology transfer centre, 
two  hospitals,  two  industrial  SMEs  (small  and 
medium-sized enterprises) and an SME expert in 
regulatory aspects.

The work involves developing an integrated as-
say system based on two steps: the first concerns 

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71

 
 
 
 
 
 
NeuroScreen

the concentration of the disease markers and the 
second involves the molecular detection of these 
markers. The application of the work for biologi-
cal  diagnosis  of  Alzheimer’s  disease,  CJD  and 
possibly  other  neurodegenerative  diseases  too, 
presents  incontestable  advantages  in  compari-
son with current technologies, and also in guar-
anteeing  increased  protection  of  public  health. 
The tests will meet the requirements of the end 
users,  namely  the  medical  biology  laboratories 
involved  in  carrying  out  the  tests  following  the 
clinicians’ prescriptions. 

•	

The	 experimental	 work	 is	 divided	 into	 7	
Work Packages (WP): WP1: design, optimi-
sation and production of the early test. 

aim:  neuroaptamer  prototypes,  neuro-strips, 
neuro-magnetic  beads,  validation  of 
packaging  and  sterilisation  process,  and 
stabilised and validated supports.
WP2:	 Alzheimer	 Diagnostic:	 tau-181	 and	
-231 markers.

•	

aim:  choice  of  the  marker  candidate  and  the 
prototype to be tested in a multiplex trial.
WP3:	Dementia	diagnostic	and	Lewy	bod-
ies: α-synuclein marker. 

•	

2) 

2) 

3) 

aim:  development and validation of a suitable 

4) 

assay for α-synuclein oligomers.
WP4:	Creutzfeldt-Jakob:	PRION.	

•	
aim:  validation of aptamers, neurostrips and i-

PCR.
WP5:	Therapeutic	follow-up.	

•	
aim:  biological  markers  for  future  therapeutic 

•	

follow-up validation
WP6:	Integrative	section	and	fundamental	
knowledge derived from the other WPs. 
aim:  validation of the multiplex assays systems.
WP7:	 Accompaniment	 and	 regulatory	
•	
follow-up.

Expected outcome:

5) 

6) 

7) 

Medical objectives
The  project  concerns  public  health  for  neuro-
degenerative  diseases,  which  are  experiencing 

72

Diagnostics - Genetic Testing and Biomarkers

constant  growth. The  medical  objectives  are  as 
follows:
1) 

to diagnose the kind of disease (especially 
CJD,  Alzheimer’s  disease,  Lewy  Body  De-
mentia)  with  specific  markers,  e.g.  patho-
logical  Prion  Protein  (PrPsc),  abnormally 
phosphorylated  tau  proteins  (tau-181  and 
tau 231) and pathological α-synuclein pro-
teins	with	an	ultra-sensitive	detection	level;
to  determine  if  any  of  the  diagnostic 
markers studied in this project would be 
suitable  as  a  potential  marker  for  thera-
peutic follow-up, notably with regards to 
patients affected by Alzheimer’s disease.

Scientific objectives
1)  

to develop scientific knowledge (i.e. adhe-
sion /non-adhesion) of surfaces and inter-
faces	in	the	field	of	life	sciences;	
to  develop  ultra-sensitive  quantitative  i-
PCR  dosing  tests,  already  established  for 
prion proteins, in order to adapt them for 
other	disease	markers;
to  develop  a  biochemical  procedure  for 
the concentration and purification of pri-
on	proteins	from	blood	and	CSF	samples;
to  develop  new  binding  molecules 
(aptamers) for the purification and detec-
tion of direct and indirect markers of neu-
rodegenerative	disorders;
to  develop  biofunctional  supports  and 
magnetic  beads  (or 
‘neuro  supports’) 
whose  specific  chemical  and  physico-
chemical features will enhance ¬— via in-
tegrated systems — the different markers 
of	interest	capture	and	detection;
to investigate the usefulness of α-synuclein 
as a biochemical diagnostic marker for ‘sy-
nucleinopathies’;
to  develop  new  biochemical  preparation 
protocols for samples containing markers 
of interest to be analysed by (q)-iPCR. 

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DIAGNOSTICS

Jean-Francois delforge, Benjamin Klein, 
Isabelle Zitte, Julien Lacauste
ALCIS
Besançon, France

awad Osman, daniela Liche, 
Heinrich Ina, Ingolf Lachmann
AJ ROBOSCREEN
Leipzig, Germany

Fabienne Poncin-Epaillard
Université du Maine
Le Mans, France

armand Perret-Liaudet, 
Isabelle Quadrio, Jérémie Seguin
CHU-Lyon 
Hôpital Neurologique
Laboratoire Diagnostic Maladies à prions
Bron, France

Miran Mozetic, anton Zalar, Janez Kovac, alenka 
Vesel, Tatjana Filipic, Uros Cvelbar, Janez Trtnik
Institut Jozef Stefan 
Slovenia, Ljubljana

david allsop 
Lancaster University
Lancaster, UK

Gabor Kovacs, Zsuzsanna Földvári, Katalin Majtényi 
Orszagos Pszichiatriai es Neurologiai Intezet
Hungary, Budapest

andreas Kage and Kathleen Grüttner
Charité – Universitätsmedizin Berlin
Institut für Laboratoriumsmedizin und Pathobiochemie
Berlin, Germany

Technological objectives:
1) 

To adapt engineering technologies (nota-
bly, surface technology adapted to manu-
factured  storage  and  analysis  supports), 
generating  higher  signal/background, 
such  as  q-iPCR  tubes  and  the  magnetic 
beads. These latter will be in encapsulated 
magnetite,  surfactant-free,  with  a  high 
binding capacity, a high surface area, and 
an  excellent  lot-to-lot  reproducibility,  as 
well as with mechanical and chemical sta-
bility.
To allow the partnership to acquire indus-
trial property rights in a sector which may 
become  very  competitive  in  the  near  fu-
ture,  and  thus  give  the  European  market 
the  opportunity  to  be  at  the  forefront  of 
this technology,
To make small pilot production of proto-
types  validated  for  the  neurodegenera-
tive disease area, with a view to rapid in-
dustrial development. 

2) 

3) 

Coordinator 

Willy Zorzi
Université de Liège
Centre de Recherche sur les Protéines Prion 
Institut de Pharmacie
B36, n°1 avenue de l’Hôpital
4000 Liège, Belgium
E-mail: willy.zorzi@ulg.ac.be

Partners

Gilbert Legeay and arnaud Coudreuse
Association pour les Transferts de Technologies du Mans
Le Mans, France

Thierry daviet
EUDICA
Annecy-le-Vieux, France

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Diagnostics

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DIAGNOSTICS

DiMI

diagnostic Molecular Imaging (diMI): a European network of excellence for 
the development of new molecular imaging strategies aiming to improve the 
diagnostic and therapy of human diseases

LSHB-CT-2005-512146
Contract No 
Project type  Network of Excellence 

EC contribution  e 10 700 000
Starting date   1 april 2005

duration  60 months

Website  www.dimi.eu

Background and objectives:

Neuroscience
Phenotyping of animal
 models/patients for early
diagnosis and imaging 
disease progression 

Cardiovascular 
Early detection of atherosclerosis 
and cardiac dysfunction 
and imaging disease progression

Animal Models 
Animal Imaging Library for 
Animal Imaging Library for 
validation of molecular markers in vitro and in vivo
 in vivo
validation of molecular markers in vitro and in vivo
validation of molecular markers in vitro and
validation of molecular markers in vitro and
validation of molecular markers in vitro and in vivo

Diagnostic Molecular Imaging Probes
Development of improved 
smart diagnostic imaging agents 

Diagnostic Molecular Imaging Technology 
Integration multimodal imaging technology
(MRI, PET, SPECT, OI)

Inflammation 
& Regeneration 
In vivo detection of
 transcriptional regulation 
 transcriptional regulation 
and migration of 
inflammatory 
and stem cells

Integrating Activities
Sharing facilities, equipment
Exchange of personnel 
Integration of SMEs

Dissemination Activities
Training/Education 
Communication 
Exploitation 

Innovations, Exploitations, Publications,
Innovations, Exploitations, Publications,
Innovations, Exploitations, Publications,
Training, Meetings, Common Knowledge

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DiMI

The main objective of the DiMI project is the cre-
ation of a Network of Excellence:
•	

to	
integrate	 multidisciplinary	 research	
aiming towards the development of new 
probes  and  novel  multimodal  non-inva-
sive  imaging  technology  for  early  diag-
nosis,  assessment  of  disease  progression 
and  treatment  evaluation  of  diseases  of 
the  central  nervous,  cardiovascular  and 
immune	system;
to	 achieve	 efficient	 training	 of	 young	 re-
searchers, dissemination of new common 
knowledge  and  integration  of  SMEs  and 
industry;
to	 reach	 the	 European	 leadership	 role	 in	
topics related to molecular imaging for di-
agnostic purpose, especially with respect 
to the creation of common data platforms, 
standards and guidelines.

•	

•	

Approach and methodology:

The  Network  consists  of  research  groups  from 
13  European  countries  with  expertise  covering 
nearly the entire field of molecular imaging. The 
consortium  is  performing  research  tasks  within 
the fields of probe and technology development, 
generation and evaluation of animal models, as 
well as preclinical and clinical evaluation and di-
agnostics in cardiology, neuroscience, inflamma-
tion and regeneration. Furthermore, the project 
features 12 training platforms with a wide offer 
in imaging modalities and topics.

Expected outcome:

The Joint Production Agreement of DiMI will join 
and  reinforce  researchers  and  scientists  from 
all  specialties  in  the  six  main  topics  of  the  field 

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DIAGNOSTICS

of  molecular  imaging  for  diagnostic  purposes. 
These  main  topics  are  inter-related  on  horizon-
tal tasks for developing technological aspects of 
molecular imaging, like integration of multimo-
dal radiotracer, magnetic resonance and optical 
imaging methods, as well as creating new diag-
nostic and smart imaging probes and validating 
animal  models.  Results  obtained  within  these 
horizontal activities will serve as the basis for the 
vertical  tasks  that  target  applications  in  major 
disease models and patients (CNS, heart, inflam-
mation). Besides these scientific results and their 
uses,  the  main  focus  within  the  DiMI  Network 
lies  in  strengthening  the  Diagnostic  Molecular 
Imaging research activities at the European level, 
the formation of a European Society of Molecular 
Imaging (ESMI), and the education of scientists, 
clinicians and society about the potential impact 
of molecular imaging for diagnostic purposes.

Main findings:

•	

•	

•	

•	

•	

•	

New	ultra-high	resolution	SPECT	with	re-
construction	software;
The	 SimSET+GEANT4	 (SimG4)	 simulation	
programme has been extended to model 
the microPET P4 detector and end shield 
geometry;
Various	 new	 radiotracers	 and	 MR-based	
and  optical  imaging  probes  were  devel-
oped  and  tested  with  regards  to  toxicity 
and	imaging;	
A	 number	 of	 animal	 models	 useful	 for	
imaging  studies  of  neurological  and  car-
diovascular  diseases  were  characterised 
by imaging to test new tracers, to validate 
the  biological  targets,  to  investigate  the 
fate of transplanted cells, and to test the 
effect	of	therapeutic	agents;
Over	 200	 cases	 and	 controls	 have	 been	
screened  for  suitability  for  identification 
of  novel  neuroimaging 
in 
neurodegenerative	disease;
Clinical	 protocols	 were	 prepared	 and	
harmonised  to  enable  imaging  studies 

targets 

Post-contrast (0.5 mmol/kg GdDTPA) T1W image of a rat 
acquired at 4.7T following infection with Streptococcusp-
neumoniae. Note the significant meningeal 

•	

•	

for  early  diagnosis  of  neurodegenerative 
disease;
Various	experimental	and	clinical	imaging	
studies have been performed by multiple 
partners	for	imaging	neuroinflammation;	
Protocols	 to	 allow	 multimodal	 imaging	
of arteriosclerotic lesions, as well as stem 
cells  in  the  CNS  and  heart  have  been 
developed.

Major publications:

Kopka, K., et al., ‘5-Pyrrolidinylsulfonyl Isatins as a 
Potential Tool for the Molecular Imaging of Cas-
pases  in  Apoptosis’,  J  Med  Chem,	 2006,	 Nov	 16;	
49(23):6704-6715.

Ottobrini,  L.,  et  al.,  ‘Molecular  imaging:  A  new 
way to study molecular processes in vivo’, Mol Cell 
Endocrinol, 2006, 246, 69-75.

Himmelreich, U., et al., ‘A responsive MRI contrast 
agent to monitor functional cell status’, NeuroIm-
age, 2006, 32:1142-1149.

‘Pharmacological  Charac-
Chalon,  S.,  et  al., 
(E)-N-(4-Fluorobut-2-enyl)-2β-
terization 
carbomethoxy-3β-(4’-tolyl) nortropane (LBT-999) 

of 

Diagnostics - Imaging, Nanoparticles and Biosensors

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DiMI

as a Highly Promising Fluorinated Ligand for the 
Dopamine Transporter’, JPET, 2006, 317, 147-152.

Lucas,  A.J.,  et  al., ‘Development  of  a  Combined 
microPET®-MR  System.  Technol  Cancer  Res  Treat, 
2006,	Aug;	5(4):337-341.

Vercammen,  L.,  et  al.,  ‘Parkin  Protects  against 
Neurotoxicity  in  the  6-Hydroxydopamine  Rat 
Model  for  Parkinson’s  Disease’,  Mol  Ther,  2006, 
Nov;14(5):716-723.

Fulton,  D.A.,  et  al., ‘Glycoconjugates  of  gadolin-
ium complexes for MRI applications’, ChemComm, 
2006, 1064-1066.

Soraya Benderbous
University of Tours
Laboratoire Biophysique Médicale et parmaceutique
Tours, France

ann Planas
Institut d’Investigacions Biomèdiques August Pi i 
Sunyer (IDIBAPS)
Barcelona (Spain) 

adriana Maggi
University of Milan
Centre of Excellence on Neurodegenerative Diseases
Milan, Italy

Gitte Moos Knudsen
Copenhagen University Hospital Rigshospitalet
Neurobiology Research Unit
Copenhagen, Denmark

Coordinator 

andreas H. Jacobs
University of Cologne
Laboratory for Gene Therapy and Molecular Imaging
Gleuelerstr. 50
50931 Cologne, Germany
E-mail: dimi.admin@nf.mpg.de

annemie van der Linden
University of Antwerp
Vision-Lab, Bio-Imaging Lab
Laboratory of Cell Biology and Histology, 
and Digital Cell Imaging Labs
Antwerp, Belgium

Partners 

John Clark
University of Cambridge
Wolfson Brain Imaging Centre
Cambridge, UK

Silvio aime
University of Torino
Department of Chemistry IFM and
Centre for Molecular Imaging
Turin, Italy

denis Guilloteau
University Hospital Tours
Unit INSERM 316
Tours, France

Chrit Moonen
Université Victor Segalen Bordeaux
Molecular and Functional Imaging: From Physiology
 to Therapy Technological Research Team
Bordeaux, France

Pascal Laugier
Université Paris VI
Targeted and Functional Ultrasound
Laboratoire d’Imagerie Paramétrique
UMR 7623 CNRS
Paris, France

Roland Matrippolito
University of Paris Sud
Institute of Nuclear Physics 
UMR 8608 CNRS
Paris, France

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DIAGNOSTICS

Markus Schwaiger
Technical University of Munich
Department of Nuclear Medicine
Munich, Germany

Harald Carlsen
University of Oslo
Faculty of Medicine
Institute for Nutrition Research and
 Institute of Immunology
Oslo, Norway

Bertrand Tavitian
CEA - Experimental molecular 
medicine laboratory 
Orsay, France

Philippe Hantrave
CEA – The ImaGene Program
Fontenay-aux-Roses / Orsay, France

Philippe Rizo
CEA – LETI: Département Systèmes
 pour l’Information et la Santé
Grenoble, France

Elena Ceccarelli and Corinne Carreaux
CEA – National Institute for Nuclear 
Science and Technology
Saclay, France

Bruno Brisson
Biospace Lab
Paris, France

Veerle Baekelandt
University of Leuven
Division of Molecular Medicine
Leuven, Belgium

Luc Mortelmans
University of Leuven
Division of Nuclear Medicine, Medical Imaging
Leuven, Belgium

deniz Kirik
Lund University 
Department of Physiological Sciences
Lund, Sweden

Rikard Holmdahl
Lund University Medical Faculty
Medical Inflammation Research (MIR) at
 the Biomedical Center
Lund, Sweden

david Brooks
Imperial College
Neurology Group
MRC Clinical Sciences Centre
London, UK

Hazel ann Jones
Imperial College
College of Science Technology and Medicine
London, UK

Ignasi Carrió
Hospital Sant Pau and CETIR Foundation Autonomous 
University of Barcelona
Department of Nuclear Medicine
Barcelona, Spain

Klaus P. Ebmeier
University of Edinburgh
SHEFC Brain Imaging Centre for Scotland
Edinburgh, UK

Bernd Fleischmann
University of Bonn
Institute of Physiology I
Bonn, Germany

Christer Halldin
Karolinska Institute
Department of Clinical Neuroscience
Psychiatry Section
Stockholm, Sweden

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DiMI

agneta Nordberg
Karolinska Institute
Department Neurotec
Division of Molecular Neuropharmacology
Uppsala, Sweden

andreas Bauer
Research Centre Juelich
Institute of Medicine
Juelich, Germany

Matthias Hoehn
MPI for Neurological Research
In vivo NMR Laboratory
Cologne, Germany

Chris Reutelingsperger
Cardiovascular Research Institute Maastricht
Maastricht, Netherlands

Michael Horn
University of Göteborg
Center for Bio-Imaging
Gothenburg, Sweden

Sabina Pappata
University of Naples ‘Federico II’
CNR Naples and Department of Clinical
 and Experimental Medicine
Naples, Italy

alberto auricchio
University of Naples
Telethon Institute of Genetics and Medicine
Biostructure and Bioimaging Institute 
of the National Research Center
Naples, Italy

david Parker
University of Durham
Department of Chemistry
Durham, UK

Ferrucio Fazio
Vita-Salute San Raffaele University
Scientific Institute Hospital San Raffaele
Institute of Bioimaging and Molecular Physiology 
CNR
Milan, Italy

andreas Jacobs and Wolf-deiter Heiss
University Medical Center Groningen
Department of Neurology and Neuroimaging Center
Groningen, Netherlands

adriana Gittenberger-de Groot
Leiden University Medical Centre
Department of Anatomy and Embryology
Leiden, Netherlands

Philip Elsinga
Groningen PET-Center
Groningen, Netherlands

Christopher Morris
University of Newcastle
Institute for Ageing and Health
Wolfson Research Centre
Newcastle, UK

Klaas Nicolay
Eindhoven University of Technology
Biomedical NMR
Department of Biomedical Engineering
Eindhoven, Netherlands

Hans Romijn
Leiden University Medical Centre
Endocrinology Research Laboratory
Department of Endocrinology
Leiden, Netherlands

Eric Salmon
University of Liege
Cyclotron Research Centre
Liege, Belgium

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Eva Sykova
Charles University
Institute of Experimental Medicine ASCR
Department of Neuroscience and Center for Cell Therapy 
and Tissue Repair
Prague, Czech Republic

Ulrich Bogdahn
University of Regensburg
Department of Neurology
Regensburg, Germany

Karl Herholz
University of Manchester
Wolfson Molecular Imaging Centre and
Centre for Clinical Neuroscience
Manchester, UK

andrian Lammertsma
VU University Medical Centre
Department of Nuclear Medicine and PET Research
Amsterdam, Netherlands

Bodo Levkau
University of Duisburg-Essen
Institute of Pathophysiology
University Hospital Essen
Essen, Germany

Michael Schäfers
University of Muenster
Interdisciplinary Molecular Imaging 
Network for Cardiovascular Diseases
Muenster, Germany

Walter Heindel
University of Muenster
Department of Clinical Radiology
Muenster, Germany

denis Vivien
University of Caen
Cerebral Imaging Centre for Research 
on Neuroscience
Caen, France

Harald Carlson and Jan O. Moskaug
Cgene AS (former MiceTech)
Oslo, Norway

Jose Masdeu
University of Navarre
Neuroscience Centre
Pamplona, Spain

Jean Bernard deloye
Cyclopharma Laboratories
Saint Beauzire, France

Stefan Wecker
Medical Research GmbH
Cologne, Germany

Ivan Lukes
Charles University
Department of Inorganic Chemistry and 
Department of Organic Chemistry
Prague, Czech Republic

Renata Mikolajczak
POLATOM
Research and Development Department 
of Radioisotope Centre
Otwock, Poland

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DASIM

diagnostic applications of Synchroton Infrared Microspectroscopy

Contract No 
Project type 

LSSB-CT-2005-005326
Specific Support action

EC contribution  e 280 000
Starting date   1 July 2005
duration  36 months

Website  www.dasim.eu

Background and objectives:

Diagnosis  of  disease  is  the  basis  for  all  clinical 
medicine. The primary requirement is reliability, 
in order to ensure that therapies are appropriate 
and  successful.  However,  the  modern  require-
ments  of  clinicians  from  diagnostic  services  go 
beyond a simple yes or no to a particular disease. 
Successful  therapy  requires  information  on  dis-
ease  subtype  classification,  assessment  of  the 
disease stage and extent such as the grading of 
tumours,  as  well  as  the  monitoring  of  disease 
progress  and  therapeutic  success.  Rapid  patho-
logical  analysis  can  also  be  a  requirement,  to 
ensure timely clinical intervention and maximise 
the chances of therapeutic success. 

Synchrotrons are particle accelerators dedicated 
to the production of light for scientific research. 
Within  a  synchrotron,  electrons  are  accelerated 
almost to the speed of light around an approxi-
mately circular path several hundreds of meters 
in length. As the electrons fly around the curves, 
they emit extremely broadband radiation cover-
ing the entire spectral range from hard x-rays to 
millimeter waves. The primary advantage of a syn-
chrotron light source for infrared spectroscopy is 
its  high  brilliance  -  that  is,  a  high  intensity,  low 
divergence  beam  from  an  almost  point  source. 
When a sample area of only a few microns is to 
be  investigated,  a  synchrotron  light  source  can 
put up to a 1000 times more infrared light onto 
the sample than a conventional instrument.

New technologies are thus constantly sought to 
assist  pathologists  in  this  demanding  and  im-
portant  clinical  area.  Infrared  spectroscopy  can 
deliver  a  very  quick ‘biochemical  fingerprint’  of 
cells and tissues, and it has been demonstrated 
convincingly in many studies that infrared spec-
troscopy  can  be  used  to  classify  tissues  as  nor-
mal  or  pathological,  as  well  as  for  classifying 
and  grading  pathological  samples.  This  is  the 
motivation for more than 70 scientists and clini-
cians from 9 European countries involved in the 
DASIM project, who have joined forces to investi-
gate whether a practical tool for pathologists can 
be developed on this basis. The common factor 
in this diverse group is their interest in using syn-
chrotrons as high-performance light sources for 
infrared spectroscopy of cells and tissues.

At  each  of  Europe’s  synchrotrons  offering  infra-
red  spectroscopy  —  ANKA  and  BESSY  in  Ger-
many,  DAFNE  and  ELETTRA  in  Italy,  SRS  and 
DIAMOND in the UK, SOLEIL and ESRF in France, 
MAX  in  Sweden  and  SLS  in  Switzerland  —  lo-
cal collaborations exist or are being established 
to  explore  biomedical  applications.  The  DASIM 
project is networking this research effort on a Eu-
ropean scale, providing a forum for international 
cross-fertilisation  of  ideas  and  multidisciplinary 
expertise, facilitating access to synchrotrons for 
researchers from EU countries without their own 
facility,  and  promoting  methodological  valida-
tion  by  adding  a  multi-centric  quality  control 
perspective.  In  this  way,  DASIM  is  accelerating 
the  transfer  of  this  emerging  technology  into 
clinical practice.

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Main findings:

In this framework, several workshops and a sum-
mer  school  on  synchrotron  infrared  microspec-
troscopy  have  been  organised.  The  first  DASIM 
meeting was organised by the University of Leeds 
(19-20 July 2005) and hosted at the SRS synchro-
tron radiation facility in Daresbury. The meeting, 
chaired  by  Dr  Mark Tobin,  triggered  the  DASIM 
activity  presenting  the  capabilities  of  the  avail-
able European synchrotrons and, in order to use 
IR  microspectroscopy,  the  needs  of  the  clinical 
environment covering screening, diagnosis, sur-
gery, post operative investigation and therapeu-
tics. Teams already working on clinical problems 
through the use of spectroscopic tools presented 
contributions about diagnostic applications and 
the  international  collaborations  in  the  scientific 
areas already operative. At the meeting, working 
parties began identifying the key issues of the re-
search areas involved in the project. 

Cooperation  between  teams  of  biologists,  cli-
nicians  and  synchrotron  scientists  started  and 
continuous progress was achieved as witnessed 
by the programme of the second DASIM meet-
ing. The event was chaired by Dr Augusto Mar-

Infrared microspectroscopy image of protein, lipid and 
nucleic acid distributions in a single human prostate cancer 
cell (picture courtesy of DASIM consortium member Dr Peter 
Gardner, University of Manchester, UK)

DIAGNOSTICS

celli  and  hosted  at  the  Laboratori  Nazionali  di 
Frascati  of  the  INFN  (21-23  June  2006)  where 
one  of  the  IR  synchrotron  radiation  facilities  is 
now  running.  During  the  meeting  specific  is-
sues  such  as  the  full  understanding  of  the  ad-
instruments, 
vantages  of  synchrotron-based 
the  coordination  of  the  ongoing  research,  the 
attempt to define standard methodologies and 
the support to new research teams joining the 
initial  participating  teams  were  discussed. The 
admission of new teams has been a unique op-
portunity to discuss the status and the perspec-
tives  of  the  European  IR  synchrotron  facilities 
working in this area, including those under con-
struction, like DIAMOND, and to extend the in-
ternational collaborations to overseas countries 
such as Australia, China and the USA.

The  most  recent  DASIM  workshop  was  organ-
ised by the University of Reims and held at the 
French  synchrotron  facility  SOLEIL  in  Saint-
Aubin  (10-11  September  2007),  chaired  by  Dr 
Pascale  Roy,  Dr  Paul  Dumas  and  Dr  Ganesh 
Sockalingum.  A  greater  and  interdisciplinary 
community  of  scientists  working  in  both  aca-
demic and medical environments attended the 
third workshop. The event was arranged with for 
parallel sessions dedicated to the DASIM work-
groups: Clinical trials, Single Cell Spectroscopy, 
Unified  Merit  Parameters  and  Complementary 
Spectroscopy Approaches.

A central feature of the DASIM project is indeed 
the formation of working parties to address spe-
cific  aspects  of  the  project  at  the  annual  meet-
ings and at their own special meetings, such as 
the Joint Single Cell Spectroscopy/Raman Work-
ing Group Meeting held in Krakow, Poland on 7 
and 8 February 2008. 

Detailed information is available on the DASIM 
website  (http://www.dasim.eu/)  —  the  ac-
tive ‘virtual’ forum of the initiative open to the 
whole  EU  community  where  the  entire  DASIM 
databank is available.

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DASIM

Poster advertising the second DASIM meeting in 
Frascati, 21-23 June 2006 

In addition to the results of the cooperation among 
teams, their scientific exchange and the publica-
tions, workgroup reports will represent the main 
feedback of this SSA to the European community. 
Their summaries are the main achievements fore-
seen for the fourth and final workshop that will be 
held  in  Dublin  (12-13  June  2008),  hosted  by  the 
Dublin Institute of Technology.

Among the DASIM initiatives to be mentioned is 
the International Summer School on synchrotron 
infrared  microspectroscopy  and  biomedical  ap-
plications, the first in the world that will be held 
at  Karlsruhe  (23-27  June  2008),  hosted  by  the 
ANKA  laboratory. The  school  is  open  to  a  wide 
range of students both undergraduate and post-
graduate, and scientists belonging to the differ-
ent  disciplines  involved  in  DASIM. The  summer 
school will be organised in small groups attend-
ing  parallel  modules  that  will  cover  all  aspects 
of the field, both theoretically and with practical 
training of the IR instrumentations.

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Diagnostics - Imaging, Nanoparticles and Biosensors

Finally,  DASIM  members  are  working  to  com-
plete an original textbook that will be published 
by the Royal Society of Chemistry and will repre-
sent a guide for future generations of scientists 
involved  in  the  scientific  areas  covered  by  this 
SSA. The interdisciplinary book written for non-
experts  with  an  accessible ‘language’  has  been 
organised in several chapters presenting the var-
ious aspects of the field plus a limited number of 
‘case studies’ discussed in great details.

Major publications:

Conti, C., Ferraris, P., Giorgini, E., Rubini, C., Sab-
batini,  S.,  Tosi,  G.,  Anastassopoulou,  J.,  Arapan-
toni,  P.,  Boukaki,  E.,  Konstadoudakis,  S.,  The-
ophanides, T., Valavanis,  C., ‘FT-IR  microimaging 
spectroscopy:  discrimination  between  healthy 
and  neoplastic  human  colon  tissues’,  Journal  of 
Molecular Structure, 2008, in press.

Gazi, E., Dwyer, J., Lockyer, N.P, Gardner, P., Shanks, 
J.H, Roulson, J-A., Hart, C.A., Clarke, N.W., Brown, 
M.D., ‘Biomolecular  profiling  of  metastatic  pros-
tate cancer cells in bone marrow tissue using FTIR 
microspectroscopy: a pilot study’, Analytical and 
Bioanalytical Chemistry, 2007, 387, 1621–1631.

Gazi, E., Gardner, P., Lockyer, N.P., Hart, C.A, Clarke, 
N.W.,  Brown,  M.D.,  ‘Probing  Lipid  Translocation 
Between  Adipocytes  and  Prostate  Cancer  Cells 
with Imaging FTIR Microspectroscopy’, Journal of 
Lipid Research, 2007, 48, 1846-1856.

Generosi, J., Piccinini, M., Marcelli, A., Belardinelli, S., 
Pozzi, D., Congiu Castellano, A., ‘Characterization of 
solid supported lipoplexes by FTIR microspectros-
copy’, Infrared Physics Technology, 2007, 50, 14-20.

Kwiatek,  W.M.,  Banas,  A.,  Banas,  K.,  Cinque,  G., 
Dyduch,  G.,  Falkenberg,  G.,  Kisiel,  A.,  Marcelli, 
A.,  Podgórczyk,  M.,  ‘Micro  and  bulk  analysis  of 
prostate  tissues  classified  as  hyperplasia’,  Spec-
trochimica Acta Part B: Atomic Spectroscopy, 2007, 
62, 707-710.

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Lyng, F., Ó Faoláin, E., Conroy, J., Meade, A., Knief, 
P.,  Duffy,  B.,  Hunter,  M.,  Byrne,  J.,  Kelehan,  P., 
Byrne, H.J., ‘Vibrational spectroscopy for pathol-
ogy,  from  biochemical  analysis  to  diagnostic 
tool’, Experimental and Molecular Pathology, 2007, 
82, 121-129.

Paluszkiewicz, C., Kwiatek, W.M., Banas, A., Kisiel, 
A., Marcelli, A., Piccinini, M., ‘SR-FTIR spectroscop-
ic preliminary findings of non-cancerous, cancer-
ous,  and  hyperplastic  human  prostate  tissues’, 
Vibrational Spectroscopy, 2007, 43, 237.

DIAGNOSTICS

Coordinator

david Moss
Synchrotron Light Source ANKA
Forschungszentrum Karlsruhe
P.O. Box 3640
76021 Karlsruhe, Germany
E-mail: david.moss@anka.fzk.de

Partners: 

augusto Marcelli
INFN-LNF
Frascati, Italy

Ganesh Sockalingum
University of Reims
Reims, France

Marco Colombatti
University of Verona, Italy 

Fiona Lyng
DIT
Dublin, Ireland

Sheila Fisher
University of Leeds
Leeds, UK

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NeuroTAS

Microfluidic total analysis system for the early diagnostic  
of neurodegenerative disorders

Contract No 
Project type 

LHSB-CT-2006-037953
Specific Targeted
  Research Project 

EC contribution  e 2 499 999

Starting date   1 January 2007
duration  36 months

Website  www.neurotas.eu

Background and objectives:

The  NeuroTAS  project  aims  to  develop  a  proto-
type  of  a  miniaturised  system  for  diagnostics  in 
the  early  stage  of  Alzheimer’s  disease  and  other 
neurodegenerative diseases, or as a point-of-care 
instrument for patient follow-up. The system to be 
developed belongs to the emerging field of lab-
on-chip  systems.  It  incorporates  several  innova-
tive enabling technologies, including microfluidic 
flow control, highly sophisticated nanobiodevices 
with integrated detection, and novel magnetic na-
noparticles. These approaches will lead to unprec-
edented  integration  and  automation,  and  allow 
routine  implementation  of  tests  that  can,  at  the 
moment, only be performed in a small number of 
specialised research laboratories. 

The system will use biomarkers present in blood, 
such  as  differently  cleaved  β  amyloid  peptides 
and  post-translational  modifications  of  the  tau 
protein.  The  miniaturisation  and  integration  of 
innovative detection technologies are intended 
to extend the sensitivity of biomarker detection, 
and thus improve the precocity of diagnosis. This 
is of paramount importance for the treatment of 
neurodegenerative  diseases,  since  therapeutic 
approaches  able  to  retard  the  evolution  of  the 
diseases are progressing and appear promising, 
but  little  hope  exists  for  the  repair  of  existing 
brain damage. 

The method also aims at allowing the simultane-
ous study of a wide range of markers, improving 

88

Diagnostics - Imaging, Nanoparticles and Biosensors

the  early  discrimination  between  different  neu-
rodegenerative  diseases,  and  thus  the  choice  of 
treatment. Indeed, the NeuroTAS system will have 
a modular and evolving structure, and will be able 
to progressively test and integrate new biomark-
ers into its diagnostic scheme that may be discov-
ered during development of the prototype. 

The consortium is a combination of four academic, 
methodology-oriented laboratories (with comple-
mentary competences in biochemistry, analytical 
chemistry,  biophysics  and  microfabrication),  two 
small and medium-sized enterprises in the field of 
microfluidics, and two end-users directly involved 
in patient diagnosis and treatment.

Approach and methodology: 

The envisioned device will present the following 
advantages: 
•	

full	automation	(from	plasma	to	result)	for	
low  cost,  reproducibility  and  usability  in 
routine	diagnosis	or	patient	follow-up;
fast	 analysis	 (the	 ultimate	 objective	 is	
one  hour,  and  the  criterion  for  success 
will  be  set  at  three  hours  total  time,  to 
be compared with present protocols that 
last	several	days);
high	sensitivity;	
multi-parameter,	 multiplexed	 analysis	 to	
allow  for  differentiation  between  differ-
ent  types  of  neurological  diseases  that 
cannot  presently  be  distinguished  at  an 
early  stage,  and  to  permit  a  detailed  in-

•	

•	
•	

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DIAGNOSTICS

detection  will  be  performed  directly  after 
immunocapture. The  system  to  be  devel-
oped will have the capability of detecting 
in parallel biomarkers from several capture 
chambers, using a secondary antibody la-
belled with an enzyme that is able to trans-
form a substrate into an electrochemically 
active compound. For Aβ peptides, specific 
antibodies  against  several  β  amyloid  spe-
cies exist, so that a direct capture and elec-
trochemical detection strategy of the ELISA 
type can be contemplated.
Microchannel	 electrophoresis-laser	
in-
duced  fluorescence  profiling  module 
(ME-LIF).  For  some  other  biomarkers,  a 
more elaborate profiling strategy (electro-
phoretic  profiling  track)  should  be  used. 
In  this  approach,  the  preconcentrated 
proteins/peptides  will  be  transferred  to 
an  electrokinetic  profiling  module, 
in 
which  they  will  be  profiled  by  high-res-
olution  capillary  electrophoresis  (CE)  on 
chips.  Two  different  detection  strategies 
will	 be	 developed;	 the	 first	 one	 will	 be	
based on fluorescent labelling and direct 
on-chip  detection  using  an  innovative 
technology centred on the incorporation 
of planar waveguides integrated into the 
chip  during  fabrication.  It  dramatically 
simplifies the detection scheme, avoiding 
complicated and expensive optics, and is 
thus particularly well-suited to the devel-
opment  of  an  integrated  lab-on-chip.  As 
part of the project, this approach will be 
implemented  in  an  ‘all-polymer’  scheme 
to retain full compatibility with the other 
modules of the project.
Hyphenated	 microchannel	 electrophore-
(‘Micro-
sis-immunodetection  module 
Western’). As an alternative to the ME-LIF 
module outlined above, a second strategy 
will  combine  CE  separation  followed  by 
translation  into  a  secondary  multiplexed 
immuno-immobilisation  element.  This 
new approach, which will be a major pre-

•	

•	

Diagnostics - Imaging, Nanoparticles and Biosensors

89

vestigation of the evolution of biomarkers 
in patients. It is hoped that this will help 
researchers to better understand the dis-
ease,  and  also  be  useful  in  the  patients’ 
follow-up routine.

The  prototype  to  be  developed  in  the  project 
is  an  automated  system  capable  of  performing 
sequential  capture,  analysis  and  detection  of 
protein  and  peptide  biomarkers.  For  both  Aβ 
peptides and tau proteins, two strategies will be 
considered.
1. 

immunocapture 

Direct track: this strategy consists of mul-
followed  by 
tiplexed 
direct  detection  by  miniaturised  ELISA. 
This strategy will be relevant if antibodies 
specific enough for a complete medically 
relevant profiling are available.
Electrophoretic  profiling  track:  this  strate-
gy, more powerful but also more demand-
ing on the instrumental side, involves im-
munocapture  followed  by  electrokinetic 
separation and post-separation detection.

2. 

The lab-on-chip instruments will be designed in 
a  modular  format  incorporating  the  following 
principal modules.
•	

The	multiplexed	immunocapture	module	
(MI) is common to both tracks. The protein 
capture  will  be  performed  by  circulating 
plasma in a sequential series of immunoaf-
finity microcolumns dedicated to the cap-
ture of specific peptides (one Aβ species) 
or one specific tau form per chamber. The 
main  strategy  will  rely  on  an  innovative 
approach  based  on  magnetic  nanoparti-
cles. This system uses self-organisation of 
the nanoparticles to create a compact mi-
crocolumn  with  auto-calibrated  micron-
sized  pores.  It  combines  a  high-loading 
capacity and fast affinity reaction, thanks 
to a high surface-to-volume ratio and ex-
tremely thin diffusion layer.
Electrochemical	detection	module	(ECD).	In	
the direct track option, an electrochemical 

•	

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NeuroTAS

scient and innovative aspect of the project, 
will combine the resolution of CE with the 
sensitivity  and  specificity  of  ELISA-type 
immunoassays.  Essentially,  this  develop-
ment will introduce the power of Western 
blotting to the lab-on-chip world.

This  option  will  be  selected  if  either  the  online 
fluorescent  labelling  strategy  (ME-LIF)  does  not 
provide  sufficient  resolution  (this  may  be  the 
case in particular for tau proteins, since differenc-
es  in  phosphorylation  levels  only  lead  to  small 
differences in mobilities that may be hidden by 
the labelling step), or to increase the sensitivity 
and  the  specificity  of  the  detection.  Sensitivity 
enhancement will be made possible, particularly 
because  this  approach  allows  for  an  ELISA-type 
amplification step.

The  final  system  will  comprise  two  sequential 
blocks,  one  dedicated  to  Aβ  peptides,  and  the 
other  to  tau  proteins.  Depending  on  the  op-
tions chosen for each family of biomarkers, the 
corresponding block will itself comprise several 
‘modules’,  selected  among  the  ones  described 
above, depending on the option chosen for pro-
filing. The direct track involves an immunoaffin-
ity  module  and  an  electrochemical  detection 
module,  whereas  electrokinetic  profiling  will 
involve  an  immunoaffinity  module,  followed 
by an electrokinetic profiling module, involving 
either  the  MELIF  strategy  or  the  MicroWestern 
strategy.  The  modular  strategy  will  allow  for 
parallel  development  and  optimisation,  but  a 
requirement  of  compatibility  between  the  dif-
ferent  modules  will  be  included  from  the  start 
to  allow  the  integration  of  all  elements  into  a 
single microfluidic system. 

Coordinator 

Jörg P Kutter
Technical University of Denmark 
Department of Micro and Nanotechnology
Building 344
2800 Lyngby, Denmark
E-mail: jku@mic.dtu.dk

Scientific coordinator 

Jean Louis Viovy
UMR 168 CNRS/Curie Institute
26 Rue d’Ulm
75005 Paris, France
E-mail: jean-louis.viovy@curie.fr

Partners 

Myriam Taverna
University of Paris-Sud
Paris, France

Zusana Bilkova
University of Pardubice
Pardubice, Czech Republic

Frédéric Reymond
Diagnoswiss
Lausanne, Switzerland

Markus Otto
University of Ulm
Ulm, Germany

Jens Wiltfang
University of Erlangen-Nürnberg
Erlangen, Germany

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DIAGNOSTICS

POC4life

Multiparametric quantum dot bioassay for point of care diagnosis

Contract No 
Project type 

LSHB-CT-2006-037933
SME-Specific Targeted

EC contribution  e 2 497 820

  Research Project

Starting date   1 January 2007
duration  36 months

Website  www.poc4life.eu

Background and objectives:

This  project  aims  to  improve  the  healthcare  of 
patients  by  elaborating  a  unique  Point  of  Care 
(POC)  diagnosis  platform  that  will  help  special-
ists to deliver an earlier diagnosis and to decide 
on appropriate treatment. The goal is to provide 
the clinicians with multiparametric measurement 
of the main 4/5 essential markers and to support 
decisions with a software tool. This will be a cost-
effective breakthrough in the diagnosis market.

Each year, 377 000 new European citizens devel-
op lung cancer and 340 000 die from it. Studies 
show  that  early  diagnosis  and  accurate  cancer 
typing could save a number of lives. Laborato-
ries  nowadays  have  a  wide  panel  of  reproduc-
ible diagnostic tests at their disposal: these are 
mostly routine tests realised in centralised labo-
ratories. The needs for early diagnosis, multipar-
ametric analysis of results and quick monitoring 
of  disease  progression  or  therapeutic  sensitiv-
ity  were  progressively  left  aside,  whereas  they 
could be fulfilled with using decentralised diag-
nostic tools, close to the patient.

Among  the  possible  applications  of  this  new 
concept,  the  partners  have  chosen  to  work  on 
the primary diagnosis of the histological types 
of lung cancer to help give an improved initial 
diagnosis  and  to  eliminate  the  15–20%  prob-
lematic or late diagnosed cases. The study will 
pay  special  attention  to  women  (lung  cancer 
death  rates  for  women  have  been  increasing 

in Europe since the 1990s and marker patterns 
may  be  different).  It  will  then  have  a  huge  im-
pact  on  health  by  contributing  to  the  fight 
against cancer and the development of gender 
dimension  in  research.  For  this  purpose,  the 
multidisciplinary  project  will  involve  academic 
researchers  (from  Germany,  Spain  and  France) 
and small and medium-sized enterprises (SMEs) 
(from  Sweden  and  the  UK)  gathering  around 
the  initiators  of  the  project  (the  SME  Cezanne, 
the  University  of  Strasbourg  in  France  and  the 
University of Potsdam in Germany) which have 
the  skills  to  build  a  multiparametric  device,  to 
develop immunoassays and to design an inter-
pretation software.

The project’s objectives are: 
•	

to	elaborate	an	innovative	medical	device:	
a unique point of care diagnosis platform 
which will help specialists to make earlier 
diagnosis  and  provide  more  appropriate 
treatments;
to	 provide	 the	 best	 possible	 integration	
of parameters by means of a consortium 
composed of public and private partners 
such as research intensive SMEs and aca-
demic	entities	in	Europe.;
to	elaborate	the	new	device	for	a	specific	
application:  the  primary  diagnosis  of  the 
different types of lung cancer. The project 
will then have a huge impact on health by 
contributing  to  the  fight  against  cancer 
and  the  development  of  gender  dimen-
sion in research.

•	

•	

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POC4life

Approach and methodology:

Expected outcome: 

The project should attain the following challeng-
ing objectives:
The  development  of  a  functional  prototype  of 
im-
POC  multi-parametric  measurement  for 
munoassays,  based  on  Homogeneous Time  Re-
solved Fluorescence (HTRF), for which main char-
acteristics are:
•	

it	 is	 equivalent	 to	 an	 A4	 sheet	 of	 paper,	
costs  less  than  EUR  2  000,  works  with  a 
sample droplet deposited on a disposable 
reagent	vessel	containing	dried	reagents;
it	 defines	 the	 panel	 of	 assays	 and	 how	
to combine them into a decision making 
software (to be developed).

•	

Potential applications:

Multiparametric diagnostics in the following fields: 
cancer, prenatal diagnostics, sepsis, cardiac

The  objective  of  the  project  is  to  generalise  this 
approach  to  combinations  of 
immuno-assay 
measurements to deliver a clear diagnosis of the 
disease  or  monitoring  information.  The  gener-
alisation means first that the diagnosis should be 
accessible  to  various  types  of  medical  practices 
(medical doctor to hospitals) and thus a low cost, 
easy-to-use  POC  device  should  be  developed. 
However, this should not be done to the detriment 
of quality and precision. A homogeneous technol-
ogy known for high-level precision can therefore 
be a judicious choice. Generalisation also means 
that various pathologies could be addressed: typi-
cally from two to four or five immuno-assays. The 
project therefore aims to allow the simultaneous 
measurement  of  four  to  five  immuno-assays  on 
the POC device with one draw of patient sample 
(one  droplet).  Finally,  generalisation  means  uni-
versality  of  the  measurement  technique  and  of 
the  data  reduction  process.  In  this  way,  fluores-
cent measurement based on FRET (Fluorescence 
Resonance  Energy  Transfer)  seems  an  excellent 
choice, since it may be extended in the future to 
other diagnostics such as DNA analysis, coagula-
tion, microbiology, etc.

Role of SMEs

The SMEs will bring to the consortium the comple-
mentary  and  comprehensive  expertise  required 
by  the  other  public  researchers  (CEZA  brings 
competence in two complementary scientific and 
technical  fields:  immunoassay  development  and 
scientific  instrumentation,  which  over  the  years 
CEZA managed efficiently to cross-fertilise, FDAB 
brings competence related to antibody develop-
ment  and  characterisation  (hybridoma  technol-
ogy,  phage  display,  gene  expression  analysis, 
c-DNA immunisation, DNA-shuffling, affinity mat-
uration)  and  competence  in  assay  development, 
and EI brings experience in flash lamps, laser di-
odes, fluorescence spectrometry and a prototype 
nanosecond plate reader.

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DIAGNOSTICS

Scientific coordinator

Emmanuel Bois
Cezanne SAS
280 allée Graham Bell
Parc Scientifique Georges Besse
30035 Nîmes cedex 1, France
E-mail: contact@cezanne.fr

Partners

Olle Nilsson
Fujirebio Diagnostics (FDAB)
Gothenburg, Sweden

S. desmond Smith
Edinburgh Instruments
Livingston, Scotland, UK

Philippe Pieri
Centre National de la Recherche Scientifique (CNRS)
Paris, France

Hans-Gerd Löhmannsröben
University of Potsdam
Potsdam – Golm, Germany

Yves Caristan
Commissariat a l’Energie Atomique (CEA)
Grenoble, France

Klaus-dieter Weltmann
Institute of Low Temperature Plasma Physics
Greifswald, Germany

Rafael Molina
Hospital Clinic Barcelona
Barcelona, Spain

Petra Stieber
Institute for Clinical Chemistry
University Hospital Munich-Grosshadern
Munich, Germany

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93

DIAGNOSIS

development of new and cost-effective methods for non-invasive diagnosis  
of human pathogens

Contract No 
Project type 

LSHB-CT-2006-037212
SME-Specific Targeted 

EC contribution  e 2 499 999

  Research Project

Starting date   1 January 2007
duration  36 months

Background and objectives:

Infectious  diseases  continue  to  be  a  serious 
burden  around  the  world,  in  both  developing 
and  industrialised  countries.  The  main  objec-
tive  of  DIAGNOSIS  is  to  deal  with  the  issue  by 
developing  a  novel,  easy  to  use,  low-cost  and 
mostly  non-invasive  biotechnological  platform 
for infectious diseases detection. The challeng-
ing aim is to reach a short and efficient sample 
treatment, which can be implemented into ex-
isting and newly developed portable PCR labo-
ratory  for  multiplex  fluorescent  pathogen  de-
tection. The concept will be proven on human 
critical pathogens but will be applicable also for 
animals, and plants pathogens. The concept will 
be  applicable  for  samples  taken  from  affected 
organisms, as well as from food/feed and envi-
ronments (water, air, soil, etc.).

The  scientific  and  technological  objectives  will 
include the development of: 1) new principles of 
nucleic	acids	sorption/desorption;	2)	innovative	
concentrating methods and materials for the en-
richment of viruses, micro-organisms and nucleic 
acids;	3)	the	adaptation	of	the	phosphoramidite	
chemistry to alternative fluorescence dyes in or-
der to broaden the labelling assortment for mul-
tiplex PCR analyses — a portable non-dependent 
on	 external	 power	 supply	 PCR	 laboratory;	 and	
4)  the  exemplary  demonstration  of  the  whole 
technological  chain  on  several  groups  of  hu-
man  pathogens,  including  the  Mycobacterium 
complex, the periodontal pathogens, the causal 

agents of population shifts within the intestinal 
microflora  associated  with  inflammatory  bowel 
diseases  and  fungal  skin  infections,  completed 
by the diagnosis of main representatives of food-
borne pathogens.

Infectious diseases are a global concern. Of the 
annual  12  million  deaths  attributable  to  infec-
tious  diseases  on  the  planet,  95%  occur  in  the 
developing  world,  particularly  in  the  most  im-
poverished  areas  where  individual  and  general 
hygiene standards remain very low and preven-
tion policies are non-existent, poorly adapted or 
insufficiently funded. 

Conversely,  economic  and  industrial  develop-
ment also accounts for the emergence of infec-
tions,  such  as  food-borne  pathogens  that  take 
advantage  of  the  increasing  industrialisation  of 
the	food	chain;	nosocomial	infections	in	the	in-
creasingly	 complex	 hospital	 environment;	 and	
travel-related  infections.  In  addition,  the  demo-
graphic  trend  towards  an  ageing  population  in 
Europe enhances the risk of increasing infection 
as elderly people are prone to invasive medical 
procedures and are, in general, more susceptible 
to infectious diseases.

European science must play a major role in this 
fight  to  curb  infectious  diseases,  particularly 
through  the  establishment  of  a  stronger  and 
more coherent surveillance and control system, 
and  through  a  substantially  increased  invest-
ment in research to underpin this endeavour.

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DIAGNOSTICS

workshops  and  staff  exchange  between 
the  relevant  entities.  A  detailed  plan  of 
staff exchange will be implemented dur-
ing the project.
The	 consortium	 includes	 three	 partners	
from  INCO  countries  that  are  highly  rec-
ommended	by	the	EU;	one	of	them	is	an	
SME  (DNAT)  and  the  other  two  are  re-
search institutes which will provide essen-
tial know-how for the project.

Expected outcome: 

DIAGNOSIS  will  realise  new  technologies  and 
products as listed below:

Novel technologies New products

New principles for 
NA separation 
and purification

New sorbent 
methods and 
materials

Kits for ultra-rapid 
separation and 
purification of DNA 
and RNA

Kits for separation 
and purification of NA 
from difficult (inhibi-
tor rich) samples

Protocols for sample 
preparation 

Kits for separation of 
different classes of NA

Protocols for samples 
target concentration

Chemistry for oligo-
nucleotides synthesis

Multiplex PCR

Kits for non-cultural 
enrichment of 
micro-organisms

Kits for diagnostic 
assays of critical 
pathogens

Prototype instrument 
for fluorescent
detection

Protocols for 
diagnostic assays

Portable PCR 
laboratory

Protocols for POC 
(point of care) sample 
preparation

Kits for sample 
preparation outside 
the laboratory

Diagnostics - Imaging, Nanoparticles and Biosensors

95

Only  with  this  investment  will  Europe  be  able 
to  manage  infectious  diseases  within  its  own 
boundaries.  Furthermore,  Europe  will  have  the 
capacity  to  help  prevent  the  emergence  and 
spread of infections prevailing elsewhere in the 
world and to pursue its historical tradition of pro-
viding assistance to the poorest countries.

•	

The challenging aim is to reach a short and effi-
cient sample preparation followed by highly sen-
sitive, accurate, cost-efficient multiplex diagnosis 
implemented i.a. into a portable PCR fluorescent 
laboratory.  The  concept  will  be  proven  on  hu-
man  critical  pathogens  but  will  be  applicable 
also for animals, plants and environmental, and 
food samples.

Role of SMEs

DIAGNOSIS  attempts  to  enhance  the  competi-
tiveness  of  Europe’s  biotechnology  industry  by 
the  development  of  fast  and  reliable  nucleic 
acids separation and purification, as well as the 
creation of new methods for separation from in-
hibitor  enriched  samples  and  new  instruments 
and  kits  for  fast  and  cost-effective  detection  of 
critical  human  pathogens.  Most  of  the  partners 
are industrial partners, thus taking the outcome 
of the project directly to the European biotech-
nology industry:
•	

The	 consortium	 consists	 of	 73%	 SMEs,	
all  of  which  are  involved  in  innovative 
technologies  and  research.  Of  the  over-
all budget, 67% is allocated to SMEs. The 
main idea is to promote their technologies 
and develop new products by enhancing 
their business plans.
The	 project	 management	 is	 fully	 per-
formed  by  two  SMEs:  one  an  expert  in 
technological  work  and  the  other  in  ad-
ministrative  management  and  coordina-
tion of EU-funded projects. 
DIAGNOSIS	 is	 allocating	 one	Work	 Pack-
age  to  exploitation  and  dissemination 
by  its  SMEs  partners,  including  internal 

•	

•	

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Camilla Giammarini
DIATHEVA Srl
Fano, Marche, Italy

Martin Gehri
PreentTec AG
Fribourg, Switzerland

Ronald arthur Bosch
Hilbrands Laboratorium BV
Wijster, Netherlands 

Sergey Zavriev
M.M. Shemyakin-Yu.A. Ovchinnikov 
Institute of Bioorganic Chemistry of RAS
Moscow, Russia

Hamlet Balayan
Institute of Fine Organic Chemistry of NAS
Yerevan, Armenia

Ulf Goebel
Charité – Universitätsmedizin Berlin
Institut für Mikrobiologie und Hygiene
Berlin, Germany 

Pnina dan
OSM-DAN Ltd
Rehovot, Israel

DIAGNOSIS

Potential applications:

The  application  Work  Package  will  focus,  but 
not limit, its activities on the following groups of 
pathogens  and  critical  sample  sources  for  mul-
tiplex PCR systems with fluorescence detection, 
thus  approving  and  demonstrating  the  broad 
and beneficial universal applicability of the tech-
nological  development 
in  the  technological 
Work Packages:
•	
•	

mycobacterium	complex:	in	sputum;
difficult	culturable	fastidious	periodontal	
pathogens	in	gingival	crevicular	fluid;
predominant	
pathogens;
gut	 flora	 pathogens	 in	 stool	 samples	 for	
analyses of intestinal microbiota associated 
with	inflammatory	bowel	disease;	
fungal	 pathogens	 in	 hair,	 skin	 and	 nail	
samples.

food-borne	

•	

•	

•	

human	

Scientific coordinator

Robert-Matthias Leiser
Agrobiogen GmbH
Thalmannsdorf 25
Larezhausen
86567 Hilgertshausen, Germany
E-mail: matthias.leiser@agrobiogen.de 

Partners

denis Rebrikov
DNA-Technology
Moscow, Russia

Claus-detlev Bauermeister
Labor Dr. Bauermeister & Co
Moers, Germany

Vendula Pachmanova
Generi Biotech s.r.o.
Hradec Kralove, Czech Republic 

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DIAGNOSTICS

USDEP

Capture and enrichment of emerging pathogens for multiple  
and ultra-sensitive diagnostic

Contract No 
Project type 

LSHB-CT-2006-037560
SME-Specific Targeted

EC contribution  e 2 004 952

  Research Project

Starting date   1 November 2006

duration  36 months

Website  www.usdep.eu

In  the  1970s,  the  World  Health  Organization 
(WHO)  proclaimed  that  eradication  of  smallpox 
should be attempted. This goal was successfully 
achieved in 1979. Nonetheless, presently there is 
a general consensus that the list of newly emerg-
ing  or  re-emerging  pathogens  is  continuously 
growing. Indeed, during the last decades, patho-

gens such as Marburg, Ebola, Hepatitis-C, Hanta-
virus,  HIV  and  more  recently,  SARS  coronavirus, 
have emerged. Furthermore, the apparent risk of 
a  new  influenza  pandemic  again  highlights  the 
global threat of infectious diseases. In addition, 
the possibility of bioterrorist attacks using highly 
pathogenic  viruses  and  bacteria  cannot  be  ig-

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97

 
 
 
 
 
 
 
USDEP

nored.  As  a  consequence,  the  current  require-
ments for novel, highly sensitive and specifi c di-
agnostics technologies have increased. 

A major obstacle for the detection of pathogens 
in  clinical  or  environmental  samples  are  false 
negative  results,  e.g.  for  HCV “occult  infections”. 
This is mainly due to the lack of a rapid and reli-
able pathogen concentration methodology, and 
the inability of most of the currently used tech-
nologies  to  eliminate  or  neutralise  interfering 
molecules  —  “natural  inhibitors”  —  present  in 
most complex samples. 

The aim of this research programme is to exploit 
the “non-self”  recognition  and  binding  proper-
ties  of  human  apolipoprotein  H  (ApoH)  for  the 

development of novel tools to isolate pathogens 
from  complex  biological  mixtures.  ApoH  binds 
pathogens  enabling  their  capture  and  concen-
tration  from  diff erent  biological  samples.  Mag-
netic beads coated with ApoH protein can be ef-
fi ciently used as a pre-treatment step to greatly 
improve  the  detection  threshold,  thereby  in-
creasing the sensitivity for diagnosis of emerging 
pathogens, regardless of the molecular or immu-
nological techniques used in the fi nal diagnostic 
step. The project will focus on increasing the sen-
sitivity  and  specifi city  of  the  currently  available 
detection methods used for pathogenic bacteria 
and  viruses,  and  on  the  development  of  novel 
techniques for pathogen detection from clinical 
and environmental samples including those that 
could be used in bioterrorism. 

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While the publicly funded partners — as well as 
the Robert Koch Institut (RKI), the Institut de Re-
cherches  pour  le  Développement  (IRD),  and  the 
privately  funded  Pontifica  Universidad  Catolica 
de Chile — working in virology and public health 
will incorporate ApoH technology into their panel 
of regular techniques for pathogen detection, the 
SME will develop and standardise novel technolo-
gies for rapid, multiple and ultra-sensitive patho-
gen diagnosis such as mini-array systems. 

ApoH-Technologies  develop  ApoH-coated  sup-
ports  for  diagnostic  purposes,  GenExpress  spe-
cialises  in  the  development  and  optimisation 
of  molecular  biology  assays,  the  Institut  für  Sil-
iziumtechnologie  (ISIT)  specialises  in  the  devel-
opment and production of microelectronic com-
ponents and will supply the electronic biochips, 
eBiochip Systems is focused on manufacturing of 
technology  for  electronic  biochip  applications, 
SKULD-TECH  is  developing  a  mini  array  system 
for  virus  detection  and  IMMUNOCLIN  provides 
strategic  direction  as  well  as  management  and 
laboratory services for clinical development and 
preclinical contract research.

DIAGNOSTICS

Scientific coordinator

Heinz Ellerbrok
Robert Koch-Institut
Centre for Biological Safety
Nordufer 20
133353 Berlin, Germany 
E-mail: EllerbrokH@rki.de

Partners

dorothy Bray
ImmunoClin Ltd
London, UK

Elias Stefas
ApoH-Technologies
Montpellier, France

Francisco Veas
University of Montpellier 1
Faculty of Pharmacy
Montpellier Cedex 5, France

Marcelo Lopez Lastra
Pontificia Universidad Católica de Chile
Santiago, Chile

Roland Lauster
GenExpress Gesellschaft für Proteindesign mbH
Berlin, Germany

Rainer Hintsche
Fraunhofer Institut für Silizium Technologie
Itzehoe, Germany

Ralf Wörl
eBiochip Systems GmbH
Itzehoe, Germany

didier Ritter and Stamatis Varsamos
Skuld-Tech
Montpellier, France

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NEMO

Nano based capsule-endoscopy with molecular imaging and optical biopsy

Contract No 
Project type 

LHSB-CT-2006-037362
Specific Targeted
  Research Project

EC contribution  e 2 832 020

Starting date   1 November 2006

duration  36 months

Website  www.nemo-strep.org

Background and objectives:

Gastrointestinal (GI) malignancy, especially color-
ectal  cancer,  makes  a  significant  impact  on  the 
quality of life and well-being of European citizens, 
and has significant economic consequences. The 
World Health Organization reported that in 2000, 
940  000  of  the  10  million  cancer  deaths  were 
colorectal  in  origin,  870  000  were  derived  from 
the  stomach,  and  410  000  were  of  oesophageal 
origin.  The  ageing  of  the  European  population 
means that the death rate will continue to rise.

GI cancer in general, and more specifically color-
ectal  cancer,  develops  slowly  and  usually  takes 
years before expressing symptoms. It is most cur-
able during its early stage. Consequently, earlier 
detection of cancer using screening methods is 
likely to be the most practical way of addressing 
the epidemic of gastrointestinal cancers. 

Today,  gastrointestinal  cancers  are  detected 
mainly  by  gastroscopy  or  colonoscopy,  fol-
lowed  by  biopsy.  There  is  good  evidence  that 
such  screening  can  locate  early  cancers  and 
that  lives  can  be  saved  if  they  are  discovered 
and  removed.  Many  patients,  however,  are  re-
luctant  to  have  screening  gastroscopies  and 
colonoscopies because of the discomfort of the 
procedures. Women  are  especially  reluctant  to 
undergo screening colonoscopy.

The  acceptability  of  capsule  endoscopy,  which 
is  pain-free,  requires  no  sedation  and  does  not 

necessarily entail a hospital visit, is attractive for 
patients.  It  is  likely  that  they  would  find  such  a 
screening  method  much  more  acceptable  than 
screening colonoscopy, for example. 

It  would  be  very  helpful  if  capsule  endoscopic 
video  imaging  could  be  combined  with  more 
sensitive and specific methods for the detection 
of early cancer, to avoid the need for biopsy.

The aim of the NEMO project is to develop a new 
and  advanced  cancer  screening  method,  which 
is  user-friendly  enough  to  significantly  increase 
compliance, simplify the diagnosis procedure and 
enhance  the  sensitivity  and  specificity  of  early 
detection. The focus is on advanced non-invasive 
method for cancer screening of the GI tract, that 
on the one hand, will be user-friendly enough to 
increase  the  compliance  of  the  population,  and 
on  the  other  hand,  will  raise  the  sensitivity  and 
capability of early detection of colorectal cancer. 

Approach and methodology:

The concept of the proposed medical device is to 
combine capsule endoscopy with molecular rec-
ognition  that  highlights  cancerous  and  precan-
cerous lesions in the GI tract, in a way that revo-
lutionises the accuracy and ease of screening for 
this major cause of death. The system unites the 
verity  of  technological  platforms:  immunoassay 
technology is used for targeting the disordered 
tissue	or	body	fluid;	nanotechnology	is	used	for	
marking	 and	 optical	 tagging;	 advanced	 in	 vivo	

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capsule  endoscopy,  based  on  spectral  technol-
ogy,	is	used	to	detect	the	marked	disorder;	and	
manoeuvring  and  navigation  is  based  on  mag-
netic fields and forces technologies. 

Two types of miniaturisation are required to en-
able the assembly of the new imaging system, 
coils,  wireless  communication  and  batteries 
into a capsule that will remain a reasonable size: 
mechanical (increasing space) and electrical (re-
ducing  power  requirement).  Technologies  like 
MEMs  switches  and  improved  electronic  pack-
aging,  based  on  array  of  chips  using  flip-chip 
bonding, are essential. 

The  ability  of  light  to  penetrate  the  tissue  de-
pends  on  its  wavelength.  Blue  light  has  limited 
penetration  capacity,  while  NIR  can  reach  deep 
tissue  layers.  By  comparing  the  light  scattered 
in  a  short  wavelength  (providing  information 
from  the  surface)  to  light  scattered  in  a  long 
wavelength (providing deep tissue information), 
optical  biopsy  can  be  achieved.  A  new  medical 
diagnostic  tool  may  be  set  up  by  fusing  visual 
imaging and analytical data based on molecular 
recognition technology. 

The NEMO partners will explore the use of spe-
cific optical filters used in conjunction with light 

DIAGNOSTICS

emitting diodes (LEDs) in order to make a mini-
ature narrow band imaging device which can be 
contained within a capsule endoscope. Narrow 
band imaging reduces the surface reflection of 
broad band illumination, and can allow small or 
flat  precancerous  lesions  to  be  seen  clearly,  in 
comparison with conventional illumination. The 
combination of conventional and narrow band 
imaging  may  provide  an  overview  of  the  gas-
trointestinal tract, indicating one of many sites 
of interest. It could be alternated with conven-
tional imaging.

Expected outcome: 

The  project  partners  expect  that  the  new  cap-
sule endoscopy screening method will offer im-
proved  clinical  solutions  for  cancer  screening: 
wireless	capsule	endoscopy	is	painless;	does	not	
need	to	be	administered	in	hospital;	does	not	re-
quire a team of nurses to clean the devices since 
it	is	disposable;	and	does	not	require	great	skill	
to  perform  (although  skill  in  interpretation  of 
the  images  is  needed).  It  is  much  preferred  by 
patients to gastroscopy or colonoscopy. The new 
device will be free to manoeuvre in stomach. By 
combining this capability with molecular recog-
nition,  which  highlights  cancerous  and  precan-
cerous lesions in the GI tract, would revolution-
ise the accuracy and ease of screening for gastric 
cancer. Moreover, by combining the capability to 
analyse secretions with localisation, the solution 
offers pancreatic and liver cancer detection as a 
by-product of stomach screening.

The  partners  hope  to  develop  a  combination 
of  miniature  spectral  and  Magnetic  Resonance 
nanotechnology  so  as  to  create ‘virtual  biopsy’ 
methods, and incorporate these within the cap-
sule  endoscope.  They  also  anticipate  that  the 
new autonomous NEMO capsule will be able to 
move  backwards  and  forwards  in  the  gastroin-
testinal tract, for example, in order to re-examine 
a suspicious lesion. 

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101

Elie Berdugo
Ernst & Young (Israel) Ltd
Tel Aviv, Israel

NEMO

Coordinator 

Elisha Rabinovitz
Given Imaging Ltd
2 Hacarmel Street
20692 Yoqneam, Israel
E-mail: elisha.rabinovitz@givenimaging.com

Partners 

Mikael Svensson
Zarlink Semiconductor AB 
Jarfalla, Sweden

avraham Rubinstein 
The Hebrew University of Jerusalem
Jerusalem, Israel

Meike Reimann-Zawadzki
Fraunhofer-Gesellschaft zur Foerderung 
der Angewandten Forschung e.V. (FhG) – 
Institute for Biomedical Engineering (IBMT)
Sulzbach, Germany

alberto Lui
Fondazione Bruno Kessler
 (Istituto Trentino di Cultura)
Trento, Italy

Jutta Keller
Israelitisches Krankenhaus
Hamburg, Germany

Paul Swain
Imperial College of Science, 
Technology and Medicine (Imperial College London)
London, UK

Heinz Jochim List
Indivumed GmbH
Hamburg, Germany

Emil Katz
Novamed Ltd
Jerusalem, Israel

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DIAGNOSTICS

FLUOROMAG

Multiparameter sensing for high sensitivity diagnostics using fluorescent  
and magnetic nanoparticles

Contract No 
Project type 

LHSB-CT-2006-037465
Specific Targeted Research Project

EC contribution  e 2 552 300

Starting date   1 November 2006

duration  36 months

Website  www.mpibpc.gwdg.de/groups/jovin/
index.php/Main/Fluoromag

Background and objectives: 

The  objective  of  the  FLUOROMAG  project  is  to 
produce  noble  metal  nanoclusters  or  nanodots 
(NDs), and core-shell (CS) nanoparticles by a va-
riety  of  methods  that  will  ensure  uniform  size 
distributions and the transfer of this technology 
to  partner  NANOGAP-sub-nm-powders  SA.  NA-
NOGAP will then scale up the synthesis of these 
nanoparticles  for  commercial  production  and 
supply the consortium with nanoparticles (NPs) 
for the characterisation of their extinction, fluo-
rescent and magnetic properties, and the further 
development of diagnostic tests.

FLUOROMAG, as a STREP (Specific Targeted Re-
search  Project),  will  devise  conjugation  strate-
gies to couple biomolecules to noble metal NDs 
and commercially available quantum dots (QDs) 
to  produce  probes  that  can  specifically  target 
macromolecules,  such  as  proteins  and  DNA/
RNA in vitro, and in cells and tissues. The consor-
tium will take advantage of ND electrochemical 
synthesis to introduce specific molecules in the 
shells  that  permit  efficient  derivatisation  and 
coupling to biomolecules.

The  consortium  is  also  targeting  the  develop-
ment of multiparametric diagnostic assays, using 
combinations  of  bioconjugated  QDs  and  noble 
metal  NDs  as  novel,  fluorescent  and  extinction 
probes.  The  goal  is  to  achieve  high  sensitivity 
(down to single virus/biomolecule detection) in 
molecular  and  cellular  recognition.  New  assays 

are being proposed that will monitor several an-
tigens in multiplexed kinetic and end-point de-
terminations. 

Another objective is development of a commer-
cial,  low-cost  programmable  array  microscope 
(PAM)  module  for  wide-field  microscopes,  that 
utilises a spatial light modulator to achieve high-
speed  sectioning  and  simultaneous  measure-
ment  of  multiple  fluorescence  modalities  as  a 
detection system for single and multiplexed di-
agnostic  assays,  using  nanoparticles  developed 
within the project.

The  research  consortium  will  test  and  improve 
the  capabilities  of  this  instrument  in  collabora-
tion with the partner, Cairn Research Ltd, so as to 
bring it to market for both research and clinical 
laboratories, by the end of the project. 

Approach and methodology:

Controlled  electrochemical  as  well  as  micro-
emulsion  techniques  for  NP  synthesis  are  be-
ing  pursued.  New  methods  for  separation  and 
characterisation  of  the  nanoparticles  are  also 
under development. The NP technology is being 
transferred to NANOGAP, which is increasing the 
syntheses of these nanoparticles for commercial 
production  proportionally,  as  well  as  supplying 
the consortium with NPs. 

AFM,  STM,  X-RAY,  SQUID,  Raman,  fluorescence 
and  mass  spectrometry  measurement  tech-

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103

 
 
 
 
 
 
 
 
 
FLUOROMAG

niques  are  being  used  for  the  characterisation 
of  NPs.  Prospective  candidate  material  is  being 
directed  into  bioconjugation  for  diagnosis  and 
fluorescence  microscopic  studies.  An  alpha  ver-
sion of PAM is undergoing rigorous testing and 
development  at  Max  Planck  Institute  (MPI)  for 
Biophysical  Chemistry,  Germany,  in  collabora-
tion with Cairn Research Ltd. Two beta units are 
under construction at Cairn Research Ltd for the 
Biophysical  Engineering  Department  at  Univer-
sity of Twente, Netherlands, and for the Analyti-
cal Chemistry Department of Nottingham Trent 
University, UK.

Expected outcome: 

The  consortium  will  have  identified  a  range  of 
well-characterised NDs and CSs with interesting 
properties  and  potential  that  can  be  produced 
commercially  for  the  research  and  diagnostic 
market.  New  assays  with  high  sensitivity  for  di-
agnosis using unique nanoparticle material will 
be	 developed;	 some	 of	 these	 will	 use	 the	 new	
PAM  platform.  PAM  units  will  enter  the  market 
for both the research and medical communities 
at  the  later  stages  of  the  FLUOROMAG  project. 
This powerful, new high-speed fluorescence sec-
tioning microscope will have capabilities not yet 
combined in other microscope systems.

Main findings:

•	

•	

•	

•	

A	 market	 analysis	 for	 the	 nanoparticles	
produced by NANOGAP is to be finalised 
in mid-2007.
The	 alpha	 version	 of	 the	 PAM	 at	 the	
MPIBPC has been improved and two beta 
units  for  Twente  and  Nottingham  Trent 
Universities  are  under  development  at 
Cairn Research Ltd, and will be delivered 
to the partners in the very near future. 
Characterisations	of	nanoparticle	synthe-
ses made by the University of Santiago de 
Compostela  and  NANOGAP  are  ongoing 
at the MPIBPC and Twente. Scientists from 
all 3 universities met in February 2007 to 
conduct  tests  jointly  and  discuss  further 
experiments.
Scientists	
Trent	
University  have  visited  the  University  of 
Santiago to set up toxicity studies on the 
nanoparticles. 

from	 Nottingham	

Major publications:

Hagen, G., Lidke, K., Rieger, Β., Caarls, W., Arndt-
Jovin,  D.,  Jovin,  T., ‘Dynamics  of  membrane  re-
ceptors:  single  molecule  tracking  of  quantum 

(B) X-ray diffraction of large clusters.

 (A) Transmission electron micrograph image of large 
Au clusters. The size of clusters is 2.1 ± 0.5 nm. 

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dot  liganded  epidermal  growth  factor’,  In Single 
Molecule Dynamics,  2007,  in  press, Y.  Ishii  and T. 
Yanagida, editors. 

Hagen, G., Caarls, W., Thomas, M., Hill, A., Lidke, K., 
Rieger, B., Fritsch, C., van Geest, B., Jovin, T., Arn-
dt-Jovin,  D., ‘Biological  applications  of  an  LCos-
based  Programmable  Array  Microscope  (PAM)’, 
Proc. SPIE, 2007, 6441:64410S1-12.

DIAGNOSTICS

Coordinator: 

donna J. arndt-Jovin 
Max Planck Institute for Biophysical Chemistry 
Department of Molecular Biology 
37070 Göttingen, Germany 
E-mail: djovin@gwdg.de

Partners

Vinod Subramaniam 
University of Twente
Department of Biophysical Engineering 
Enschede, Netherlands

M. arturo López-Quintela
University of Santiago de Compostela
Faculty of Chemistry
Department of Physical chemistry
Santiago de Compostela, Spain

Quentin S. Hanley
Nottingham Trent University
School of Biomedical and Natural Sciences
Nottingham, UK

Martin Thomas
Cairn Research Ltd
Faversham, UK

Tatiana López de Rio
NANOGAP-subnm-powders SA
Santiago de Compostela, Spain

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BONSAI

Bio-imaging with smart functional nanoparticles

Contract No 
Project type 

LSHB-CT-2006-037639
Specific Targeted
  Research Project 

EC contribution  e 2 909 005

Starting date   1 November 2006

duration  36 months

Website  www.bonsai-project.eu

Background and objectives:

Approach and methodology:

The  overall  objective  of  the  BONSAI  project  is 
the development of ultrasensitive bio-imaging 
techniques based on novel multifunctional na-
noparticles (NPs) with tailored optical and mag-
netic properties for visualising complex cellular 
structures  (tissues  and  organs),  receptors,  tu-
mour cells and masses. 

True  innovation  rests  on  the  capability  to  com-
bine  the  preparation  of  ‘ad-hoc’  nanoparticles, 
having  different  properties  and  functions,  with 
the development of advanced bio-imaging tech-
niques,  in  the  same  project.  The  expected  im-
provements  of  labelling  cells  and  cellular  struc-
tures  with  tailored  nanoparticles  are  sensitivity, 
speed and specificity in the visualisation of bio-
logical systems. 

The improved resolution, sensitivity and versatil-
ity of diagnostics based on the NPs developed by 
BONSAI is likely to have a strong impact on bio-
medical research, by allowing the unravelling of 
some aspects of the cellular response to patho-
logical perturbation and tissue repair, including 
signal transduction and cell-cell interaction.

The  success  in  reaching  the  project  objectives 
would contribute both to a better understanding 
of  the  molecular  mechanisms  of  cellular  proc-
esses, and to achieving higher sensitivity in early 
detection of tumour cells and lesions. 

Currently,  cells  are  visualised  through  fluoro-
phores, such as organic dyes. These have several 
drawbacks, including their tendency to blink (that 
limits their efficiency), photo-oxidation (that lim-
its the detection time) and the necessity of differ-
ent wavelengths to activate each dye (that slows 
data  acquisition).  Semiconductor  nanocrystals 
(quantum dots) were recently introduced for bio-
labelling, since one wavelength can make them 
glow in a rainbow of colours depending on their 
size. The most widely used quantum dots, how-
ever, are cytotoxic. 

BONSAI’s goal is the preparation by laser pyrolysis 
(Fig.  1)  of  sizeable  quantities  of  light-emitting  Si 
(Fig. 2) and Si-based NPs that have a broad-band 
pumpability,  size-dependent  optical  emission 
(Fig. 3), a reduced tendency to photo-bleach, and 
are not cytotoxic as compared with largely inves-
tigated, toxic CdSe quantum dots. Si-NPs, with dif-
ferent colours of fluorescence, can be excited with 
one single wavelength, which can be selected to 
minimise  the  cell  autofluorescence  that  usually 
masks signals from labelled molecules. This is an 
added advantage in high-resolution bio-imaging.

The applications in biology and medical diagnosis 
(Fig. 4) require that the NPs do not interfere with 
biological processes or poison the cells. Thus, the 
second task of BONSAI is the development of sta-
ble  colloidal  solutions  containing  non-cytotoxic, 
colloidally stable Si-based NPs, which are properly 

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DIAGNOSTICS

Fig. 1: Schematic of laser pyrolysis set-up (courtesy of 
partner CEA).

Fig. 2: Si nanoparticles 
prepared at ENEA by laser 
pyrolysis (HREM-TEM 
image: care of partner 
UNIPD)

functionalised on the surface in order to improve 
and  tune  their  optical  properties  and  increase 
their selectivity in specific biological targets. 

•	

Fig. 3: Photoluminescence (PL) emission from size-selected 
Si nanoparticles (NPs) under illumination with UV lamp. 
The arrow indicates NP size variation from 8 nm to 2.5 nm. 
(Courtesy of partner MPI for Astronomy). 

through  the  capillary  system  of  organs 
and	tissues	with	little	vessel	embolism;
narrow	 size	 distribution	 for	 differential	
uptake of various tissues (Fig. 5,6). 

Imaging  can  also  be  generated  by  exposure  of 
cells or tissues to ultrasound and by measuring 
the  resulting  signal  with  the  help  of  contrast 
agents, as in MRI (Magnetic Resonance Imaging). 
MRI shows excellent spatial resolution, but as its 
sensitivity is relatively low, MRI requires amplifi-
cation mechanisms for its use in molecular imag-
ing. To this purpose, the help of suitable contrast 
agents is required. 

The objective of BONSAI is the development of 
stable  colloids  of  nontoxic,  non-immunogenic 
NPs with: 
•	

high	 magnetisation,	 so	 that	 NP	 can	 be	
moved  in  the  blood  and  accumulated  in 
the	target	organ;
particle	size	that	is	small	enough	to	remain	
in  circulation  after  injection  and  to  pass 

•	

Nanoparticle coating and hydrodynamic size are 
key features for driving the pharmacokinetics of 
NPs and their access to ‘deep’ compartments of 
the body. 

A  very  ambitious  and  risky  objective  of  the 
project is to combine optical (for optical detec-
tion  and  imaging)  and  magnetic  (for  manipula-
tion and/or MRI) properties in the same NP that 
will acquire the capability to be moved, followed 
and  eventually  energised  when  introduced  in 
specific biological tissues. 

Prior  to  using  nanoparticles  in  biological  and 
medical diagnostics, the partners will verify that 
they  have  no  adverse  effect  on  cells’  health  or 
development.  Non-toxic,  luminescent  nanopar-
ticles  will  then  be  used  to  develop  optical  bio-
imaging techniques that aim for the following:

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BONSAI

Fig. 4: Bio-applications of Diffuse Reflectance and 
Fluorescence Spectroscopy of nanoparticles (courtesy of 
GPI-Natural Sciences Center).

Fig. 5: HREM-TEM image of Fe2O3 magnetic nanoparticles 
prepared by laser pyrolysis at CSIC.

Fig. 6: HREM-TEM image 
of siloxane polymer-iron/
iron oxide shell-core 
nanoparticles prepared 
at the National Institute 
for Lasers, Plasma and 
Radiation Physics Institute in 
Bucharest, Romania.

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•	

•	

•	

better	understanding	of	how	the	genome	
instructs and orchestrates the function of 
cell,	organs	and	organisms;
whole-cell	labelling	for	cell	or	pathogen	
detection,  cell  tracking  and  cell  lineage 
studies;
optical	imaging	of	in	vitro	and	in	vivo	tu-
mour cells for early cancer diagnostics.

Expected outcome: 

The primary aim of the BONSAI project is to achieve 
a real industrial breakthrough, based on scientific 
and  technological  excellence  through  interdisci-
plinary  work.  In  this  respect,  BONSAI  has  joined 
together 11 participants from 4 EU Member States 
(Germany,  Spain  France  and  Italy)  and  a  Russian 
partner  with  complementary,  well-documented 
and high-profile expertise in the following:
•	

material	 science	 (synthesis	 of	 new	 nano-
particles  through  bottom-up  strategies, 
like laser synthesis from gas-phase precur-
sors	and	laser	ablation	in	liquids);	
nanotechnology	
(exploration	 and	 ex-
ploitation  of  novel  optical  and  magnetic 
properties that appear only at nanoscale 
and	are	truly	size	dependent);	
colloidal	chemistry	(bio-compatibilisation	
of the colloidal nanoparticles by building 
up a passive interface between the artifi-
cial	material	and	the	physiological	fluids);	
biotechnology  (advanced  imaging  tech-
nologies  in  biological  samples,  develop-
ment of magnetic NPs as contrast agents 
in	Magnetic	Resonance);
biomedicine	 (toxicity	 studies	 of	 NPs,	 up-
take  of  NPs  by  specific  tumour  models, 
NPs’ distribution to specific organs in rela-
tion to administration routes).

•	

•	

•	

Specific magnetic Fe-based nanoparticles will be 
prepared for the project at the National Institute 
for Lasers, Plasma and Radiation Physics Institute 
in Bucharest, Romania. Moreover, the European 
dimension  of  the  project  will  contribute  to  the 

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DIAGNOSTICS

Giovanni Mattei
Università di Padova
Dipartimento di Fisica
Padova, Italy

dayang Wang
Max Planck Gesellschaft
Max Planck Institute of Colloids and Interfaces
Potsdam, Germany

Friedrich Huisken
Max Planck Institute for Astronomy 
Heidelberg, Germany

Giuseppe Miserocchi
Università di Milano-Bicocca
Dipartimento di Medicina Sperimentale, Ambientale e 
Biotecnologie Mediche
Milan, Italy

Jean Marc Idee
GUERBET
Aulnay-sous-Bois, France

Vladimir Pustovoy
General Physics Institute
Natural Sciences Centre
Moscow, Russia

Klaus Palme
University of Freiburg
Center for Applied Biosciences
Inst. Biology II
Freiburg, Germany

Maria Rosa GaSCO
NANOVEC-NANOVECTOR srl
Turin, Italy

Rainer UHL
TILL-TILL Photonics GmbH
Graefelfing, Germany

strengthening of the European Research Area.

The  expected  breakthrough  is  related  mainly  to 
the development of advanced bio-imaging diag-
nostics  made  possible  by  the  availability  of ‘ad-
hoc’  nanoparticles,  produced  within  the  project 
and  having  superior  properties  with  respect  to 
commercially available nanoparticles. After a care-
ful testing process, which is needed for pharma-
ceutical products, these materials will make up a 
source of long-term innovation of contrast agents 
for  medical  imaging,  especially  in  MRI.  Alterna-
tive  long-term  implementation  and  exploitation 
approaches  of  the  project’s  diagnostics  in  early 
tumoural cell and tissues detection will be consid-
ered in the course of the project, with the coop-
eration of hospitals and oncological centres. 

Coordinator 

Elisabetta Borsella
ENEA (Ente Nazionale per le Nuove Tecnologie, l’Energia 
e l’Ambiente)
Via Enrico Fermi 45
Frascati (Roma), Italy
E-mail: borsella@frascati.enea.it

Partners 

Nathalie Herlin-Boime
CEA 
Commissariat à l’Energie Atomique-Direction des 
Sciences de la Matière
Gif-sur-Yvette, France

Sabino Veintemilas Verdaguer
Consejo Superior de Investigaciones Cientificas 
Instituto de Ciencia de Materiales
Madrid, Spain

Miguel angel Garcia
Universidad Complutense Madrid
Instituto de Magnetismo Aplicado
Madrid, Spain

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NanoSense

Moving sensitive immunoassays from slow and expensive to fast  
and affordable nanoparticle-based methods

Contract No 
Project type 

LSHB-CT-2006-037245
SME-Specific Targeted

EC contribution  e 1 433 600

  Research Project 

Starting date   1 January 2007
duration  36 months

Website  www.nanosense.eu

Background and objectives: 

Role of SMEs

There is a need for high sensitivity non-separation 
immunoassay  technology  for  general  clinical 
chemistry  instrument  platforms,  in  particular  for 
large  protein  disease  markers  of  low  concentra-
tion, such as NT-proBNP and PSA, and a long list of 
other plasma proteins, protein hormones and spe-
cific antibodies. Such new technology will signifi-
cantly change the diagnostic industry and health-
care providers, in a step towards greater efficacy. 

Traditionally,  immunoassays  have  been  separa-
tion based, meaning that the analyte of in¬terest 
goes through several steps of antibody binding, 
washing  and  separation  before  final  detection. 
This type of assay requires high use of consuma-
bles, which is expensive as well as time-consuming 
due to all the steps involved. While no separation 
steps are involved and the use of consumables is 
limited in a non-separation assay, making the as-
say less expensive and with a much shorter assay 
time is key. A non-separation assay will typically 
be run on a clinical chemistry platform intended 
for  high-throughput  of  analytes,  making  homo-
geneous  non-separation  immunoassays  a  high 
potential market-growth opportunity.

The aim of the NanoSense project is to move im-
munoassays  from  slow  and  expensive  methods 
to  fast,  high-throughput  super-sensitive  nano-
particle-based methods, to demonstrate that it is 
working within the specifications, and to gener-
ate intellectual property for such technology.

There	 are	 five	 participants	 in	 this	 project;	 three	
of them are small and medium-sized enterprises 
(SMEs). Coordinator of the project is Dalen Diag-
nostics  AS,  a  Norway-based  SME.  In  addition  to 
the coordination, the company has the necessary 
expertise for improved signal generation in ho-
mogeneous  nanoparticle  assays. The  other  two 
SMEs are 77 Elektronika Kft in Budapest, Hungary 
(i.e. a specialist in the field of medical electron-
ics  and  manufacturer  of  blood  glucose  meters, 
urine analysers and rapid test readers) and Get-
ica  AB  (i.e.  a  specialised  Swedish  small  biotech 
company concentrating on bioorganic coupling 
chem¬istries and bioprocessing of protein con-
jugates  and  nanoparticles).  The  consortium 
also  includes  a  large  industrial  company,  Merck 
Chimie SAS, which is Europe’s largest producer of 
nanoparticles, and an academic participant, the 
Groningen University Medical Center, providing 
a reference laboratory for measurements in large 
epidemiological studies.

Expected outcome:

To achieve the goal of this project, the consortium 
will  use  specific  methods  and  techniques  so  as 
to optimise each component in the assay. When 
technology, as described above, was developed 
for  small  molecule  markers  15  years  ago,  a  big 
change in the diagnostic industry was seen and 
two SMEs grew into big industrial corpora¬tions. 
The NanoSense partners foresee that similar ef-

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fects will emerge when such technology is devel-
oped for large molecule markers as well.

Potential applications: 

New  assay  high  sensitivity,  high-speed  assay 
products  on  automated  clinical  chemistry  plat-
forms  for  use  in  laboratories  throughout  the 
healthcare  system,  for  higher  throughput  and 
improved cost-effectiveness.

DIAGNOSTICS

Coordinator

Guri Skjeltorp
Dalen Diagnostics AS
Kolsroedveien 120
1599 Moss, Norway
E-mail: email@dalendiagnostics.no

Partners 

Erling Sundrehagen and Ingrid Hulthén 
Getica AB
Tösse, Sweden

Richard Vidal and Cécile Genies 
Merck Chimie SAS Estapor
Fontenay–Sous–Bois, France

Uzonka Farkas and Péter Jakus 
77 Elektronika Muszeripari Kft
Budapest, Hungary

dick de Zeeuw and Stephan J. L. Bakker 
Groningen University Medical Center 
Department of Clinical Pharmacology
Groningen, Netherlands

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111

 
DiaNa

Predictive diagnostics for diabetic nephropathy — novel nanotechnology 
based test platforms

Contract No 
Project type 

LSHB-CT-2006-037681
SME-Specific Targeted

EC contribution  e 2 977 400

  Research Project 

Starting date   1 december 2006

duration  36 months

Website  www.diana-eu.fi

Background and objectives:

The DiaNa project uses the latest knowledge of 
the  pathophysiology  of  diabetic  nephropathy 
and  newly  identified  urinary  markers  to  devel-
op  predictive  diagnostic  tests  to  follow  disease 
progression. Through metabolomic approaches, 
DiaNa aims to find additional markers from dia-
betic urine. In parallel, two separate approaches 
will be used to develop diagnostic tests: one will 
be based on nanobead technology and the oth-
er on a multiplexing platform allowing a combi-
nation of several parameters in a single test. This 
will translate into early identification of patients 
at high risk of rapid loss of kidney function. Af-
ter  validation  with  clinical  material,  subsequent 
steps  will  include  a  transfer  of  the  test  into  pa-
tient use by a small and medium-sized enterprise 
(SME). This approach — directly aimed at devel-
oping a clinical urinary test — will be supported 
by extensive basic research on the mechanisms/
biomarkers of diabetic nephropathy. DiaNa com-
bines the expertise accumulated from the previ-
ous  FP5  EU  project,  Mechanisms  of  Proteinuria 
(QLG1-2000-00691) and the FP6 project, ADDNET 
(LSHB-CT-2003-503364).

Diabetic nephropathy is the main cause of end-
stage  renal  failure  in  the  western  world.  The 
World  Health  Organization  (WHO)  estimates 
that  presently  there  are  over  200  million  peo-
ple with diabetes worldwide. The prevalence is 
constantly rising and is estimated to reach over 
300 million by the year 2025. Overall, up to 40% 

of  diabetic  patients  will  develop  debilitating 
kidney  complications.  Diabetic  nephropathy  is 
becoming not only a severe health problem for 
individual  patients  but  a  major  economic  bur-
den of all societies as well. With DiaNa, the part-
ners  aim  to  achieve  a  better  understanding  of 
the  pathophysiologic  mechanisms  underlying 
the development of diabetic nephropathy — a 
major  complication  shared  by  both  type  I  and 
type II diabetes. 

Role of SMEs

The SMEs involved will (1) utilise their expertise 
to pull out antibodies specific for the molecules 
involved in the pathogenetic sequelae of diabetic 
nephropathy and used for diagnostics (Philogen 
S.P.A,	 Siena,	 Italy);	 (2)	 combine	 the	 antibodies	
produced to novel test platforms, including the 
appropriate  packaging  into  existing  and  to-be-
developed concepts (Future Diagnostics B.V., Wi-
jchen,	The	Netherlands);	(3)	develop	and	screen	
for appropriateness of the platforms developed 
for daily routines with incoming patient samples 
(United	 Laboratories	 Ltd,	 Helsinki,	 Finland);	 and	
(4)  develop  novel  magnetosensors  for  detect-
ing low amounts of target molecules in patients’ 
urine  (Philips  Electronics  Netherlands  BV,  The 
Netherlands).  In  addition,  market  analysis  and 
surveys,  IPR  strategies,  competitor  analysis  will 
be  provided  by  an  additional  party  as  subcon-
tractor of Partner University of Helsinki.

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Expected outcome:

The  ultimate  goal  of  DiaNa  is  to  develop  novel 
diagnostic tests based on the best molecular un-
derstanding reflections in the urine to reveal the 
early diabetic damage during the premicroalbu-
minuric stage of the disease.

Potential applications:

The applications will include novel magnetosen-
sor-based sensors for detection of diabetes-dia-
betic kidney damage.

DIAGNOSTICS

Coordinator 

Harry Holthofer 
Haartman Institute
Haartmaninkatu 3
FI-00014 University of Helsinki, Finland. 
E-mail: harry.holthofer@helsinki.fi

and

National Centre for Sensor Research/
BioAnalytical Sciences 
Dublin City University
Dublin 9, Ireland
E-mail: harry.holthofer@dcu.ie

Partners

Per-Henrik Groop
Samfundet Folkhälsan
Helsinki, Finland

Rob van der Heijden
Universiteit Leiden
Leiden, Netherlands

dario Neri
Swiss Federal Institute of Technology
Zurich, Switzerland

Reinerio Gonzales
Philogen SpA
Siena, Italy 

Menno Prins
Philips Electronics Nederland BV
Eindhoven, Netherlands

Mike Martens
Future Diagnostics BV
Wijchen, Netherlands

Jussi Vilpo
United Laboratories Ltd
Helsinki, Finland

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NANOMYC

Multiparametric detection of bio-molecule conjugated nanoparticles for the 
diagnostic investigation of mycobacterial infections of humans and animals

Contract No 
Project type 

LSHB-CT-2006-036812
Specific Targeted
  Research Project 

EC contribution  e 2 194 020

Starting date   1 January 2007
duration  36 months

Background and objectives: 

The  WHO  reports  that  tuberculosis  causes  mil-
lions of deaths or disabilities each year, especially 
in poorer areas of the planet. The problem is also 
exacerbated by the AIDS epidemic that increases 
disease incidence in developed countries. How-
ever,  in  addition  to  tuberculosis,  exposure  to 
mycobacteria has also been linked to the patho-
genesis  of  sarcoidosis  and  Crohn’s  disease  that 
affect  millions  of  people  in  Europe  alone.  Diag-
nostic  investigation  of  mycobacterial  infections 
is hampered by the difficulty to detect – in a spe-
cific manner – low populations of mycobacteria 
or the immunology markers associated with the 
infections they cause. 

The NANOMYC project aims to develop a highly 
sensitive and specific quantifiable detection sys-
tem  for  molecular  and  immunology  diagnostic 
markers associated with infection caused by M. 
tuberculosis complex (human and animal tuber-
culosis, implicated in sarcoidosis) and M. paratu-
berculosis  (animal  paratuberculosis,  implicated 
in Crohn’s disease). To meet this goal, the consor-
tium will combine nanotechnology and molecu-
lar biology incorporating the recent advances in 
the  sequencing  of  mycobacterial  genomes  to 
routine diagnostics.

NANOMYC  will  develop  a  set  of  functionalised 
quantum  dots  (QDs)  with  different  emission 
characteristics  that  will  allow  a  sensitive,  differ-
ential and quantifiable detection of mycobacte-

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rial-specific  oligonucleotides  and  polypeptides 
in  solid  and  liquid  clinical  samples. The  consor-
tium  will  focus  on  Mycobacterium  tuberculosis 
(MTB) complex (the cause of human and animal 
tuberculosis,  and  possibly  a  causative  agent  of 
sarcoidosis)  and  Mycobacterium  avium  subsp. 
paratuberculosis (MAP), (associated with Crohn’s 
disease  of  man  and  causative  agent  of  paratu-
berculosis of ruminants). 

The project partners will also develop the assay 
for:
•	

in-field	diagnostics	using	portable	devices	
for	evaluation	of	liquid	samples;
manual	and	automated	evaluation	of	sol-
id samples using fluorescence resonance 
energy transfer (FRET). 

•	

Approach and methodology:

Currently, in vitro diagnostic investigation of my-
cobacterial infection relies on two kinds of tests: 
those that aim to detect the pathogen and those 
that target specific antibody. Of the former, cul-
ture and microscopic examination of specimens 
by  auramine-rhodamine  or  Ziehl-Neelsen  stain-
ing  are  among  those  more  traditionally  used, 
but have been largely substituted by molecular 
techniques  that  can  allow  detection  and  differ-
entiation of mycobacterial pathogens in a clini-
cal  sample,  and  in  a  rapid  (culture  may  require 
up to 8 months in the case of MAP), highly sen-
sitive  and  specific  manner.  Numerous  assays  of 
the polymerase chain reaction (PCR) have been 

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DIAGNOSTICS

proposed for this. More recently, Real Time PCR 
(ReT-PCR) has further increased sensitivity (low-
er  minimum  detection  limit)  and  has  allowed  a 
quantifiable  assessment  of  the  result.  However, 
the latter method has not yet been incorporated 
in	practice;	not	only	does	it	require	very	detailed	
calibration but it also requires costly equipment. 

All  the  techniques  mentioned  above  share  the 
same  disadvantage  of  low  negative  predictive 
value  (NPV),  i.e.  although  positive  results  mean 
definite presence of mycobacteria in the sample, 
negative results require further confirmation. The 
problem  of  low  NPV  of  these  tests  is  solved  by 
assays that focus on the detection of substances 
produced  as  a  consequence  of  infection.  How-
ever,  tests  in  this  category  (e.g.  ELISA,  CFT,  AGIT, 
g-inteferone,  tuberculin  testing,  etc)  often  fail  to 
produce  specific  results  due  to  cross  reactions 
with  other  mycobacterial  species.  Furthermore, 
immuno-compromised patients, especially those 
infected with HIV representing a very considera-
ble risk-population for tuberculosis, often produce 
false negative results due to the impaired ability 
of their immune system to respond to infections. 

It becomes evident that a method that will com-
bine the advantages of the diagnostic tests men-
tioned  above  will  greatly  improve  diagnostic 
investigation of mycobacterial infections. NANO-
MYC, however, will go a step further since it is be-
ing developed to allow, in addition to the above, 
the assessment of mycobacterial viability through 
detection of proteins produced exclusively by vi-
able  cells  (this  assessment  currently  relies  on  re-
verse transcriptase PCR or NASBA, both of which 
have  failed  to  be  used  routinely  mainly  because 
of their low reliability, i.e. positive results do not al-
ways signify microbial death and negative results 
are often false due to RNA degradation). 

The consortium will develop QDs with different 
oproelectrochemical characteristics. To this pur-
pose,  the  approach  will  involve  construction  of 
QDs  (CdSe,  ZnS,  Au)  that  have  already  proven 

their  efficiency  for  conjugation  with  biomol-
ecules  and  detection  of  specific  target  regions, 
and  new  ones  that  can  revolutionise  the  diag-
nosis of mycobacterial infections (InN, and GaN) 
since they can be combined with other semicon-
ductor-based QDs for direct and indirect immo-
bilisation  onto  biomolecules.  These  substrates 
are unique, in that they have enhanced stability, 
selectivity, but most of all surface characteristics 
that are dependent on the surrounding chemical 
environment. Conjugation of these biomolecules 
with the QDs will be performed. 

Know-how for the completion of this stage is al-
ready well established and thus the only foresee-
able  risk  is  a  delay  in  timely  completion. This  is 
associated with the fact that QDs are expected to 
show a shift in their optical characteristics after 
their conjugation with the biomolecules. There-
fore,  the  final  products  of  this  stage  will  have 
to be described in detail with reference to their 
electrical-physico-chemical characteristics. 

The  QD-conjugates  that  will  be  constructed 
will be used for the development of NANOMYC 
for  application  with  liquid  samples  (in-field  di-
agnosis)  and  with  solid  samples  (manually  and 
automated).  For  the  former,  QDs  will  become 
soluble by coating with siloxane shells and spe-
cific	capping	macromolecules;	for	the	latter,	GaN	
and InN will be used as matrixes for biomolecule 
and polymer immobilisation for the production 
of  reversible  sensor  arrays  through  Fluorescent 
Resonance Energy Transfer combined with Field 
Effect Transistors. 

Expected outcome:

The  consortium  expects  to  improve  quality  of 
life through better and more effective diagnosis, 
prevention  and  treatment  of  mycobacterial  in-
fections  with  reference  too  to  children  who  are 
by definition more susceptible. Considering indi-
cations that early exposure to mycobacteria may 
lead not only to tuberculosis but also to immune-

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115

NANOMYC

dysregulation that has been associated with vari-
ous  manifestations,  including  soarcoidosis  (the 
primary  cause  of  eye-loss  in  children),  Crohn’s 
disease and asthma, the NANOMYC project will 
provide  considerable  support  to  health  main-
tenance  and  disease  prevention.  This  is  also  in 
agreement with the efforts of the EU to combat 
poverty-related  diseases  –  one  of  which  is  cer-
tainly tuberculosis.

The  partners  anticipate  improving  competitive-
ness  of  the  European  biotechnology  sector  by 
providing a World Innovative diagnostic tool that 
addresses  a  market  of  several  million  euros  per 
year and has strong commercialisation potential.

The project will also allow more effective detec-
tion of mycobacterial pathogens among animals 
and  animal  products  which  will  decrease  the 
loss  of  capital  and  revenue  associated  with  the 
relevant diseases. Moreover, it will gradually de-
crease the level of the required alertness of the 
European Food Industry.

Coordinator

John Ikonomopoulos 
Agricultural University of Athens
Faculty of Animal Science
Department of Anatomy and
 Physiology of Farm Animals
Iera Odos 75
11855 Athens, Greece
E-mail: ikonomop@aua.gr

Scientific coordinator 

Maria Gazouli
University of Athens
School of Medicine
Department of Biology
E-mail: mgazouli@med.uoa.gr

Partners

Nikos Chaniotakis
University of Crete
Laboratory of Analytical Chemistry
Heraklion, Crete, Greece

Leonardo Sechi 
University of Sassari
Sezione di Microbiologia
Dipartimento di Scienze Biomediche
Sassari, Italy

Mirjana Čomor
Vinca Institute for Nuclear Sciences
Laboratory for Radiation Chemistry and Physics
Belgrade, Serbia 

Nikos Goutas
Eugenidion Infirmary Agia Trias
Athens, Greece

Spanos Stamatios
Biosure Cell & Co
Athens, Greece 

Palmiro Poltronieri
Biotecgen Srl
Lecce, Italy

Joers Titt
Quattromed Ltd Molecular
 Diagnostic Laboratory
Tartu, Estonia

Birgit Glaubitz
Medizone GmbH
Munich, Germany

Panos Malamis
Malamis & Malamis Co
Athens, Greece 

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DIAGNOSTICS

DETECTHIV

Sensitive nanoparticle assay for the detection of HIV

Contract No 
Project type 

LSHP-CT-2006-037118
Specific Targeted
  Research Project

EC contribution  e 2 026 260

Starting date   1 January 2007
duration  36 months

Background and objectives:

The  DETECTHIV  project  aims  to  develop  a  new 
platform and assay for the detection of the HIV 
p24 antigen in serum or blood. The p24 test has 
two  advantages:  it  can  detect  HIV  at  an  early 
stage of the infection, before antibodies develop, 
and it is quantitative. This STREP will develop an 
extremely simple viral load test with only one re-
actant (grafted colloids). 

In the first phase of the project, the DETECTHIV 
partners will set up a magnetic nanoparticles as-
say to be used in a microtiter plate with the goal 
of  detecting  concentrations  as  low  as  1  ng/ml. 
In  the  second  phase,  the  use  of  nanoparticles 
on a microfluidic chip will allow the detection of 
p24,  to  levels  as  low  as  0.1  picog/ml  —  one  to 
two  orders  of  magnitude  more  sensitive  than 
classical Enzyme Linked Immuno-Sorbent Assay 
(ELISA) p24 tests. The partners will use both re-
combinant p24 and patient samples to validate 
the platform.

Approach and methodology:

The  test  primarily  involves  optically  detecting 
the formation of a colloidal gel of magnetic na-
noparticles (‘agglutination test’). The gel forms in 
a magnetic field under the presence of antigens 
that are capable of irreversibly linking two colloi-
dal particles. Therefore, the latter are grafted with 
antibodies  that  are  specific  to  the  p24  antigen. 
The detection is achieved through simple optical 

absorbance measurements, owing to the strong 
optical  scattering  modification  when  passing 
from nanometric colloids to the gelled state.

In the microfluidic chip test, a sample solution 
of  serum  or  blood  is  transported  through  sus-
pended  magnetic  nanoparticles  that  are  mag-
netically retained within a microfluidic channel. 
When brought into a magnetic field, the parti-
cles  will  be  able  to  approach  each  other,  form 
chains and will be irreversibly linked if the p24 
antigen is present. Subsequently, on-chip light 
scattering  techniques  will  be  used  to  quantify 
the concentration of permanent chains or clus-
tered beads, which are proportional to the p24 
antigen concentration.

Given  that  immunoassays  are  the  most  widely 
used  assays  in  clinical  diagnostics,  the  impact 
of lowering their cost while enhancing their ef-
ficiency  would  provide  a  much-needed  boost 
towards  lowering  healthcare  costs.  The  chosen 
assay, i.e. the p24 antigen-based viral test, would 
be  of  great  benefit  in  the  global  battle  against 
HIV  infection  and  AIDS,  especially  in  the  devel-
oping  world  that  constitutes  over  70%  of  the 
affected world population. An arsenal of labora-
tory methods is available to screen blood, diag-
nose infection and monitor disease progression 
in individuals infected by HIV. ELISA is the most 
commonly used test to screen for HIV infection.

One advantage of using magnetic colloids arises 
from the fact that the particle surface has a very 

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For ultimate sensitivity, magnetic retention and 
actuation  will  be  used  to  separate  nanoparticle 
clusters from nonreactive nanoparticles in a mi-
crofluidic chipbased system. By means of an op-
tical detection system, with integrated polymer-
based waveguides, it will be possible to exploit 
the  scattered  light  to  retrieve  information  from 
the nanoparticles.

Potential applications:

With the recent availability of low-cost/free anti-
HIV drugs, a remaining major hurdle is the avail-
ability of an affordable viral load test. Viral load 
tests  help  determine  the  correct  regimen  of 
anti-HIV drugs. The current gold standard for vi-
ral load testing (the Polymerase Chain Reaction-
based test) is unfortunately out of reach for the 
budgets  of  developing  nations.  Consequently, 
most  of  these  countries  commence  treatment 
without  viral  load  monitoring. The  new  p24  as-
say  platform  developed  within  the  DETECTHIV 
project  will  be  of  considerable  benefit  to  the 
development of a low-cost viral load test for HIV. 
The aim is to use South Africa as the beta test site. 
The total number of people with HIV infections 
in South Africa is currently estimated at around 
4.7 million. South Africa is the ideal pilot site be-
cause it has conditions approximating both the 
developed  and  developing  world,  as  well  as  an 
established medical infrastructure.

DETECTHIV

strong colloidal stability in any type of buffer, se-
rum or plasma, and has functional groups or re-
ceptors so that the particles can be further grafted 
with the biomolecules of interest. After trapping 
molecules (present in small amounts in solution) 
on  the  nanoparticles,  the  latter  can  be  handled 
with applied magnetic fields. There is a net advan-
tage due to faster reaction rates, trapping of the 
analyte and separation without losses.

With  this  innovative  and  sensitive  p24  assay, 
DETECTHIV seeks to approximate the sensitivity 
of  the  current  viral  load  assays  with  the  added 
advantage of being more robust (because of the 
superior  physical  stability  of  the  p24  antigen). 
Although measurement of HIV-1 RNA (viral load) 
is the acknowledged ‘gold standard’ marker for 
monitoring disease activity in patients receiving 
highly  active  antiretroviral  therapy,  it  remains 
a  very  expensive  test  in  resource-constrained 
settings.  As  this  STREP  promises  to  establish  a 
more  sensitive,  faster  and  simpler  test  than  a 
conventional  ELISA  p24  test,  as  well  as  a  more 
affordable test than an HIV-1 RNA viral load test, 
it has the full potential to set a new standard in 
the diagnosis and follow-up of HIV-infected and 
AIDS  patients  during  the  complete  duration  of 
the infection.

Expected outcome:

The final goal of this project is the development 
of an agglutination test for the HIV p24 antigen, 
with  a  detection  sensitivity  that  is  one  to  two 
orders  of  magnitude  better  (0.1  pg/ml)  and  up 
to one order of magnitude faster than standard 
ELISA  p24  tests.  A  single  platform  that  handles 
magnetic  actuation,  microfluidics,  optical  de-
tection  and  signal  processing  on  a  disposable 
microfluidic chip will be provided. Magnetic na-
noparticles  with  appropriate  surface  chemistry 
for selective recognition of the p24 antigen will 
be  the  first  to  be  developed.  Clinical  validation 
of  the  assay  for  the  detection  and  quantifica-
tion of p24 antigens is an important milestone. 

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Coordinator

Martin Gijs
Ecole Polytechnique Fédérale de Lausanne 
Swiss Federal Institute of Technology Lausanne
Institute of Microelectronics and Microsystems
1015 Lausanne, Switzerland
E-mail: Martin.Gijs@epfl.ch

Partners

Marc Van Ranst
Katholieke Universiteit Leuven
Clinical and Epidemiological Virology
Aids Refrence Lab
Leuven, Belgium

Solly Makholiso
Ayanda Biosystems SA
Lausanne, Switzerland

Bruno Vallayer
Bertin Technologies
Biotech Systems Department
Montigny-le-Bretonneux, France

Jérôme Bibette
Ecole Supérieure de Physique et
 de Chimie Industrielles de la ville de Paris
Laboratoire Colloïdes et Matériaux Divisés
Paris Cedex 05, France

Jörg P. Kutter
Technical University of Denmark
MIC – Department of Micro and Nanotechnology
Lyngby, Denmark

Bernard Plichon
ADEMTECH SA
Pessac, France

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NACARDIO

Nanoparticle-based electronic biosensor for diagnostics  
of cardiovascular disease

Contract No 
Project type 

LSHB-CT-2006-037672
Specific Targeted
  Research Project 

EC contribution  e 2 221 185

Starting date   1 October 2006
duration  36 months

Website  www.nacardio.com

Background and objectives:

Approach and methodology:

NACARDIO  is  a  multidisciplinary  project  aiming 
to develop and commercialise a nanobiosensor 
technology, capable of analysing extremely small 
amounts of protein in small sample volumes. The 
technology can be used to quantify proteins in-
volved in lipid storage to investigate whether any 
of these proteins are potential biomarkers for the 
development of insulin resistance and cardiovas-
cular disease.

The sensor technology is based on single electron 
tunnelling (SET), a phenomenon well explored for 
low  temperature  applications.  State–of-the-art 
nanofabrication  utilising  metallic  nanoparticles 
now make this technology platform available for 
operation at room temperature. SET-technology 
provides unique possibilities for biosensing.

To achieve the goals, the NACARDIO network will 
perform extensive multidisciplinary work to ad-
dress questions at the interface between nanote-
chnology, physics, electrical engineering, surface 
chemistry, biotechnology and medical sciences. 
Frontline  experimental  approaches  encompass-
ing  peptide-stabilised  gold  nanoparticles,  elec-
tron-beam lithography, nano-imprint, molecular 
self-assembly,  engineered  antibody-fragments, 
protein expression and fluidic simulations will be 
used to fabricate the sensor and ensure biologi-
cal functionality and usability.

Figure shows how the different Work Packages of 
NACARDIO are assembled into an instrument prototype

The  individual  scientific,  technical  and  innova-
tion objects of NACARDIO are as follows.

1. 

To express proteins, which have been iden-
tified as potential biomarkers for insulin re-
sistance and cardiovascular disease through 
investigation  of  the  mechanism  for  the 
storage of lipids in the cell. The proteins will 
be  used  to  obtain  a  few  specific  antibody 
fragments directed against each of the re-
spective  biomarkers.  A  unique  route  for 
the  production  of  small,  highly  stable  sin-
gle chain antibody fragments will be used, 
giving antigen-binding fragments that are 
perfectly suited for the SET-biosensor. The 
antibody fragments will have a tailored af-
finity ligand that meets the immobilisation 
requirements for the biosensing by SET

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DIAGNOSTICS

2. 

3. 

4. 

5. 

To  evaluate  different  methods  for  the 
preparation  of  gold  nanoparticles  to  be 
used  for  the  island  and  active  site  of  the 
biosensing SET. The gold nanoparticles will 
be fabricated with different sizes (between 
3 nm and 15 nm) and narrow size distribu-
tion. The  surface  of  the  nanoparticles  will 
be provided by appropriate chemistry that 
stabilises the particles and allows chemical 
coupling to sensor electrodes and antibody 
fragments. Frontline approaches, including 
peptide  stabilised  gold  nanoparticles,  will 
be  used  in  order  to  create  the  nanoparti-
cle-antibody fragment conjugates that are 
needed in the sensor.
To use advanced lithography for the fab-
rication  of  metallic  electrodes  on  silicon 
separated  by  5  to  20  nm,  and  to  evalu-
ate the reproducibility of this fabrication. 
Reproducible fabrication on this scale is a 
giant leap forward for the state of the art 
in  lithographic  methods.  The  extremely 
small  nanostructures  are,  together  with 
nanoparticles,  making  up  the  SET,  which 
is  the  foundation  of  the  sensor. To  make 
the  nanogaps,  three  innovative  lithogra-
phy methods will be used: electron-beam, 
nanoimprint and focused ion beam.
To couple tailored antibody fragments to 
the  nanoparticle  and  to  provide  the  sur-
faces  surrounding  the  active  site  of  the 
SET with chemical functionality, modified 
in order to reduce unspecific proteins in-
teraction using self-assembly techniques. 
Innovative  instrumental  approaches  uti-
lising  surface  plasmon  resonance,  ellip-
sometry and quartz crystal microbalance 
with dissipation makes it possible to dis-
tinguish  unspecific  protein  binding  from 
specific antigen-antibody binding.
To  fabricate  fluidic  microchips  in  elastic 
polymer  material  to  be  easily  positioned 
on  top  of  the  biochip.  The  fluidic  micro-
chip should enable optimal sample trans-
fer  to  the  active  sites  of  the  biochip  with 

6. 

minimised unspecific binding, allowing for 
extremely  sensitive  detection. The  inven-
tive design of the fluidic chip will also seal 
the biochip so as to avoid leakage during 
sample screening. Simulations will be per-
formed in order to optimise microfluidics 
regarding parameters, such as channel de-
sign, temperature, density, concentration, 
electric fields, flow speed, etc. 
To assemble electrode structures and gold 
nanoparticles  to  achieve  functional  SET-
devices  for  operation  at  room  tempera-
ture.  To  perform  biosensing  experiments 
and  develop  a  model  for  SET-biosensing. 
An electrical measurement set-up with an 
associated  fluidic  system  is  available.  The 
purpose of these experiments is also to op-
timise the sensor chips and provide impor-
tant information concerning fabrication of 
the SET-biosensor. The knowledge gained 
will  then  be  used  to  refine  the  measure-
ment set-up into a first prototype. 

Expected outcome:

The  project  partners  anticipate  the  following 
results:

•	

•	

•	

•	

•	

•	
•	
•	

small,	highly	stable	single	chain	antibody	
fragments  with  great  specificity  towards 
identified  potential  biomarkers  within 
cardiovascular	disease;
successful	functionalisation	of	gold	nano-
particles	with	these	fragments;
routes	to	avoid	unspecific	binding	to	the	
device;
a	method	to	fabricate	device	electrodes	in	
an	industrial	way;
a	 method	 to	 assemble	 a	 device	 in	 an	 in-
dustrial	way;
a	sensing	mechanism	model;
market	analysis;
a	SET	biosensing	prototype.

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NACARDIO

Main findings:

Whilst  NACARDIO  has  only  been  running  since 
autumn 2006, the project partners already have 
some  progress  to  report.  The  first  potential  bi-
omarker  has  been  identified  and  is  now  ready 
for  production  of  small,  highly  stable  single 
chain antibody fragments via the immunisation 
of  camels.  As  regards  the  investigation  of  the 
design  and  synthesis  of  biologically  functional 
metallic nanoparticles, the preparation of robust 
biocompatible  and  functional  gold  nanoparti-
cles  has  begun  and  the  initial  results  look  very 
promising.  Low  temperature  measurements  of 
SET device confirm room temperature measure-
ments and show that the partners can fabricate 
the devices.

Coordinator

Olle Isaksson 
Göteborgs Universitet
Department of Medicine
Gröna stråket 8
413 45 Göteborg, Sweden
E-mail: Olle.Isaksson@medic.gu.se

Partners

Linda Olofsson
Midorion AB
Göteborg, Sweden

albert van den Berg
University of Twente
Twente, Netherlands

Serge Muyldermans
Vlaams Interuniversitair Instituut Biotechnologie
Brussels, Belgium

Sergey Kubatkin
Chalmers University of Technology
Göteborg, Sweden

d Mathias Brust
The University of Liverpool
Liverpool, UK

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SLIC

SLIC-Biosensors in molecular diagnostics: nanotechnology for the analysis  
of species specific microbial transcripts

Contract No 
Project type 

LSHB-CT-2005-513771
Specific Targeted
  Research Project 

EC contribution  e 1 999 980

Starting date   1 January 2005
duration  36 months

Website  www.fp6-slic.eu

Background and objectives:

Molecular diagnostics of microbial pathogens is 
an integral part of modern medicine. The growing 
need for direct genotyping and/or the screening 
of the transcriptome calls for the development of 
alternative technologies. The consortium of SLIC, 
a Specific Targeted Research Project, planned to 
develop a cost-effective platform for the identi-
fication  of  bacterial  species  based  on  the  SLIC-
Nanobiosystem. Using tmRNA transcripts of the 
bacterial  ssrA  gene,  the  partners  were  able  to 
detect,  quantify  and  identify  bacterial  species 
in a single homogenous assay format. The SLIC-
Nanobiosystem consists of a self-assembled lipid 
bilayer membrane that integrates a synthetic lig-
and-gated ion channel (SLIC). The SLIC compris-
es a capture molecule that can specifically bind 
a given analyte, a process that is monitored via 
electrical impedance spectroscopy. 

With  this  system,  the  effect  from  even  a  few 
channels can be resolved, thus providing an ul-
tra-sensitive, highly stable and versatile biosen-
sor platform. The consortium utilised transcripts 
(tmRNA) of the ssrA gene in order to identify bac-
terial  species  present  in  clinical  samples.  These 
transcripts occur in high abundance and contain 
a core sequence that is species specific, a feature 
that was exploited to identify infectious disease 
pathogens. Identification of the different bacte-
rial tmRNA transcripts was accomplished by dis-
playing  a  library  of  nucleic  acid  capture  probes 
on  the  SLIC. This  enabled  species  identification 

and discrimination between one or more species 
present in the sample if there was mixed species 
infection.  Since  the  detection  equipment  was 
based on electronics, miniaturised/compact and 
cost-effective instrumentation was possible. The 
consortium’s approach aimed to lay the founda-
tion for a new generation of multiparametric mo-
lecular testing systems, which would open novel 
opportunities  within  the  area  of  point-of-care 
applications in the clinical diagnostics market.

Approach and methodology: 

In the first half of the project, one particular path-
ogen, S. pneumoniae, out of the three (S. pneu-
moniae,  H.  influenza  and  M.  tuberculosis)  was 
selected  as  the  initial  focus.  During  this  phase, 
the  consortium  focused  on  developing  and  as-
sembling the building blocks of the biosensor for 
the assay to detect the S. pneumoniae pathogen. 
The RTD activities involved in this period can be 
broadly classified into the following categories: 
•	

development	of	a	panel	of	capture	probes	
that can bind target RNA, as well as meth-
odologies and strategies to optimise cap-
ture	probe	performance;
development	 of	 simplified	 methods	 for	
producing the SLIC biosensor constituent 
elements,  such  as  the  SLIC  peptide  units 
and  ligation  of  capture  of  capture  probe 
on	biosensor	platform;
development	 of	 a	 microfluidics-based	
sample  pre-treatment  platform  in  order 
to  carry  out  on-chip  target  RNA  extrac-

•	

•	

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SLIC

•	

tion,  purification  and  transportation  to 
SLIC	analysis	site;
assessment	 of	 SLIC	 biosensor	 robustness	
when  in  contact  with  media  of  complex 
mixtures (e.g. blood) as would be the case 
with clinical samples.

Patent

ALU: Vulto,  P.,  Urban,  G., ‘A  microfluidic  chip  for 
RNA  purification  and  hybridisation  detection’, 
German patent, filed end of 2006.

Expected outcome:

Coordinator

The following outcomes are expected:

•	

•	

novel	 automated	 sample	 preparation	
platform for both cell lysis extraction and 
separation	of	RNA;
methodology	 on	 a	 bioinformatics	 plat-
form for optimising oligo probe design for 
RNA target.

Major publications:

Vulto,  P.,  Medoro,  G.,  Igel,  G.,  Kieninger,  J.,  Ur-
ban,  G.,  Tartagni,  M.,  Guerrieri,  R.,  Manaresi,  N., 
‘Phaseguide structures for pipette actuated lami-
nar  flow-based  selective  sample  recovery’,  Proc. 
of MicroTAS, 2005, pp. 1093-1095.

Vulto,  P.,  Medoro,  G.,  Altomare,  L.,  Urban,  G.A., 
Tartagni, M., Guerrieri, R., Manaresi, N., ‘Selective 
sample recovery of DEP-separated cells and par-
ticles  by  phaseguide-controlled  laminar  flow’,  J. 
Micromech. Microeng., 16, 2006, pp. 1847-1853 

Glynn, B., Lacey, K., Reilly, J., Barry, T., Smith, T., Ma-
her, M., ‘Quantification of Bacterial tmRNA using 
in vitro Transcribed RNA Standards and Two-Step 
qRT-PCR’, Research Journal of Biological Sciences, 2, 
2007: 564-570.

Vulto, P., Klaunick, C., Igel, G., Urban, G., ‘tmRNA 
purification by electrophoretic filtration
for genomic identification of bacteria’, Submitted 
to MicroTAS, 2006.

Healthtech  Institute’s ‘Nucleic-Acid  Based  Tech-
nologies’ conference, 2006.

124

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Solomzi a. Makohliso
Ayanda Biosystems SA
PSE Parc Scientifique 
Swiss Federal Institute of Technology
CH-1015 Lausanne, Switzerland
E-mail: s.makohliso@ayanda-biosys.com

Partners 

Horst Vogel 
Swiss Federal Institute of Technology
Institute of Chemical Sciences & Engineering
Lausanne, Switzerland 

Gerald a. Urban
IMTEK Albert Ludwigs Universitat Freiburg
Freiburg, Germany

Majella Maher
DNA Diagnostics Laboratory 
The National Diagnostics Centre
National University of Ireland
Galway, Ireland

ants Kurg
University of Tartu
Estonian Biocentre, Laboratory of 
Gene Technology
Tartu, Estonia

andrea degen Iseli
eurelations AG
Zurich, Switzerland

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DIAGNOSTICS

eBIOSENSE

Electrical biosensor arrays for analyses of harmful micro-organisms  
and microbial toxins

Contract No 
Project type 

LSHB-CT-2004-512009
Specific Targeted 
  Research Project 

EC contribution  e 2 370 900

Starting date   1 January 2005
duration  36 months

Website  www.ebiosense.org

Background and objectives: 

The eBIOSENSE project is developing a platform 
for the analysis of harmful micro-organisms and 
their toxic products. The platform is based on sili-
con  chips,  which  are  manufactured  with  stand-
ard  silicon  technology.  These  chips  are  then 
activated for specific analyses via the  immobili-
sation of different sample binding molecules on 
an array of microelectrodes on the chip surface. 
The  electric  biochip  arrays  enable  parallel  and 
simultaneous  identification  and  quantification 
of specific nucleic acids (DNA or RNA), microbial 
proteins and toxic microbial products. 

Figure 1 shows a silicon chip with electrodes for 
the analysis of 16 different molecules in a sample. 

The  use  of  DNA-  and  antibody-based  analyses 
for 
identification  of  micro-organisms,  rather 
than  traditional  classification  in  species,  offers 
a  great  advantage  in  the  assessment  of  health 
hazards, since in many cases only certain strains 
of a species are pathogenic and many toxins are 
produced by several species. Thus, eBIOSENSE is 
seeking to assess the pathogenicity factors, rath-
er than the species name. 

Approach and methodology: 

Two  versions  of  arrays  are  being  developed:  nu-
cleic acid-based chips and antibody-based chips. 

Fig. 1. An electric biochip. Left: The 9x10 mm electric chip 
array with 16 positions. Right: The biochip reader with 
chip-holding cassette, and sample-handling equipment 
for the assay.

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The function of an electric DNA-chip is illustrated 
in Figure 2. 

When the chip surface is exposed to a sample, 
the  target  DNA  molecules  simultaneously  hy-
bridise  with  the  capturing  DNA-probe  on  the 
electrode  and  with  a  soluble  detection  probe. 
The  detection  probe  is  subsequently  labelled 
with  an  enzyme.  The  signal  is  then  generated 
by the addition of a chemical substance (pAPP). 
pAPP  reacts  with  the  enzyme  and  generates 
p-aminophenol (pAP), which is oxidised to qui-
noneimine  (QI)  at  the  positive  electrode.  The 
two  electroactive  components  pAP  and  QI  are 
then  redox  recycled  between  the  anode  and 
cathode, generating a current from the chip, as 
illustrated in Fig. 2. 

In an antibody-based biochip, the DNA capture 
probe is replaced by a specific antibody which 
recognises and binds the target molecule where 
an enzyme-antibody conjugate is then used to 
label  the  bound-target  molecules.  Enzyme  re-
action and signal generation are the same as for 
the DNA chip. The different steps in the analysis 
are  automatically  controlled  by  an  instrument 

Fig. 2. Left: Principle of signal generation with an electric 
DNA chip. Right: responses from 16 electrodes of a chip. 
The left arrow shows time of pAPP application. The second 
arrow shows the subsequent stop-flow. The initial slope 
(nA/sec) generated during the stop-flow is used as signal.

(Fig. 1), so the operator only prepares and adds 
the sample to a container in the instrument and 
then collects the signal from the different elec-
trode positions.

Expected outcome:

Time  chips  will  be  developed  for  pathogenic 
strains of the Bacillus cereus group, shiga-toxin 
producing  E.  coli  strains  (usually  called  EHEC), 
pathogenic  Staphylococcus,  Salmonella  en-
terica  and  the  mycotoxins  ochratoxin  A  and 
fumonisin.  However,  the  electric  biochips  are 
generic  and  can  be  applied  to  varied  analyses 
by  altering  the  DNA  probes  or  the  antibodies. 
Many applications are found in clinical and food 
analyses, and in the future, environmental anal-
yses may also be based on electric biochips.

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DIAGNOSTICS

based  identification  of  bacterial  colonies  with 
an  electric  chip’,  Analytical  Biochemistry,  2005, 
Vol. 345, pp. 270-276.

Los, M., Los, J., Blohm, L., Spillner, E., Grunwald, 
T., Albers, J., Hintsche, R., Wegrzyn, G., ‘Rapid de-
tection of viruses using electrical biochips and 
anti-virion  sera’,  Letters  in  Applied  Microbiology, 
2005, Vol. 40, pp. 479-485.

Coordinator 

Sven-Olof Enfors
School of Biotechnology
Royal Institute of Technology (KTH)
Roslagstullsbacken 21
10691 Stockholm, Sweden
E-mail: enfors@biotech.kth.se

Partners 

Rainer Hintsche
The Fraunhofer Institute for Silicon Technology
Itzehoe, Germany 

Thomas Schweder
Ernst-Moritz-Arndt Universität
Greifswald, Germany 

Peter Neubauer
University of Oulu
Oulu, Finland 

Grzegorz Wegrzyn
University of Gdansk
Gdansk, Poland 

Lars Blohm
eBiochip Systems GmbH
Itzehoe, Germany 

antje Breitenstein
Scanbec Oy
Oulu, Finland

Main findings:

Silicon chip arrays with 16 positions have been 
designed and manufactured for the analysis of 
several  pathogens  and  toxins:  a  DNA  chip  has 
been applied for the simultaneous detection of 
all genes involved in synthesis of all known tox-
ins  produced  by  many  strains  of  the  common 
food pathogens of the Bacillus cereus group. In 
this way, the toxin-producing capacity of Bacil-
lus strains, causing different types of food poi-
soning, could be assessed in one assay. 

A DNA chip for the analysis of the pathogenic E. 
coli strains called EHEC has also been developed. 
This chip gives information on whether the sus-
pected E. coli strain can produce the feared shi-
ga-like toxin or not. These chips are intended for 
rapid confirmative analysis of suspected bacte-
rial  colonies  from  the  primary  enrichment  cul-
ture,  which  is  usually  applied  in  food  analysis. 
Such  an  assay  takes  about  30-40  minutes  with 
the DNA chips, in comparison with standard ISO 
methods that require at least one extra day, due 
to the demand for repeated cultivations. Similar 
chips for analysis of Salmonella and fumonisin-
producing fungi will also be delivered. The per-
formance of the Salmonella chips is compared 
with commercial methods and the ISO method.

An antibody-based chip has been developed for 
analysis of several staphylococcal toxins and its 
performance is compared with standard meth-
ods. The chip for quantitative analysis of staphy-
lococcal  enterotoxin  B  currently  detects  15  ng 
toxin in a 250 µL sample.

Major publications:

Liu, Y.,  Elsholz,  B.,  Enfors,  S.O.,  Gabig-Ciminska, 
M., ‘Confirmative  electric  DNA  array-based  test 
for  food  poisoning  Bacillus  cereus’,  Journal  of 
Microbiological Methods (in press), 2007.

Gabig-Ciminska,  M.,  Liu,  Y.,  Enfors,  S.O., ‘Gene-

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eBIOSENSE

Cees Waalwijk
Plant Research International BV
Wageningen, Netherlands 

Julien Bourjault
Centre de Recherche et d’Étude 
pour l’Alimentation
Paris, France 

Mika Tuomola
Raisio Benecol Ltd
Raisio, Finland

FP7 PROJECTS

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FP7 PROJECTS

Biomedical imaging

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Diagnostics - Imaging, Nanoparticles and Biosensors

CARS Explorer

Innovative contrast imaging by non-linear optics (NLO) for the observation  
of biological tissues in vivo and in real time, at cellular and molecular levels

 Grant agreement No  HEaLTH-F5-2008-200820

Project type  Collaborative Project

EC contribution  e 3 091 129

Starting date   1 March 2008
duration  36 months

Website  http://www.carsexplorer.eu

Background and objectives:

The CARS Explorer project seeks to demonstrate 
the  concept  of  innovative  light-based  contrast-
ing  technologies  for  functional  in  situ  imaging 
in life science and biomedical research. The part-
ners’  ultimate  goal  is  to  develop  an  endoscope 
based on non-linear optics (NLO) and laser pulse 
phase  shaping.  Non-linear  laser  pulse  interac-
tions with living tissues provide unique possibili-
ties, such as an absence of sample preparation, 
direct multiparametric visualisation with molec-
ular specificity and cellular resolution, and deep 
sample  penetration.  Nevertheless,  the  effective 
transfer of NLO to biomedical applications faces 
major  technological  challenges  that  are  related 
to  the  delivery  of  ultra-short  laser  pulses,  the 
weakness  of  the  signal  produced  in  biological 
samples and the difficulty in interpreting gener-
ated contrasts.

The  CARS  Explorer  interdisciplinary  consortium 
includes  partners  with  expertise  ranging  from 
optical physics to the clinic. The work plan is split 
into five research and technology development 
(RTD) Work  Packages  (WPs):  three  are  intended 
to  overcome  specific  technological  problems 
and the other two will determine the assets and 
constraints in NLO imaging through appropriate 
experimental biological models. 

Finally,  to  bring  the  concept  to  the  diagnostic 
level,  the  consortium  will  explore  the  molecu-
lar  and  morphological  NLO  signatures  associ-
ated  with  tumour  development  in  skin  cancer. 
In addition to the challenge of developing pulse 
shaped NLO-based endoscope technology, this 
project  will  have  a  strategic  and  economic  im-
pact by providing a non-invasive functional ex-
ploration method.

Approach and methodology:

The work plan is broken down into WPs that are 
partially  or  totally  interdependent  and  will  be 
developed in parallel. As the structure of the WPs 
reflects the complementarity of the approaches 
and  expertise  of  the  individual  partners,  each 
partner contributes to several WPs. 

The WPs that will overcome the specific techno-
logical problems and validate the CARS Explorer 
project are the following:
•	

WP2,	 NLO	 contrast	 propagation	 using	
pulse	shaping;	

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DIAGNOSTICS – FP7

Partners

Hervé Rigneault
Centre National 
 de la Recherche Scientifique (CNRS)
Institut Fresnel
Marseille, France

Benoît Van den Eynde
De Duve Institute 
Brussels, Belgium

andreas Volkmer
Universität Stuttgart
Stuttgart, Germany

Jonathan Knight
University of Bath
Bath, UK

François Lacombe
Mauna Kea Technologies
Paris, France

Christiane dascher-Nadel
Inserm Transfert SA
Marseille, France

•	

•	

WP3,	 photonic	 crystal	 fibres	 for	 NLO	
imaging;	
WP4,	
processing.

recovery	 and	

imaging	

signal	

WP1  and  WP5,  which  are  more  biologically  re-
lated, will delineate through appropriate experi-
mental models the assets and constraints in NLO 
in a microscopy mode and in an endoscope con-
figuration, respectively: 
•	

WP1,	assets	and	constraints	in	imaging	tis-
sues	by	NLO;	
WP5,	molecular	&	morphological	NLO	signa-
tures associated with tumour development.

•	

Coordinator

didier Marguet
Institut National de la Santé  
et de la Recherche Médicale (INSERM)
18 Avenue Mozart
13276/09 Marseille, France
E-mail: marguet@ciml.univ-mrs.fr

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FLUODIAMON

Ultra-high resolution and ultra-sensitive fluorescence methods for objective sub-cellular 
diagnosis of early disease and disease progression in breast and prostate cancer

 Grant agreement No  HEaLTH-F5-2008-201837

Project type  Collaborative Project 

EC contribution  e 4 197 774
Starting date   1 July 2008
duration  42 months

Background and objectives:

FLUODIAMON seeks to develop and validate a 
quantitative, minimally invasive diagnostic tool 
for  early  and  conclusive  detection,  diagnosis 
and monitoring of breast and prostate cancer. 
By  making  use  of  a  combination  of  what  are 
probably the most exciting recent advances in 
the  field  of  light  microscopy,  the  partners  will 
develop a methodology for fluorescence-based 
optical imaging of individual sample cells. The 
methodology  will  include  advances  that  will 
take the spatial resolution far beyond the fun-
damental  limits  of  optical  resolution  and  the 
sensitivity  down  to  an  ultimate  single-mole-
cule level. Multi-parameter detection schemes 
will  significantly  increase  the  fluorescence  in-
formation  by  which  these  cellular  images  can 
be analysed. 

Apart  from  detecting  and  identifying  tumour 
markers  in  the  samples,  FLUODIAMON  will  ex-
ploit  tumour-specific  spatio-temporal  molecu-
lar  distributions  within  the  intact  sample  cells. 
To date, this has been an almost unexploited di-
mension of diagnostic information. By combin-
ing and supporting these novel optical methods 
with state-of-the-art affinity molecule biotech-
nology,  fluorophore  chemistry,  proteomics-
based  biomarker  identification,  and  bioinfor-
matic  validation  tools,  all  possible  means  will 
be exploited to extract a maximum amount of 
information out of very small amounts of sam-
ple material. 

The partners expect that an improved, early and 
reliable diagnosis of breast and prostate cancer 
will be possible from amounts of sample mate-
rial  which  are  small  enough  for  a  minimally  in-
vasive procedure such as Fine-needle aspiration 
(FNA) to be used. In addition, with the minimally 
invasive  FNA-based  sampling,  serious  sampling 
related side effects, such as seeding and spread 
of cancer cells, can be completely avoided. Given 
the  high  incidence  of  breast  and  prostate  can-
cer, and the utmost importance of an early and 
conclusive  diagnosis  for  the  prognosis  of  these 
diseases, the relevance of this project cannot be 
overestimated.

Approach and methodology:

Recent biophysical research has made remarkable 
progress in the field of fluorescence-based opti-
cal imaging. With an attainable spatial resolution 
of a few tens of nanometres, a detection sensitiv-
ity down to the single-molecule level and multi-
parameter  fluorescence  detection  schemes,  the 
amount  of  information  that  is  now  obtainable 
has reached a quantitatively new level. However, 
despite  shortcomings  in  the  current  analytical 
methods, clinical diagnostics have so far had lit-
tle  benefit  from  these  developments.  The  FNA 
technique is a prominent example where these 
developments can lead to considerable improve-
ments. Being minimally invasive and without ma-
jor side effects, like tumour cell spreading, FNA is 
a superior sample extraction method for breast 

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DIAGNOSTICS

for the microscopy methods. Clustered cells, tis-
sue fat or cell detritus will cause additional light 
scattering. This could be addressed by established 
wash- and filter-clean up of the aspirates and/or 
by  shifting  the  employed  wavelengths  into  the 
near-infrared region and using time-gated detec-
tion. Possible failures in the labelling or delivery 
of labelled antibodies/affibodies into cells or nu-
clei of clinical tissue can be circumvented by us-
ing multiple alternative penetration techniques. 

In  summary,  as  far  as  risks  for  the  project  are 
concerned, alternative approaches — both with 
respect to affinity molecules, the arsenal of com-
plementary  imaging  techniques  and  tumour 
markers — will make it possible to define combi-
nations by which one can overcome the practical 
problems that may arise.

Coordinato

Jerker Widengren
Albanova University Center
10691 Stockholm, Sweden
E-mail: jerker@biomolphysics.kth.se

Partners

Hans Wiksell
VibraTech AB 
Stockholm, Sweden

Gert auer
Karolinska Institutet
Stockholm, Sweden

Stefan Hell
Max-Planck-Gesellschaft zur Förderung der 
Wissenschaften e.V.
Institute for Biophysical Chemistry
Goettingen, Germany

Diagnostics - FP7 Projects - Biomedical Imaging

133

and prostate cancer sampling, for example. How-
ever, providing only small amounts of (often low-
quality) sample, the investigation of the material 
is  often  impossible  with  the  currently  available 
analytical methods.

To address this particular problem, the FLUODIA-
MON consortium seeks to bring together experts 
from  both  clinical  and  biophysical  research,  as 
well as from the instrument development side to 
devise new diagnostic methods to analyse FNA 
samples  reliably  and  without  the  requirement 
of  expert  knowledge.  The  partners  are  distin-
guished researchers in their respective fields and 
cover the following fields of expertise:
•	
•	
•	
•	

super-resolution	fluorescence	nanoscopy;	
transient-state	microscopy;	
multidimensional	fluorescence	detection;	
low-level	
light	 detection	 and	 data	
acquisition;	
fine-needle	aspiration,	FNA;	
cancer	proteomics;	
affinity	molecules	and	fluorescent	labels;
bioinformatics.

•	
•	
•	
•	

Potential  risks  can  be  identified.  However,  the 
partners do not consider them as being signifi-
cant,  but  more  localised  to  the  detailed  activi-
ties along the whole chain of activities. Being a 
field-tested  method,  the  consortium  does  not 
expect  major  risks  related  to  FNA-based  sam-
ple  extraction.  Regarding  the  identification  of 
specific  biomarkers,  some  libraries  may  not  be 
readily  available.  Difficulties  may  also  occur  in 
the  peptide  synthesis,  genetic  immunisation  of 
camels,  and  development  of  variants  of  librar-
ies.  However,  due  to  the  numerous  biomarkers 
already known and the variants identified within 
the project, the partners anticipate that they can 
focus  on  a  moderate  number  of  markers  com-
patible with their antibody/affibody and optical 
methods. 

The use of clinical, FNA-based biopsy smears in-
stead of cell lines may pose additional challenges 

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FLUODIAMON

Claus Seidel
Heinrich-Heine University
Duesseldorf, Germany

John Murphy
SensL Inc
Cork, Ireland

Wolgang Becker
Becker&Hickl GmbH
Berlin, Germany

Jens Habermann
University of Luebeck
Luebeck, Germany

Karl drexhage
University of Siegen
Siegen, Germany

Pekka Hänninen
University of Turku
Turku, Finland

Sampsa Hautaniemi
University of Helsinki
Helsinki, Finland

Silvere van der Maarel
Academisch Ziekenhuis Leiden 
(Leiden University Medical Center)
Leiden, Netherlands

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DIAGNOSTICS

FUN OCT

Functional Optical Coherence Tomography

 Grant agreement No  HEaLTH-F5-2008-201880

Project type  Collaborative Project 

EC contribution  e 5 411 720
Starting date   1 april 2008

duration  48 months

Website  www.funoct.eu

Background and objectives:

The  aim  of  FUN  OCT  is  to  expand  the  non-
invasive  optical  biopsy  capability  of  optical 
coherence  tomography  (OCT)  and  combine 
it  with  multiphoton  tomography 
(MT)  to 
develop  novel  functional  capabilities  enabling 
‘morphofunctional’ performance, i.e. the fusion of 
anatomic and functional imaging at the cellular 
resolution 
level.  These  methodologies  will 
enable  unprecedented  non-invasive  detection 
of  depth-resolved  physiological,  metabolic 
and  molecular  specific  tissue  information.  In 
other words, a novel, powerful medical imaging 
platform is envisioned. 

This novel platform fills an important gap in to-
day’s medical imaging technology. The hypoth-
esis is that the combination of cellular resolution, 
real  time  imaging  of  morphology  and  depth-
resolved  tissue  function  could  enable  a  major 
step forward in early cancer diagnosis and in the 
early  detection  of  retinal  pathologies  that  are 
worldwide leading causes of blindness. This will 
be accomplished due to a synergistic effect from 
joining  complementary  international  expertise 
in the fields of laser sources, OCT, MT and beam 
delivery  system  technology.  The  consortium 
comprises seven research groups and two small 
and  medium-sized  enterprises  (SMEs).  It  will 
make use of its existing relations to clinical col-
laborators in order to achieve proof-of-principle 
validation of the imaging modalities.

The outcome will contribute directly to improv-
ing and maintaining the quality of life and living 
conditions  of  the  European  ageing  population 
through  early  diagnosis  of  cancer  and  retinal 
pathologies,  as  well  as  more  efficient  therapy 
monitoring.  Moreover,  the  envisaged  imaging 
modality may in the long term act as a screening 
device to investigate the prevalence of cancer as 
a function of geographic (regional) or gender-re-
lated parameters. Finally, the diagnosis of other 
age-related diseases in a variety of medical fields, 
such as cardiology, neurology, gynaecology, and 
gastroenterology, will benefit from this novel di-
agnostic platform provided by FUN OCT.

Approach and methodology:

The functional extensions of OCT comprise polar-
isation-sensitive OCT, Doppler OCT, spectroscop-
ic OCT and OCT for optophysiology. Furthermore, 
OCT  is  combined  with  MT,  thus  providing  addi-
tional functional imaging and diagnostic capabil-
ities. It should be emphasised that the choice of 
applications illustrate the general clinical impact 
and applicability of the developed novel imaging 
platform. In order to facilitate such development, 
the  consortium  has  identified  two  key  enabling 
device  and  system  technologies,  namely  novel 
light source technology and probe delivery and 
applicator  systems.  Accordingly,  in  order  to  im-
plement  the  main  project  objectives,  the  work 
plan  is  divided  into  nine  Work  Packages  (WPs), 
two of which deal with project management:

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FUN OCT

WP1:	 project	management;
WP2:  development  of  novel  light  sources  for 
multi-modal,  functional  and  ultrahigh 
speed	biomedical	imaging;

WP3:  application  systems  for  functional  OCT 

and	multiphoton	tomography;

WP4:  design  and  implementation  of  polarisa-

tion	sensitive	OCT;

WP5:  design  and  implementation  of  Doppler 
OCT  for  depth  resolved  and  quantitative 
blood	flow	imaging;

WP6:  design  and  implementation  of  spectro-
scopic  optical  coherence  tomography 
for  contrast  enhancement  and  depth  re-
solved	metabolic	tissue	information;
WP7:  design and implementation of optophysi-
ology  for  depth  resolved  physiologic  tis-
sue	information;

WP8:  combination of multiphoton tomography 
and	optical	coherence	microscopy	(OCM);

WP9:  dissemination and exploitation.

Coordinator

Peter andersen
Technical University of Denmark
1 Anker Engelunds Vej
2800 Kgs. Lyngby, Denmark
E-mail: peter.andersen@risoe.dk

Partners

Gereon Hüttmann
Universität zu Lübeck
Luebeck, Germany 

Wolfgang drexler
Cardiff University
Cardiff, UK

Robert Huber
Ludwig-Maximilians-Universität München
Munich, Germany

Christoph Hitzenberger
 and Rainer Leitgeb
Medizinische Universität Wien
Vienna, Austria 

andreas Stingl and Tuan Le
Femtolasers Produktions GmbH
Vienna, Austria 

Karsten Koenig
JenLab GmbH
Jena, Germany 

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DIAGNOSTICS

nEUROPT

Non-invasive imaging of brain function and disease  
by pulsed near infrared light

 Grant agreement No  HEaLTH-F5-2008-201076

Project type  Collaborative Project 

EC contribution  e 5 738 653
Starting date   1 april 2008

duration  48 months

Website  www.neuropt.eu

Background and objectives:

The  nEUROPT  project  targets  the  development 
and clinical validation of advanced non-invasive 
optical  methodologies  for  in  vivo  diagnosis, 
monitoring, and prognosis of major neurological 
diseases  (e.g.  stroke,  epilepsy,  ischemia),  based 
on diffuse optical imaging by pulsed near infra-
red light. Established diagnostic imaging modali-
ties (e.g. X-ray Computed Tomography, Magnetic 
Resonance Imaging, Positron Emission Tomogra-
phy) provide 3D anatomical, functional or patho-
logical information with spatial resolution in the 
millimetre  range.  However,  these  methods  can-
not be applied continuously or at the bedside. 

Diffuse  optical  imaging  is  expected  to  provide 
a  valuable  complementing  tool  to  assess  per-
fusion and blood oxygenation in brain tissue and 
their  time  evolution  in  a  continuous  or  quasi-
continuous manner. Not only will the devices be 
portable and comparably inexpensive, they can 
be  applied  in  both  adults  and  children.  Time-
domain  techniques  are  acknowledged  as  offer-
ing superior information content and sensitivity 
compared  to  other  optical  methods,  allowing 
for separation between contributions of surface 
tissues  (skin  and  skull)  and  brain  tissue.  Time-
domain imaging can also differentiate between 
scatter and absorption effects. 

The  nEUROPT  consortium  plans  major  develop-
ments  in  technology  and  data  analysis  that  will 
enhance  time-domain  diffuse  optical  imaging 

with respect to spatial resolution, sensitivity and 
robustness of quantification, as well as perform-
ance  of  related  instruments  in  clinical  diagnosis 
and  monitoring.  The  diagnostic  value  of  time-
domain diffuse optical imaging will be assessed 
by clinical pilot studies addressing specific neuro-
logical disorders, in comparison with established 
neurophysiological  and  neuroimaging 
tech-
niques.  Perspectives  regarding  clinical  applica-
tion of time-domain diffuse optical brain imaging 
will be estimated and a reliable basis for a poten-
tial commercialisation of this novel technique by 
European system manufacturers will be created.

Approach and methodology:

According  to  this  general  framework,  the  tim-
ing of the activities will be divided into two main 
parts  scheduled  for  months  1-24  and  months 
25-48.  Within  each  part,  two  parallel  research 
lines will be conducted:
•	

Applied	Research,	involving	upgrade,	ad-
aptation  to  clinical  environment,  stand-
ardisation, and use in clinical tests of exist-
ing/novel time-domain instrumentation.
Basic	 Research,	 focussing	 on	 exploration	
of novel approaches, identification of po-
tentially  successful  methodologies,  and 
development of novel instrumentation. 

•	

feedback 

A  continuous 
the  applied 
research to the basic research lines will provide 
valuable  input  for  the  optimisation  of  novel 
methodologies. 

from 

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nEUROPT

Coordinator

Rinaldo Cubeddu
Politecnico di Milano
Physics Department
32 Piazza L. da Vinci
20133 Milan, Italy
E-mail : rinaldo.cubeddu@fisi.polimi.it

Partners

Sergio Cerutti
Politecnico di Milano 
Department of Biomedical Engineering
Milan, Italy

Heidrun Wabnitz
Physikalisch-Technische Bundesanstalt
Department of Biomedical Optics
Braunschweig, Germany

Simon arridge
Department of Computer Science
Jeremy Hebden
Department of Medical Physics and 
Bioengineering
Judith Meet
Institute of Woman Health
University of College London
London, UK

adam Liebert
Institute of Biocybernetics and 
Biomedical Engineering
Warsaw, Poland

Silvana Fanceschetti
Fondazione Istituto Nazionale 
Neurologico ‘Carlo Besta’
Milan, Italy

Helmuth Obrig
Charité - Universitätsmedizin Berlin
Department of Neurology
Berlin, Germany

Ewa Mayzner-Zawadzka
Medical University of Warsaw
Warsaw, Poland

alvin Kienle
Institut für Lasertechnologien in der Medizin und 
Meßtechnik – UlmUniversität
Ulm, Germany

Fabrizio Martelli 
Universita degli Studi di Firenze
Dipartimento di Fisica
Florence, Italy

William Wadsworth
University of Bath
Centre for Photonics 
and Photonic Materials
Bath, UK

John Clowes
Fianium Ltd
Southampton, UK

Franco Zappa
Micro Photon Devices S.r.l.
Bolzano, Italy

Wolgang Becker
Becker & Hickl GmbH
Berlin, Germany

Carla Finocchiaro
CF Consulting S.r.l.
Milan, Italy

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DIAGNOSTICS

FMT-XCT

Hybrid  Fluorescence  Molecular  Tomography  –  X-ray  Computed  Tomography 
method and system

Contract No  HEaLTH-F5-2008-201792
Project type  Collaborative Project

EC contribution  e 4 512 303

Starting date   To be confirmed
duration  48 months

Background and objectives:

The  FMT-XCT  project  aims  to  combine  X-ray 
computed tomography (XCT) and fluorescence 
molecular  tomography  (FMT)  into  a  hybrid, 
quantitative system. The project builds on state-
of-the-art knowledge that has only recently be-
come available in Europe, and which is brought 
to the project by the partners herein. In return, 
it  should  deliver  the  first  such  hybrid  system 
worldwide.

The  system  will  operate  by:  (1)  co-registering 
XCT images with highly performing FMT images 
for merging anatomical, functional and molec-
ular	 contrast;	 and	 (2)	 combining	 XCT	 informa-
tion into the FMT inversion to provide a system 
with superior imaging performance. XCT-based 
correction  can  improve  FMT  performance  in  a 
more  radical  way  than  corresponding  ‘correc-
tion methods’ used for improving PET or SPECT 
images. In this way, FMT-XCT can reach the im-
aging accuracy of radio-nuclei-based tomogra-
phy hybrid systems. 

By  using  fluorescence,  FMT-XCT  can  then  en-
able high flexibility in targeting physiology and 
molecular  function,  especially  in  multi-spectral 
mode, and high dissemination potential because 
virtually any biomedical laboratory has access to 
fluorescence reporting compared to radio-nuclei 
based  research  that  requires  access  to  radio-
chemistry and cyclotron facilities.

FMT-XCT aims to advance small animal imaging 
and  drug  discovery  with  a  view  to  the  clinical 
application  of  non-invasive  breast  cancer  im-
aging.  For  this  reason,  the  focus  is  on  imaging 
breast  cancer  and  response  to  therapy.  Overall, 
the  technology  is  ideally  suited  for  commercial 
translation and has the potential to become the 
method of choice for in vivo imaging in most bio-
medical laboratories and in select clinical appli-
cations. While it appreciates the value of nuclear 
imaging methods, this project will hopefully raise 
the  funding  necessary  to  establish  in  Europe  a 
potent  new  paradigm  of  in  vivo  imaging  with 
high  dissemination  and  application  potential, 
and have a large social and health-care impact.

Approach and methodology:

The work is split into nine Work Packages (WPs). 
WP1 focuses on the management and coordina-
tion of the project while WP9 considers dissemi-
nation  and  training  activities.  WP2-WP4  build 
unique XCT and FMT technology and know-how 
that is then integrated into one system prototype 
in WP5. WP6 and WP7 research appropriate im-
aging strategies for in vivo imaging and perform 
preclinical imaging. WP8 compares the FMT-XCT 
system with a previously developed PET-XCT sys-
tem to test the hypotheses in this proposal.

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FMT-XCT

Coordinator

Vassilis Ntziachristos
Helmholtz Center Munich
1 Ingolstaeder Landstrasse
85764 Neuherberg, Germany
E-mail: vasilisn@comcast.net

Partners

Bertrand Tavitian
Laboratory for Experimental Molecular Imaging
Paris, France

Philippe Rizo
LETI, Commissariat à l’Energie Atomique 
Grenoble, France

Jorge Ripoll
Foundation for Research and Technology Hellas
Heraklion, Crete, Greece

Simon arridge
University College London
London, UK

Manuel desco
Fudacion para la Investigacion 
Biomedica del Hospital Gregorio Marañon
Madrid, Spain

Markus Rudin
Universität Zürich
Zurich, Switzerland

Willi Kalender
Verfahren und Apparate 
der Medizinischen Physik GmbH
Erlangen, Germany

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Diagnostics - Genetic Testing and Biomarkers

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DIAGNOSTICS

HYPERImage

Hybrid PET-MR system for concurrent ultra-sensitive imaging

 Grant agreement No  HEaLTH-F5-2008-201651

Project type  Collaborative Project 

EC contribution  e 4 940 000
Starting date   1 april 2008

duration  36 months

Website  www.hybrid-pet-mr.eu/

Background and Objectives:

The  HYPERImage  project  will  develop  a  novel  hy-
brid  system  for  simultaneous  whole-body  PET-MR 
(Positron  Emission  Tomography-Magnetic  Reso-
nance) imaging for humans. It will advance the re-
quired Time-of-Flight (ToF) PET technology, and the 
software for MR-mediated compensation of motion 
artefacts. The hybrid system will be validated in pre-
clinical and initial clinical studies, for application in 
cardiovascular disease and in breast cancer, as one 
of the most relevant applications in oncology. For 
the latter application, the concept will be extended 
from pure imaging towards image-guided therapy. 

PET is the most sensitive molecular imaging mo-
dality.  Hybrid  PET/CT  systems  using  Computer 
Tomography (CT) in order to provide the anatom-
ical reference for lesion localisation have evolved 
to  become  the  best  choice  for  a  number  of  ap-
plications in cardiology and oncology. However, 
PET/CT has drawbacks and limitations: CT is asso-
ciated with a radiation dose and lacks soft tissue 
contrast, and PET suffers from restrictions in small 
lesion detectability, both due to motion artefacts 
during the scan, and detector limitations. 

A  hybrid  combination  of ToF-PET  with  a  3T  MR 
has  the  potential  to  overcome  these  shortcom-
ings  by  fully  exploiting  the  superior  soft-tissue 
contrast  of  MR  in  combination  with  a  new  MR-
compatible solid-state PET detector technology. 
Sophisticated  motion  compensation  —enabled 
by concurrent acquisition of both MR and time-
stamped  PET  data  —  will  also  be  used.  In  ad-
dition,  the  versatility  of  MR  allows  imaging  of 
supplementary  functional  parameters  like  tem-
perature,  elasticity,  and  diffusion,  enabling  this 
new  hybrid  imaging  concept  to  open  up  new 
fields  of  applications  in  therapy  guidance  and 
therapy response monitoring. 

The  consortium  consists  of  one  large  company, 
four  academic  partners  and  three  research  in-
stitutes  from  six  different  EU  Member  States.  It 
combines leadership in technology with pioneer 
experience in using biomedical imaging for diag-
nosis and therapy monitoring.

Approach and methodology:

The project is divided into three major research 
topics: 
•	

development	 of	 hybrid	 PET/MR	 test	 sys-
tems	for	concurrent	image	acquisition;	
development	 of	 multimodality	 methods	
to	advance	quantitative	technologies;	
preclinical	and	clinical	tests	with	focus	on	
oncology and cardiology applications.

•	

•	

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HYPERImage

Coordinator

Volkmar Schulz 
Philips Technologie GmbH
Forschungslaboratorien
2 Weibhausstrabe
52066 Aachen, Germany
E-mail: volkmar.schulz@philips.com

Partners

Peter Fischer
University of Heidelberg
Mannheim, Germany

Claudio Piemonte
Fondazione Bruno Kessler-IRST
Trieste, Italy

Tobias Schaeffter
King’s College London
London, UK

Julia Redondo
Fundación Centro Nacional de 
Investigaciones Cardiovasculares, Carlo III 
Madrid, Spain

Gijsberta Krenn
Netherlands Cancer Institute
Amsterdam, Netherlands

Gerhard adam
Universitätsklinikum Hamburg-Eppendorf
Hamburg, Germany

Stefaan Vandenberghe 
Interdisciplinair Instituut voor Breedb
and Technologie
Ghent, Belgium

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DIAGNOSTICS

MEGMRI

Hybrid MEG-MRI Imaging System

 Grant agreement No  HEaLTH-F5-2008-200859 

Project type  Collaborative Project 

EC contribution  e 4 865 656
Starting date   1 May 2008
duration  48 months

Website  http://megmri.tkk.fi

Background and objectives:

The  MEGMRI  project  will  develop  and  validate 
hybrid  magnetoencephalography  (MEG)  and 
magnetic  resonance  imaging  (MRI)  technology 
that will allow simultaneous structural (MRI) and 
functional  (MEG)  imaging  of  the  human  brain. 
MEG  is  a  non-invasive  3D  functional  imaging 
technology  with  a  high  temporal  resolution 
compared to other functional imaging but often 
suffers from a precise structural localisation that 
will be improved by the dual modality approach 
of the MEGMRI hybrid scanner.

In parallel, low-field MRI, a new very promising al-
ternative  to  conventional  high-field  MRI,  will  pro-
vide  enhanced  image  contrast  in  certain  applica-
tions,  improved  geometric  accuracy,  improved 
safety (for patients with pacemakers and other im-
plants, pregnant women and infants), and reduced 
costs. These new opportunities are based on recent 
advances in ultra-sensitive magnetic sensors. 

Two  US  teams  recently  used  superconducting 
magnetometers based on quantum interference 
devices  (SQUIDs)  to  provide  2D-MRI  images  at 
very low fields. In parallel, the Paris group of the 
MEGMRI consortium has developed a new type of 
magnetometer  based  on  their  Nobel-prize  win-
ning (Albert Fert, 2007) GMR technology, called 
mixed sensor, and is used for low-field NMR. 

The first part of the project will focus on sensor 
optimisation and low-field MRI development. This 

covers the development of field-tolerant SQUIDs 
and optimised mixed sensors, as well as 3D-MRI 
low-field  hardware  and  software  development. 
The second part of the project will be devoted to 
a prototype building with the best kind of sensor 
and  preclinical  validation,  covering  major  brain 
disorders for adults and children. The consortium 
has the necessary skills to perform all the tasks: 
sensor developers, MRI experts, MEG developers 
and  clinical  validators.  It  comprises  13  partners 
from 5 countries, including 3 small and medium-
sized enterprises (SMEs) and 1 large medical de-
vice manufacturer.

Approach and methodology:

The partners will develop an MEG-MRI scanner 
for  brain  studies.  The  MRI  mode  will  function 
at  low  field  with  an  initial  resolution  of  3×3×3 
mm3. Partners will compare and integrate low-
field MRI and high-field MRI on volunteer sub-
jects  and  patients. This  device  will  be  the  first 
whole-head  low-field  3D  MRI  system  where 
MEG  source  localisation  maps  and  MR  images 
are obtained in the same session. To realise the 
goal  in  an  optimal  way,  they  will  develop  and 
test  both  optimised  field-tolerant  SQUIDs  and 
mixed sensors. The partners will select their op-
timal combination for the prototype. The project 
has three main tasks corresponding to the steps 
described above. To succeed in these, the work 
plan  is  divided  in  Work  Packages  (WPs),  each 
with a clear end point and a designated, respon-
sible WP leader.

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antonello Sotgiu
Imaging Technology Abruzzo
L’Aquila, Italy

Lutz Trahms
Physikalisch-Technische Bundesanstalt
Braunschweig, Germany

Giacomo Rizzolatti
University of Parma
Parma, Italy

Panu Helistö
VTT Technical Research Centre of Finland
Espoo, Finland

MEGMRI

Coordinator

Risto Ilmoniemi
Helsinki University of Technology
Box 1000
02015 Espoo, Finland
E-mail: risto.ilmoniemi@tkk.fi

Partners

Jari Sakari Penttilä
Aivon Oy
Espoo, Finland

Patrick Meneroud
CEDRAT Technologies SA
Meylan, France

dag Winkler
Chalmers University of Technology
Gothenburg, Sweden

Gian Luca Romani
Universita degli studi Gabriele D’Annunzio
Department of Clinical Sciences and 
Bioimaging
Chieti, Italy

Claude Fermon
Commissariat à l’Energie Atomique
Paris, France

antti ahonen
Elekta AB
Stockholm, Sweden

Paolo Maria Rossini
Assiociazione Fatebenefratelli per la Ricerca 
Biomedica e Sanitaria
Rome, Italy

Jyrki Mäkelä
Hospital District of Helsinki and Uusimaa
Helsinki, Finland

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DIAGNOSTICS

SKINSPECTION

Multimodal skin inspection with hybrid acoustic  
and optical spectroscopic imaging

 Grant agreement No  HEaLTH-F5-2008-201577

Project type  Collaborative Project 

EC contribution  e 4 097 585
Starting date   1 april 2008

duration  48 months

Website  http://www.skinspection-fp7.eu

This  novel  multimodal  approach  will  provide 
a  wide-field  ‘acoustic/optoacoustic’  view  with 
quantitative depth information of the dermato-
logical lesion as well as a close ‘optical’ look into 
particular  intratissue  compartments  with  quan-
titative  hyperspectral  information  and  subcel-
lular resolution. It is intended to provide a novel 
unique  tool  for  early  diagnosis  and  treatment 
control  of  skin  cancer  and  skin  disease,  which 
will significantly contribute to the improvement 
of the European healthcare system.

Approach and methodology:

The project implementation is divided into three 
logical  phases:  specification,  development  & 
in vitro / ex vivo testing and clinical evaluation. 
The work in all phases is structured into 10 Work 
Packages,  7  of  which  are  directed  towards  re-
search  and  development  with  others  covering 
management aspects, regulatory affairs for clini-
cal testing, and training and dissemination. 

Background and objectives:

The  incidence  of  skin  cancer  in  Europe,  the  US 
and Australia is rising rapidly. One in five people 
will  develop  some  form  of  skin  cancer  during 
their  lifetime.  A  person  has  a  1  in  33  chance  of 
developing melanoma, the most aggressive skin 
cancer. Melanoma is the second most common 
cancer in women aged 20-29, and the sixth most 
common  cancer  in  men  and  women.  In  2007, 
more than 1 million new cases were expected to 
be diagnosed in the US alone. About 90% of skin 
cancers  are  caused  by  ultraviolet  (UV)  sunlight. 
The World Health Organization estimates that 60 
000 people will die this year from too much sun: 
48  000  from  melanoma  and  12  000  from  other 
skin cancers. 

A  significant  improvement  of  the  current  diag-
nostic  tools  of  dermatologists  is  required  in  or-
der  to  identify  dermal  disorders  at  a  very  early 
stage,  as  well  as  to  monitor  directly  the  effects 
of  treatment.  The  SKINSPECTION  partners  aim 
in  this  project  to  develop  a  non-invasive  multi-
modal hybrid imaging system with the capacity 
to  perform  non-invasive  high  resolution  three-
dimensional  clinical  (1)  two-photon  imaging 
with	 timecorrelated	 single	 photon	 detection;	
(2)	 autofluorescence	 lifetime	 imaging;	 (3)	 high-
frequency acoustical imaging with novel minia-
turised	 multiple	 detector	 arrays;	 and	 (4)	 optoa-
coustical imaging using ultrashort near infrared 
(NIR) laser pulses. 

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SKINSPECTION

Coordinator

Volkmar Schulz 
Robert Lemor
Fraunhofer IBMT
48 Ensheimer Strasse
66386 Sankt Ingbert, Germany
E-mail : robert.lemor@ibmt.fraunhofer.de

Partners

Karsten Koenig
JenLab GmbH
Jena, Germany

Chris dunsby
Imperial College of Science, Technology and 
Medicine
London, UK

alberto Giannetti
Universita degli studi di Modena e Reggio Emilia
Modena, Italy

Hanno Wittig
tp21 GmbH
Saarbruecken, Germany

Christian Weiss
kibero GmbH
Saarbruecken, Germany

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DIAGNOSTICS

EURIPIDES

European Research initiative to develop Imaging Probes for early  
In vivo diagnosis and Evaluation response to therapeutic substances

 Grant agreement No  HEaLTH-F5-2007-201380

Project type 

Integrated Project 

EC contribution  e 6 994 850

Starting date   1 February 2008
duration  48 months

Website  www.euripides-europe.com/

Background and objectives:

The  EURIPIDES  project  partners  aim  to  develop 
an  in  vivo  imaging  biomarker  of  multi-drug 
transporter  function  as  a  generic  tool  for  the 
prediction, diagnosis, monitoring and prognosis 
of major central nervous system (CNS) diseases, 
as  well  as  to  provide  support  and  guidance  for 
therapeutic interventions. Multi-drug transport-
ers actively transport substrates (including mul-
tiple CNS drugs) against concentration gradients 
across the blood-brain barrier (BBB). 

Over-activity  of  these  transporters  results  in  in-
adequate  access  of  CNS  drugs  to  their  targets 
and  hampers  the  build-up  of  adequate  tissue 
levels of these drugs in the brain, This greatly lim-
its their therapeutic efficacy. As such, this ‘trans-
porter hypothesis’ of drug resistance is applicable 
to a broad range of CNS drugs and patients with 
a  variety  of  CNS  diseases  who  critically  depend 
on these drugs. Efflux transporters may also in-
fluence brain elimination of Aβ, the hallmark of 
Alzheimer’s  disease  (AD).  Impaired  multi-drug 
transporter  function  with  reduced  clearance  of 
Aβ could lead to accumulation within the extra-
cellular space, contributing to the pathogenesis 
of AD.

The  partners  will  determine  the  contribution 
of  multi-drug  transporters  to  impaired  brain 
uptake of drugs for the prediction of therapeu-
tic  responses,  or  the  contribution  of  impaired 
transporter  function  to  reduced  clearance  of 

toxic  substances  for  the  early  in  vivo  diagnosis 
of AD. Circumvention of pharmacoresistance, or 
increasing  clearance,  may  involve  inhibitors  of 
multi-drug transporters or sophisticated alterna-
tive therapies, but demonstration of overexpres-
sion or underactivity of transporter function is an 
essential and necessary first step. 

An  in  vivo  imaging  biomarker  of  multi-drug 
transporter  function  is  essential  for  identify-
ing altered transporter activity in individual pa-
tients. If a relation between overexpression and 
therapy resistance, or underactivity and AD, can 
be demonstrated, such a biomarker will provide 
the means for predicting treatment response, or 
early diagnosis, in individual patients.

Approach and methodology:

EURIPIDES  is  a  four-year  research  programme 
based  on  a  multidisciplinary  approach  integrat-
ing  radiochemistry,  molecular  and  cellular  biol-
ogy, physics, physiology, pharmacology, patholo-
gy and clinical research topics related to the most 
important  neurological  and  neurodegenerative 
issues. The overall goal is to provide a non-inva-
sive molecular imaging tool for the prediction, di-
agnosis, monitoring and prognosis of major CNS 
diseases,  and  to  provide  support  and  guidance 
for  therapeutic  interventions.  It  will  be  deter-
mined whether multi-drug transporters contrib-
ute to drug therapy resistance in diseases of the 
CNS. If transporters are shown to be important in 
mediating resistance, the development of strate-

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EURIPIDES

gies to modulate their function will be important, 
and are feasible with the development of highly 
specific, potent and non-toxic transporter inhibi-
tors. The work programmes selected are comple-
mentary, symbiotic and cross-fertilising, and ad-
dress the underlying methodological issues:

•	

•	

(A)  RTD  activity  area  (organised  according  to  the 
flow of developing radioactive molecular probes):
•	
•	

radiotracer	development;	
in	vitro	molecular	characterisation	of	com-
pounds;	
biological	evaluation	in	animal	models;	
proof-of-concept	studies	in	animal	models;	
evaluation	in	healthy	human	subjects;	
proof-of-concept	 studies	 in	 human	 CNS	
disease. 

•	
•	
•	
•	

In  parallel  with  activities  aimed  at  newly-devel-
oped P-glycoprotein tracers, the role of existing 
PET  tracers  for  two  major  neurotransmitter  sys-
tems  will  be  explored:  serotonin  ([18F]-MPPF) 
and GABAA ([11C]-FMZ). Use will be made of the 
unique  possibility  in  certain  CNS  disorders  to 
validate and inform in vivo imaging findings by 
comparing with autoradiography and immuno-
histochemistry  the  sacrificed  animals  and  brain 
specimens resected by surgery. 

(B) Management activity area, which consists of 
the following main activities:
•	

Technical	coordination	of	EURIPIDES	com-
ponents. Harmonisation and standardisa-
tion procedures will be implemented and 
shared  within  the  EURIPIDES  consortium 
and applied to:
a)	
b)	 acquisition	and	analysis	of	PET	data;
c) 

animal	models;

structural  imaging  (e.g.  MRI)  with 
standard protocols for the detection 
of	structural	abnormalities;
collection  of  human  biological 
samples  (brain  tissue,  blood,  cells, 
DNA,  surgical  and  post-mortem 
specimens).

d) 

Quality	 assurance	 and	 monitoring,	 espe-
cially  financial  status  and  scientific  rel-
evance of EURIPIDES.
Knowledge	 management.	 The	 major	 ac-
tivities are:
a)  

internal  dissemination  including  in-
ternal  communication,  workshops 
and	training	courses;

b)   external  dissemination  of  research 
through  peer-reviewed 
progress 
manuscripts,  through  reports  in  lay 
language  to  patient  organisations, 
the  general  public  and  through  its 
own	website;
reporting. 

c)  

WP 9:
Trainind and dissemination

WP 1:
Synthesis
of new
P-g
tracer

WP 2:
Biological
evaluation of
new P-gp tracer
animal PET
studies

WP 3:
In-tro
inhibition 
and induction
 of P-gp

WP 7:
P-gp
in AD

C-VPM
C-PIB

WP 6:
P-gp
in 
epilepsy

C-VPM
New
PgP
tracer

WP 5:
P-gp
in 
healthy
controls

C-VPM
New
PgP
tracer

WP 4:
C-FMZ
F-MPPF

human
PET
studies

WP 4:
C-FMZ
F-MPPF

animal
PET
studies

WP 8:
Ex-vivo studies

WP 10:
Project Management

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DIAGNOSTICS

Rob Voskuyl
Stichting Epilepsie Instellingen Nederland
Heemstede, Netherlands 

alexandra Varvarigou
National Center for Scientific Research 
“Demokritos”
Aghia Paraskevi, Athens, Greece 

Gitte Moos Knudsen
Rigshospitalet
Copenhagen, Denmark 

Birgit Fuchs 
GABO.mi (Gesellschaft für Ablauforganisation: 
milliarium mbH & Co. KG) 
Munich, Germany

Coordinator

Matthias Johannes Koepp
University College London
33 Queen Square
London, WC1N 3BG, UK
Email: mkoepp@ion.ucl.ac.uk

Partners

adriaan Lammertsma
VU medisch centrum
Amsterdam, Netherlands 

Ekaterina Patraia
Medizinische Universitaet Wien
Vienna, Austria

Oliver Langer
Austrian Research Centres GmbH
Seibersdorf, Austria

Wolfgang Loescher 
Stiftung Tierärztliche Hochschule Hannover
Hannover, Germany

Heidrun Potschka
Ludwig-Maximillians-Universitaet
Munich, Germany 

Philippe Ryvlin
Hospices Civils de Lyon
Lyon, France 

Karl Herholz
University of Manchester
Manchester, UK

Munir Pirmohamed
University of Liverpool
Liverpool, UK

Elizabeth de Lange
Universiteit Leiden
Leiden, Netherlands 

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ENCITE

European Network for Cell Imaging and Tracking Expertise

 Grant agreement No  HEaLTH-F5-2008-201842 

Project type  Collaborative Project

EC contribution  e 11 997 946
Starting date   1 June 2008

duration  48 months

Background and objectives:

Cell  therapy  can  be  defined  as  the  transplanta-
tion  of  living  cells  for  the  treatment  of  medical 
disorders. Three different principles underlie the 
increasing interest in cell therapy:
1. 
2. 

Transplanted cells used as an ‘active drug’.
Transplanted  cells  used  to  replace  dam-
aged and degenerated tissue.
Cells used as a drug delivery vehicle.

3. 

Promising  results  have  been  obtained  in  pre-
clinical  and  clinical  studies.  However,  success 
rates  have  been  variable  and  clinical  benefits 
have been limited. A major issue is the fact that 
the mechanisms by which cell therapy works in 
the different disease areas are still poorly under-
stood. The ability to non-invasively monitor the 
fate  and  modes  of  action  of  transplanted  cells 
over time is mandatory. The development of rel-
evant imaging tools will lead to a better under-
standing of how cell therapy works, increase the 
possibility  of  response  monitoring  in  patients, 
and offer sufficient safety of the treatment.

The  ENCITE  project  will  provide  tools  to  allow 
this by developing:
•	

new	 imaging	 methods	 to	 improve	 the	
spatio-temporal	tracking	of	labelled	cells;
dual	and	multimodality	imaging	procedures	
to	cross-validate	each	individual	approach;
new	contrast	agents	and	procedures	that	
will improve the sensitivity and specificity 
of	cellular	labelling;

•	

•	

•	

•	

•	

•	

•	

a	 combination	 of	 molecular	 biology	 for	
the  generation  of  molecular  and  cellular 
imaging reporters with multimodal imag-
ing	techniques;
novel	 cell	 and	 animal	 reporter	 systems	
detecting the location and function of in-
dividual cells and small cell subsets within 
the	target	organ;
cellular	 labelling	 that	 does	 not	 interfere	
with  cellular  functions  and  therapeutic 
efficacy;
methods	 for	 quantitative	 assessment	 to	
generate  reliable  biomarkers  of  the  cell 
fate	and	therapeutic	effects;
cell	 homing	 for	 therapeutic	 delivery	 to	
target organs.

The tools and methodologies developed will be 
validated in five key disease areas: neurological, 
cardiovascular,  musculoskeletal,  diabetes  and 
cancer.

Approach and methodology:

The  key  work  of  the  project  will  be  carried  out 
within Subprojects (SPs), which represent the rel-
evant expertise of the participating groups. While 
SPs  will  concentrate  on  the  integration  of  new 
methods, technologies and approaches, they will 
be  broken  down  into  individual  Work  Packages 
(WPs) which will concentrate on the scientific and 
technology activities, as well as provide well de-
fined, specific objectives and milestones.

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DIAGNOSTICS

Matched images of iron-labeled 
cells. (A) Light microscopy image 
showing the contours of the cells. 
(B) Fluorescent microscopy image 
showing the fluorescent labeled 
nuclei of the cells. (C) MR image 
showing the susceptibility artifacts 
caused by the intra-cellular iron 
particles. (D) Overlay of the images 
shown in A. B. and C.

Mathias Hoehn
Max Planck Gesellschaft zur Foerderung der 
Wissenschaften E.V.
Colgone, Germany

Gil Navon
Tel Aviv University
School of Chemistry
Tel Aviv, Israel

Silvio aime
Università di Torino
Turin, Italy

Milan Hájek
Institute for Clinical and Experimental Medicine
Department of Diagnostic and Interventional 
Radiology
Prague, Czech Republic

Juergen Henning
University of Freiburg
Freiburg, Germany

The  SPs  and  WPs  will  be  coordinated  at  the 
project level and the success of the project will 
be assured by well-defined interaction and com-
munication channels coordinated at the project 
level  between  the  coordinator,  and  the  SP  and 
WP leaders.

Coordinator

Gabriel Krestin
European Institute for Biomedical Imaging Research 
(EIBIR)
Neutorgasse 9/2A
1010 Vienna, Austria
E-mail: g.p.krestin@erasmusmc.nl

Partners

Monique Bernsen
Erasmus Medical Center
Department of Radiology
Rotterdam, Netherlands

Mike Modo 
King’s College London
Centre for the Cellular Basis of Behaviour & MRC 
Centre for
Neurodegeneration Research
London, UK

Michal Neeman
Weizmann Institute of Science
Rehovot, Israel

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FP7 PROJECTS

Stefan Wecker
Medres-Medical research GmbH
Cologne, Germany

Giovanni B. Giovenzana 
Cage Chemicals SRL
Turin, Italy

Ignacio Melero
University of Navarra
Gene Therapy and Hepatology
Pamplona, Spain

ENCITE

Robert Muller
University of Mons-Hainaut
General, Organic and Biomedical Chemistry
Mons, Belgium

Oliviér Clément
University Paris Descartes
Laboratoire de Recherche en Imagerie EA 4062
Paris, France

Gerold Schuler
Friedrich-Alexander University Erlangen-
Nurenberg
Department of Dermatology
Nuernberg, Germany

Clemens Lowik
Leiden University Medical Center
Endocrinology, Leiden University Medical Center, 
postal zone C4-R
Leiden, Netherlands

Francesca Granucci
The University of Milano – Bicocca
Department of Biotechnology and Bioscience
Milan, Italy

Carl Figdor
Radboud University Nijmegen Medical Centre
Department of Tumor Immunology
Nijmegen, Netherlands

Ignacio Melero
Foundation for Applied Medical Research
Gene Therapy and Hepatology- CIMA
Pamplona, Spain

diego amigorena
Institut Curie
Dept. U653, Immunité et cancer
Paris, France

Pierre-alix dancer
BioSpace
Paris, France

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FP7 PROJECTS

molecular testing

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SPIDIA

Standardisation and improvement of generic pre-analytical tools  
and procedures for in vitro diagnostics

 Grant agreement No  HEaLTH-F5-2008-222916

Project type  Collaborative Project
EC contribution  e 9 000 000 (proposed)

Starting date   To be confirmed
duration  48 months

Background and objectives:

In vitro diagnostics have allowed a great deal of 
progress in medicine but are limited by two fac-
tors: (1) the lack of guidelines in collection, han-
dling,  stabilisation  and  storage  of  biosamples 
which  limits  the  reproducibility  of  subsequent 
diagnoses, and (2) its scale is limited to the cellu-
lar level. To address this first point, the Integrated 
Project SPIDIA, comprising clinicians, academics, 
tool  developers  and  assay  developers,  aims  to 
develop quality guidelines for molecular in vitro 
diagnostics and to standardise the pre-analytical 
workflow  in  related  procedures.  Regarding  the 
second  point,  SPIDIA  aims  to  develop  modern 
pre-analytical  tools  for  diagnostics,  improving 
the stabilisation, handling and study of free bio-
molecules  within  blood,  plasma,  serum,  tissues 
and tumours. 

Recent discoveries have revealed that RNA, DNA 
or  proteins  released  from  pathological  sites  — 
such as tumour cells or Alzheimer’s disease (AD) 
brain lesions — into the blood or as a secondary 
blood  based  response  to  the  disease  can  serve 
as  biomarkers  for  early  and  reliable  molecular 
diagnosis  of  such  debilitating  diseases.  Further 
discoveries have shown that the cellular profiles 
of these molecules and structures in clinical sam-
ples  can  change  during  transport  and  storage, 
thus  making  clinical  assay  results  and  pharma-
ceutical  research  unreliable  or  even  impossible. 
It  will  therefore  be  a  decisive  prerequisite  for 
future and current diagnostic assays to develop 

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standards  and  new  technologies,  tools  and  de-
vices that eliminate the human error in the pre-
analytical steps of in vitro diagnostics. 

At  this  crucial  moment  in  the  development  of 
molecular diagnostics, SPIDIA proposes a project 
that  reunites  eight  private  research  companies 
(including  four  small  and  medium-sized  enter-
prises  (SMEs)),  six  public  research  organisations 
(including  universities,  hospitals  and  biobanks) 
and an official European Standards Organisation. 
This strong consortium is balanced and empow-
ered to maximise the impacts of in vitro diagnos-
tics on human health.

Approach and methodology:

SPIDIA  is  organised  into  three  activities,  each 
consisting of multiple Work Packages (WPs):

1.  Evidence-based,  international  guidelines  and 
quality-assurance schemes:
•	

to	 evaluate	 solutions	 developed	 by	 the	
consortium  by  using  ISO-certified  analysis 
platforms and ring-trials in order to gather 
evidence needed to improve critical steps in 
the pre-analytical workflow and gather the 
data	required	for	standardisation	activities;
to	 submit	 these	 data	 and	 quality-assur-
ance schemes to the CEN and its partner 
organisations, including ISO, and the IFCC 
and WHO  (members  of  the  club  of  inter-
est)  for  conversion  into  official  technical 
guidelines;

•	

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•	

to	discover	one	or	more	sets	of	biomark-
ers that serve as quality assurance indica-
tors  for  artificial,  post  collection  changes 
of biological samples.

3. Management, ethics and spreading of 
excellence:
•	

to	perform	training	to	diffuse	information	
about  guidelines  and  discoveries  to  con-
cerned authorities in the scientific, clinical 
and	biobanking	communities;
to	disseminate	non-proprietary	results	to	
the	community;
to	encourage	ethical	sensitivity	and	com-
pliance;
to	efficiently	manage	SPIDIA;
to	 optimise	 implementation	 and	 maxim-
ise impact.

•	

•	

•	
•	

2.  Research  leading  to  pre-analytical  tools  for 
molecular 
in  vitro  diagnostics  and  classical 
pathology:
•	

to	discover	chemical	compositions	that	en-
able the simultaneous stabilisation of mul-
tiple  cellular  and  biomolecular  targets  in 
blood, tissue and non-invasive samples (i.e. 
respiratory	and	cervical	swab	samples);
to	 create	 prototypes	 of	 integrated	 kits	
based  on  new,  innovative  collection  and 
stabilisation;
to	 develop	 technologies	 for	 tissue	 and	
blood  samples  that  can  stabilise  RNA, 
DNA, proteins and metabolites while leav-
ing  the  morphology  and  antigenicity  of 
the cells and tissues intact (these technol-
ogies  would  have  a  unique  market  posi-
tion worldwide, as no such technology is 
currently	available);
to	create	a	fully	automated	system	for	use	
with stabilised blood samples which com-
bines  the  pre-analytical  tool  described 
above  with  the  first  critical  steps  of  the 
analytical assay setup, thereby eliminating 
potential	for	human	error	in	the	workflow;
to	 provide	 a	 proof-of-principle	 for	 non-
invasive  sample  collection  techniques 
improved with respect to the stabilisation 
and recovery of biomolecules and simul-
taneous	inactivation	of	pathogens;
to	evaluate	and	provide	feedback	encour-
aging  improvement  and  innovation  of 
guidelines and tools used for the discov-
ery and validatation of biomarkers.

•	

•	

•	

•	

•	

DIAGNOSTICS

Coordinator

Uwe Oelmüller
QIAGEN GmbH
1 Qiagen Strasse
40724 Hilden, Germany
E-mail : uwe.oelmueller@qiagen.com

Partners

Kurt Zatloukal
Medical University of Graz
Graz, Austria

Ivano Bertini
Consorzio Interuniversitario Risonanze
 Magnetiche di Metalloproteine
Paramagnetiche
Sesto Fiorentino, Italy

Robert Sjöback
TATAA BIOCENTER AB
Gothenburg, Sweden

Christian Lenz
PreAnalytiX GmbH
Hombrechtikon, Switzerland

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Heinz Höfler
Institute of Pathology of the Technical 
University Munich
Munich, Germany

SPIDIA

anders Lönneborg
DIAGENIC ASA
Oslo, Norway

Mogens Kruhoffer
AROS Applied Biotechnology AS
Aarhus, Denmark

Nanna Christensen
Dako Denmark AS
Glostrup, Denmark

Bénédicte Charrin
ACIES
Lyon, France

Mikael Kubista
Institute of Molecular Genetics
Czech Academy of Sciences
Prague, Czech Republic

anna von Groote 
European Committee for Standardization 
(CEN)
Brussels, Belgium

Sébastien Weisbuch
ImmunID Technologies
Grenoble, France

Pierre Hainaut 
International Agency for Research on 
Cancer
Lyon, France

Mario Pazzagli
University of Florence
Florence, Italy

Pieter Riegman
Erasmus Medical Center Rotterdam
Rotterdam, Netherlands

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DIAGNOSTICS

EURO-GENE-SCAN

European Genetic disease diagnostics

 Grant agreement No  HEaLTH-F5-2008-223293

Project type  Collaborative Project 
EC contribution  e 2 913 807 (proposed)

Starting date   To be confirmed
duration  36 months

Background and objectives:

Molecular  techniques  have  become  more  ef-
ficient,  increasingly  precise  and  much  cheaper, 
resulting in an unprecedented discovery rate of 
inherited disease genes. In areas such as prima-
ry  immunodeficiencies  (PID),  muscle  disorders, 
growth deficiencies, hearing/vision impairments 
and  metabolic  diseases,  very  large  numbers  of 
different  genes  have  been  found  to  carry  mu-
tations  in  diseases  with  heterogeneous  clinical 
presentation.  For  example,  mutations  in  almost 
150  genes  have  been  found  to  cause  PID.  This 
means  that  even  for  well-defined  subgroups  of 
PID, mutations in different genes result in identi-
cal, or overlapping, phenotypes. 

Current  mutation  analysis  is  very  complex,  and 
often involves many different European laborato-
ries. Thus, individual laboratories carrying out mu-
tation detection normally only cover a few percent 
of all disease genes. Obtaining a correct diagnosis 
is  both  difficult  and  time-consuming.  If  multiple 
genes need to be analysed, the cost rises propor-
tionately. New sequencing approaches have been 
used for the analysis of whole genomes. 

The  EURO-GENE-SCAN  project  partners  will 
adapt  these  technologies,  based  on  massive, 
parallel  sequencing,  to  specific  disease  fields. 
This  will  involve  the  development  of  an  inno-
vative  multiplexing  technology.  The  proposed 
prototype  area  is  PID,  where  significant  col-
laboration  in  Europe  has  been  continuing  over 

the last two decades. By using high-throughput 
sequencing, the partners estimate that the cost 
for analysing all known 150 PID genes in a single 
run will be in the same range as the current cost 
for mutation detection in single disease genes. 
They  will  also  develop  chips  to  identify  single 
nucleotide polymorphisms (SNPs) for the study 
of modifier genes. In addition, they will develop 
reverse-phase protein arrays for proteomics ap-
proaches in the diagnostics of PID patients dur-
ing infancy. They will also disseminate informa-
tion and transfer the developed technologies to 
other disease areas.

Approach and methodology:

The overall strategy is to develop high-through-
put technologies, which will become available to 
all  Europeans. The  aim  is  that  parallel  sequenc-
ing of PID genes will become operational by the 
end  of  the  project. This  is  also  true  for  the  SNP 
chip and the reverse-phase protein (RPP) arrays 
technology. For RPP the aim is not to include all, 
but selected disease proteins, representing both 
secreted and intracellular targets. In order to de-
velop the massive sequencing effort in a comple-
mentary way, partners will run in parallel

the Roche 454 and the Solexa (Illumina 1G) tech-
nologies  for  high-throughput  sequencing.  Sol-
exa may be especially suitable for this purpose. 

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EURO-GENE-SCAN

Coordinator 

Edvard Smith
Karolinska Institutet
5 Nobels väg
17177 Stockholm, Sweden
Email: edvard.smith@ki.se

Partners

Bodo Grimbacher
University College London
London, UK

Johannes Regenbogen
GATC Biotech AG
Konstanz, Germany

Ewa Bernatowska
Children’s Memorial Health Institute
Warsaw, Poland

Mats Nilsson
Uppsala University
Uppsala, Sweden

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DIAGNOSTICS

NMD-Chip

development of targeted dNa-Chips for High Throughput diagnosis  
of NeuroMuscular disorders

 Grant agreement No  HEaLTH-F5-2008-223026

Project type  Collaborative Project

EC contribution  e 2 907 735

Starting date   To be confirmed
duration  36 months

Background and objectives:

Inherited Neuromuscular Disorders (NMDs) form 
a large and very heterogeneous group of genetic 
diseases that cause progressive degeneration of 
the  muscles  and/or  motor  nerves  that  control 
movements.  Most  NMD  types  result  in  chronic 
long-term disability posing a significant burden 
to the patients, their families and public health-
care.  Life  is  always  shortened  by  multiple  and 
cumulative  defects  that  occur  during  disease 
progression.  Premature  death  may  result  from 
cardiac and respiratory muscle involvement.

These pathologies are present in all populations, 
affecting  children  as  well  as  adults.  The  overall 
prevalence of NMDs is very difficult to evaluate, 
but  one  can  estimate  that,  given  the  incidence 
of every different types, around 1 among 1 000 
people  may  have  a  disabling  inherited  neu-
romuscular disease.

The  precise  diagnostics  of  NMDs require  a  con-
junction  of  extensive  clinical  examination  and 
targeted complementary tests: biological analy-
ses, electromyography, imaging, and histological 
analysis of biopsies. Since many gene mutations 
responsible  for  these  diseases  are  known,  mo-
lecular genetics analyses are performed, both to 
confirm the clinical diagnosis and to make pre-
cise the genotype configuration in each patient. 
However,  one  cannot  avoid  the  difficulties  in 
making a molecular diagnosis in those diseases 
due to frequent overlaps of clinical phenotypes, 

a  large  number  of  genes,  large  genes  that  lack 
‘hot spots’ of mutation etc.

Most  of  the  molecular  approaches  currently 
used  for  genetic  diagnosis  correspond  to  gene 
by gene explorations, starting by the most per-
tinent gene. Thus, a differential molecular geno-
typing is required, which is highly complex and 
time-consuming  (two  weeks  to  one  year)  ac-
cording  to  presently  available  technologies.  As 
a  consequence,  many  patients  remain  devoid 
of genetic confirmation of their disease: to date 
this  proportion  amounts  to  30  to  40%  of  NMD. 
Importantly,  new  cutting-edge  therapies,  such 
as exon skipping, cannot be envisaged when no 
precise genetic diagnosis is available.

To  overcome  this  situation,  novel  genomics-
based  technologies  could  present  an  efficient 
alternative to develop new molecular diagnosis 
tools, enabling quick, reliable and cost-effective 
sequencing of numerous NMD genes in parallel. 
In  particular,  the  potential  of  DNA-chip  arrays, 
designed  to  examine  all  possible  mutations  in 
relevant gene(s) in only one step process, could 
certainly help to increase the ratio of precisely di-
agnosed  patients,  ameliorate  genetics  counsel-
ling and patients management, establish pheno-
type-genotype correlations, construct dedicated 
databases and include patients in current or fu-
ture  clinical  trials  in  relation  to  the TREAT-NMD 
network  of  excellence.  Such  an  approach  will 
also dramatically reduce the costs associated to 
the diagnosis in the medium term. From a long-

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NMD-Chip

term perspective, this will probably contribute to 
decreasing the global NMD prevalence by devel-
oping an appropriate diagnostic counselling.

Aim:

The aim of NMD-Chip is to design, develop and 
validate  new  sensitive  high-throughput  DNA 
arrays  to  effi  ciently  diagnose  patients  aff ected 
by  NMDs,  namely  Duchenne/Becker  muscular 
dystrophies  (DMD/BMD),  limb  girdle  muscular 
dystrophies  (LGMD),  congenital  muscular  dys-
trophies  (CMD),  and  hereditary  moto-sensory 
neuropathies  or  Charcot-Marie-Tooth  neuropa-
thies (CMT). The new sensitive and reliable tools 
(reliability  from  95  to  >99%)  originating  from 

this project will allow assessing all known genes 
implied in a group of disease at one time (2 100 
000  probes),  and  analysing  effi  ciently  chip  data 
through optimised read-out bioinformatic tools, 
within 72 hours to 1 week and thus be cheaper 
than  any ‘gene  by  gene’  approach.  Developing 
these  NMD-Chips  could  allow  decreasing  mo-
lecular dignostics cost by a factor of 10. 

Approach and methodology:

The  present  challenge  lies  in  increasing  the 
detection rate, as well as abbreviating the time-
to-diagnosis  (down  to  72  hours  to  1  week) 
for  patients  and  families  via  characterising  all 
mutations types and reducing analyses costs by 

Today

Clinical
consulation

Clinical
diagnostic

NMD patient

Biopsy

Biochemical
characterisation

Blood

Molecular
diagnostic

Up to 10 
genes tested

Test the
most 
pertinent
gene 1

NO

Clinical consulation

Test most 
pertinent 
gene X

Diagnosed
patient

Participation
to clinical trials

Therapy

Mutation in untested gene
Undetected mutation
Unknown mutation

Undiagnosed patient
(40% of NMD patients)

2 weeks to 1 year

Tomorrow with NMD Chips

Clinical
consulation

Clinical
diagnostic

Blood

NMD CHIP
(Test 2,000,000
in one shot)

Diagnosed
patient

Participation
to clinical trials

Therapy

NMD patient

Unknown gene mutated

Undiagnosed patient
(YY% NMD patients)

72 hours to 1 week

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DIAGNOSTICS

known genes implied in a given group of NMD. 
This,  coupled  with  a  high-throughput  sequenc-
ing  technology  (pyrosequencing),  will  bring  a 
quick molecular diagnosis to patients. The project 
will  also  comprise  the  design  and  validation  of 
one CGH-array chip to scan genes for large rear-
rangements,  deletions  or  insertions. Then,  if  no 
deleterious  mutation  is  found  with  the  first  run 
on Known Genes-chips, a second series of chips 
dedicated to candidate genes will be hybridised 
with the patient’s DNA. 

That  means  that  every  gene  implied  in  a  given 
NMD group will be checked at a glance, whereas 
until  now,  diagnostic  laboratories  have  to  se-
quence  one  gene  after  another  until  the  muta-
tion is found. If deleterious mutations are identi-
fied in known genes, the delay to diagnosis will 
be reduced to less than a week.

using platforms with high diagnostic capacities. 
These  two  goals  will  also  allow  the  consortium 
to characterise the genotype in rare and atypical 
phenotypes,  in  genetically  ambiguous  sporadic 
cases  and  in  NMDs  whose  pathophysiology  is 
multiallelic or multigenic. One must keep in mind 
that patients with a well-characterised pathology, 
both  on  clinical  and  genetic  sides,  are  the  only 
ones eligible for clinical trials or protocols, which 
become  more  and  more  numerous.  DNA-Chips 
really correspond to a ‘one-shot’ technology that 
may considerably reduce both the times and the 
costs of the whole diagnostic process.

To achieve NMD-Chip aims, the partners will:

•	

•	

•	

•	

•	

•	

•	

design	specific	Sequence	Capture	DNA	ar-
rays containing all the genes already known 
to	be	involved	in	LGMD,	CMD	and	CMT;	
design	a	whole	gene	CGH	array	containing	
all the genes already known to be involved 
in LGMD, CMD and CMT. Only on CGH-chip 
will	be	designed	for	all	these	pathologies;
develop	 bioinformatic	 tools	 to	 accurately	
and	quickly	analyse	DNA-Chip	data;
assess	 the	 quality	 of	 these	 chips.	 Several	
hybridisation  tests  will  be  performed  to 
assess a good reproducibility and a strong 
efficiency.  An  important  part  of  the  work 
will be to adapt existing algorithms to the 
partners’ specific goals (e.g. lowering of the 
inclusion	threshold);
validate	 these	 DNA-arrays	 on	 pre-diag-
nosed  patient  samples  and  test  their  ro-
bustness	on	undiagnosed	samples;
design	 distinct	 candidate	 genes	 SC-	 and	
CGH-chips	for	LGMD,	CMT	and	CMD;
test	patients	with	unidentified	gene	mu-
tations with candidate genes chips. This 
last  step  will  provide  the  consortium 
with information on the reliability of the 
tools developed.

The developed chips will consist first in a series 
of chips dedicated to sequence capturing of all 

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161

alessandra Ferlini
University of Ferrara
Ferrara, Italy

Johan den dunnen
Leiden University
Leiden, Netherlands

Francesco Muntoni
University College London
London, UK

angela Huebner
University Dresden
Dresden, Germany

NMD-Chip

Coordinator

Nicolas Levy
Institut National de la Santé et de la 
Recherche Médicale (INSERM)
101 Rue de Tolbiac
75654/13 Paris, France
E-mail : nicolas.levy@medecine.univ-mrs.fr

Partners

Pascal Soularue
PARTNERCHIP
Evry, France

Thomas Sejersen
Karolinska Institutet
Stockholm, Sweden

david atlan
PhenoSystems SA
Lillois Witterzee, Belgium

Clemens Mueller-Reible
University Wuerzburg
Wuerzburg, Germany

Volker Straub
University of Newcastle upon Tyne 
Newcastle, UK

Veronika Karcagi
National Institute of Environmental Health
Budapest, Hungary

Isabelle Richard 
GENETHON
Evry, France

Thomas Voit
Association Institut de Myologie
Paris, France

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DIAGNOSTICS

TECHGENE

High throughput molecular diagnostics in individual patients 
for genetic diseases with heterogeneous clinical presentation

 Grant agreement No  HEaLTH-F5-2008-223143 

Project type  Collaborative Project
EC contribution  e 2 997 010 (proposed)

Starting date   To be confi rmed 
duration  36 months

Background and objectives:

Since  completion  of  the  sequencing  of  the  hu-
man genome, the demand for genetic analysis in 
the human healthcare system is increasing dra-
matically, and the extension of molecular genet-
ic  diagnostics  is  urgently  needed.  However,  the 
majority of genetic diseases are molecularly and 
clinically highly heterogeneous, and until recent-
ly  the  available  techniques  lacked  the  required 
capacity to analyse several genes in parallel. 

The recently introduced high-throughput whole 
genome sequencing (WGS) technology now of-
fers the unique opportunity to extend molecular 
genetic analysis by introducing these techniques, 
and developing tailor-made medical resequenc-
ing  approaches  for  molecular  genetic  diagno-
sis  of  heterogeneous  disorders.  The  TECHGENE 
project aims to deliver crucial innovations lead-
ing to these approaches, and to deliver a proof-

of-principle  for  its  implementation  in  selected 
model disorders. 

The  model  disorders  have  been  selected  with 
increasing genetic complexity and represent the 
majority of non-multifactorial genetic disorders. 
The current momentum to perform these inno-
vations by a European consortium of clinical ge-
netic diagnostic laboratories and research labo-
ratories, and industrial stakeholders will lead to a 
front-running position of European laboratories 
and small and medium-sized enterprises (SMEs) 
in this fi eld. 
The  consortium  consists  of  leading  scientists  and 
laboratories  providing  cutting-edge 
established 
knowledge with respect to quality management as-
pects, ethical and societal issues, and cost-eff ective-
ness issues. This is the only approach that will war-
rant the development of diagnostic tools designed 
to restrict genetic testing to relevant medical factors. 
For European SMEs, this project off ers the opportu-

WP8 Management of TECHGENE

WP1

WP2

WP3

WP4

Hemoglobinopathies 
Breast Cancer Few Genes 
with Multiple Mutations 

Sensory D isorders
1 Major Gene & 
Multiple Minor Genes

Ataxia & Paraplegia 
Multiple Equally 
Important Genes

Mental Retardation
Rare Mutations in 
Rare Genes

Long PCR Enrichment 

Validation

Array Enrichment

Read-out & Data Anal

WP5

WP6

WP7

Ethical Issues

Economic Issues

Dissemination & Training

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TECHGENE

nity to identify niches in the steadily increasing mo-
lecular genetic market. A specially designed training 
programme will take care of rapid dissemination of 
the acquired knowledge and tools across Europe.

Approach and methodology:

The overall objective of TECHGENE is to improve 
molecular  analysis  for  genetic  disorders,  which 
can  be  caused  by  multiple  possible  underlying 
mutations  (allelic  heterogeneity) 
in  multiple 
possible  underlying  genes  (locus  heterogene-
ity).  This  general  objective  can  be  reached  by 
the interdisciplinary genetic approach of clinical 
scientists, researchers, clinicians, and commercial 
companies  involved  in  the  project.  Obviously, 
for all molecular techniques a sliding window in 
time  will  be  present,  after  which  the  particular 
techniques may be surpassed in performance by 
others. However, the partners are convinced that 
they have chosen the most promising new tech-
nology and available platforms that are currently 
emerging for further development of novel clini-
cal applications, and they extend the application 
of genetic analysis towards clinical entities with 
extensive genetic and/or clinical heterogeneity.

Coordinator

Hans Scheffer
Radboud University Nijmegen Medical 
Centre
9 Geert Grooteplein Noord
6525 EZ Nijmegen, Netherlands
E-mail : h.scheffer@antrg.umcn.nl

Partners

Gert Matthijs
Katholieke Universiteit (KU) Leuven
Leuven, Belgium 

Milan Macek
Charles University -
2nd School of Medicine
Prague, Czech Republic

Xavier Estivill
Center for Genomic Regulation
Barcelona, Spain

Paolo Gasparini
University of Trieste
Trieste, Italy 

Olaf Riess
Eberhard-Karls-Universitaet Tuebingen
Tuebingen, Germany

Bert Bakker and Johan den dunnen
Leiden University Medical Center
 The Netherlands Bakker
Leiden, Netherlands

Sandro Banfi
Telethon Foundation
Naples, Italy

Vincenzo Nigro
Second University of Naples
Naples, Italy 

anne Cambon Thomsen
University Paul Sabatier
INSERM U558
Toulouse, France 

Katherine Payne
University of Manchester
Manchester, UK

Katrin Sak
Asper Biotech Ltd
Tartu, Estonia 

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INDEX OF PROjECTS

addNET 
antePrion 
BONSaI 
CaRS Explorer 
COBREd 
daSIM 
dETECTHIV 
dIaGNOSIS 
diaNa 
diMI 
dRoP-ToP 
eBIOSENSE 
EdaR 
ENCITE 
EURIPIdES 
EuroFlow 
EURO-GENE-SCaN 
EUROGENGUIdE 
EuroGentest 
FLUOdIaMON 
FLUOROMaG 
FMT-XCT 
FUN OCT 
GENEPaRK 

41
33
106
130
51
84
117
94 
112
77
57
125
69
150
147
54
157
19
13
132
103
139
135
64

GLYFdIS 
HYPERImage 
IBdchip 
MEGMRI 
Moldiag-Paca 
NaCaRdIO 
NaNOMYC 
NanoSense 
NEMO 
nEUROPT 
NeuroScreen 
NeuroTaS 
NMd-Chip 
POC4life 
PREGENESYS 
QuaGSIC 
SaFE 
SKINSPECTION 
SLIC 
SPIdIa 
TB-trdNa 
TECHGENE 
TSEUR 
USdEP 

44
141
30
143
47 
120
114
110
100
137
71
88 
159
91
67
28
22
145
123
154
62
163
37
97

166

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DIAGNOSTICS

INDEX OF
COORDINATORS

NETWORK OF EXCELLENCE

SME-SPECIFIC TARGETED RESEARCH PROjECT

Cassiman, Jean-Jacques (EuroGentest) 
Hughes, Kate (SAFE) 
Jacobs, Andreas H. (DiMI) 

16
24
80

INTEGRATED PROjECT

Gress, Thomas M. (MolDiag-Paca) 

49

SPECIFIC TARGETED RESEARCH PROjECT

Aguzzi, Adriano (TSEUR) 
Arndt-Jovin, Donna J. (FLUOROMAG) 
Borsella, Elisabetta (BONSAI) 
Enfors, Sven-Olof (eBIOSENSE) 
Gijs, Martin (DETECTHIV) 
Holthöfer, Harry (ADDNET) 
Ikonomopoulos, John (NANOMYC) 
Isaksson, Olle (NACARDIO) 
Kutter, Jörg P. (NeuroTAS) 
Makohliso, Solomzi A. (SLIC) 
Peterlin, Borut (GENEPARK) 
Peters, Peter J. (AntePrion) 
Rabinovitz, Elisha (NEMO) 
Van Dongen, Jacques J.M. (EuroFlow) 
Visser, Pieter Jelle (EDAR) 
Zorzi, Willy (NeuroScreen) 

40
105
109
127
119
43
116
122
90
124
66
35
102
55
70
73

Bois, Emmanuel (POC4life) 
Ellerbrok, Heinz (USDEP) 
Holthofer, Harry (DiaNA) 
Huggett, Jim (TB tr-DNA) 
Leiser, Robert-Matthias (DIAGNOSIS) 
Meiri, Hamutal (PREGENESYS) 
Ochoa, Gorka (DRoP-ToP) 
Porgador, Angel (GLYFDIS) 
Sans, Miquel (IBDchip) 
Skjeltorp, Guri (NanoSense) 
Takacs, Laszlo (COBRED) 
Weisbuch, Claude (QuAGSIC) 

SPECIFIC SUPPORT ACTION

Kent, Alastair (EUROGENGUIDE) 
Moss, David (DASIM) 

COLLABORATIVE PROjECTS (FP7)

Marguet, Didier (CARS Explorer) 
Widengren, Jerker (FLUODIAMON) 
Andersen, Peter (FUN OCT) 
Cubeddu, Rinaldo (nEUROPT) 
Ntziachristos, Vassilis (FMT-XCT)  
Schulz, Volkmar (HYPERImage) 
Ilmoniemi, Risto (MEGMRI) 
Schulz, Volkmar (SKINSPECTION) 
Koepp, Matthias Johannes (EURIPIDES) 
Krestin, Gabriel (ENCITE) 
Oelmüller, Uwe (SPIDIA) 
Smith, Edvard (EURO-GENE-SCAN) 
Levy, Nicolas (NMD-Chip) 
Scheffer, Hans (TECHGENE) 

93
99
113
63
96
68
61
46
31
111
53
29

21
87

131
133
136
138
140
142
144
146
149
151
155
158
162
164

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Diagnostics – Index of Projects

167

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