Genomics: Research and Application

ƒ Human Genome Research

ƒ Genetic Laboratory Services evolving from research
ƒ Current Organisation / National /International
ƒ External Quality Assessment
ƒ Laboratory Accreditation
ƒ Reference materials and Standards
ƒ New developments and implementation

E. Bakker
Department of Human and Clinical Genetics
Leiden University Medical Center
The Netherlands

Warsaw, 18-19 June 2002

Human Genome Project
1990-1994
Macro level
GENETIC MAP
FYSICAL MAP
1995-1999
Meso level
GENE MAP
2000-2005 (2001)
Micro level
DNA Sequence
( 99%
complete)
Warsaw, 18-19 June 2002
 Genome research’s impact
Huge stimulus on Biology and Medicine
Genes, gene tests, gene functions
Comparative studies: revealing gene functions
Animal models- and population studies:
cause of disease: Ö therapy
Pharmaceutical, agriculture and food-industry, but also
on the environmental sector:
New biological insights
Ö new solutions
Restriction Fragment Length Polymorphism (RFLP) / 1981

Taq I –restriction
side

-AACT*CGATGG-
- TTGAGC T ACC-

(DXS7)

T a T* T

T
probe T

A
Warsaw, 18-19 June 2002
 First prenatal DNA test for
Duchenne Muscular Dystrophy
Prenatal diagnosis and carrier detection of Duchenne
muscular dystrophy with closely linked RFLPs.

Lancet 1985 Mar 23;1(8430):655-8

Bakker E, Hofker MH, Goor N, et al.

Warsaw, 18-19 June 2002

 How Molecular Genetic Labs started

Early 80’s DNA tests, based on Southern blotting and linkage

tests, became available
University research groups developed new techniques and
diagnostic procedures for prenatal diagnosis (1985)
A nation wide inventory was performed and money requested
from the Health insurance agencies
In 1988 four for centers molecular genetic testing were
selected on basis of their specific expertise for some disorders
Groningen, Leiden, Nijmegen and Rotterdam were subsidized
for an initial pilot period of 4 years.

Warsaw, 18-19 June 2002

Organisation Clinical Genetic Centers

Counseling Unit
Clinical Cytogenetic Laboratory
Clinical Molecular Genetic Laboratory
Clinical Metabolic Laboratory
Prenatal Diagnosis Unit Echo/Ultra sound

Warsaw, 18-19 June 2002

 Dutch Molecular Genetic Labs
1992 - Evaluation of the first 4 years
- Medical Technology Assesment study (cost
effectiveness)
1993 - All 7 Genetic Centers subsidized
1994 - Regular meetings (4-6 a year) with of the 7 Lab s
1996 - DNA- testing for genetic disorders has become part of
the regular health care system (limited to the 9
KGC’s)
1999 - 16.000 tests /year over 25 disorders tested per center
2001- over 21.000 tests /year over 250 disorders
Warsaw, 18-19 June 2002
75% in only of the one the centers
 Monogenetic (rare) disorders
Disorder Incidence Gene Mutation

Cystic fibrosis 1: 4,000 CFTR 98%

Duchenne Muscular Dystrophy 1: 4,000* DMD 70-80%
Fragile X syndrome 1: 4,000* FMR1
100%
Huntington’s disease 1: 5-10,000 HD
100%
Hemophilia A 1:10,000* F8C 90%
Phenylketonuria 1:10,000 PAH 99%
Polycystic kidney disease 1: 4,000 PKD1(85%) 10 -15%
PKD2(15%)
Achondroplasia 1-2 :100,000 FGFR3
100%
Warsaw, 18-19 June 2002
 www.fdg.unimaas.nl /LOD/lod.htm
Newsletter for genetic testing labs in NL:
Lists the labs (9) with the disorders tested (over 250)
Gives details on genes tested
reporting time
mutation detection yes / no
Technical info on new tests or new disorders in the list
Overview of ules how to apply for tesing
Additional info eg. Patent discussion
Warsaw, 18-19 June 2002on BRCA1/2
 Table of disorders tested
Richtlijn voor uitslagtermijnen
Prenatale diagnostiek2 (maximaal 3) wekenAnalyseren van een in de familie bekende mutatie
(Voor partners van een familielid uit een familie met een bekende mutatie geldt de termijn zoals in de tabel is
aangegeven voor het opsporen van een in de familie nog onbekende mutatie)6 weken Het opsporen van een in de
familie nog onbekende mutatiezie tabelKoppelingsonderzoek (kopp.)zie tabel\
Ziekte Code1 Kopp. Termijn Mutatie Termijn14
Aarskog syndroom 5 ja 3 mnd nee
Achondro-/Hypochondroplasie
Thanatophore dysplasie 3,4,6,8 nee - ja 3 mnd
Acute intermitterende porfyrie 5 nee - ja 6 mnd
ADCA:
-SCA 12,6,7 nee - ja 2 mnd
-- SCA2 2,6,7 nee - ja 2 mnd
-- SCA3 (Machado-Joseph) 2,6,7 nee - ja 2 mnd
-- SCA6 2,6,7 nee - ja 2 mnd
-- SCA7 2,6,7 nee - ja 2 mnd
Adrenogenitaal Syndroom (21 hydr.def) 5ja 3 mnd ja 6 mnd
Adrenoleukodystrofie 5 ja 3 mnd ja 6 mnd
Agammaglobulinemie, X-gebonden 7 ja 3 mnd ja -
Alagille syndroom 6 ja 3 mnd nee -
Albinisme, X-linked (OAI) 1 ja 3-5 mnd nee -
Alport Syndroom6 4 ja 3 mnd soms -

Warsaw, 18-19 June 2002

Internal and External Quality Assessment
Internal: Blanco’ s,
Size standards,
Duplo tests (on independent samples)

External: Quality assessment schemes

UK-NEQAS
EMQN
CF EQA

Warsaw, 18-19 June 2002

 Huntingtons’ disease gene
Affected range
>35

Intermediate range
27-35

Normal range
6-26

5' 3'
CAG CCG

6-11

Warsaw, 18-19 June 2002

PCR
Fragment analysis on an ALF DNA Sequencer

PAGE
electrophoresis

Laser
Warsaw, 18-19 June 2002
 Warsaw, 18-19 June 2002
Fragment analysis on the ALF
 European Molecular Genetics Quality Network

EMQN
Supported by the European Union
c/o Regional Molecular Genetics Laboratory, St Mary’s Hospital, Hathersage Road,
Manchester M13OJH UK email relles@hgmp.mrc.ac.uk
44 161 276 6129 fax 44 161 276 6606 email relles@hgmp.mrc.ac.uk

EMQN National Partners in the European Union

updated 6.99

Austria Dr A Haselberger Vienna * EMQN management group members

Belgium Professor J.J Cassimans*, Leuven
Co-ordinator Dr Rob Elles*, Manchester
Denmark Dr Marianne Schwartz, Copenhagen
Finland Dr Arto Orpana, Helsinki
France Prof Michel Goossens*, Creteil .
Germany Prof Clemens Mueller*, Wurzburg
Greece Dr L. Florentin , Athens .
Ireland Dr David Barton*, Dublin
Italy Dr Maurizio Ferrari, Milano
Norway Dr Trond P Leren, Oslo
Portugal Dr Paula Pacheco, Lisboa
Spain Dr M Tamparillas, Zaragosa
Sweden Professor Ulf Kristofferson, Lunt
The Netherlands Dr Bert Bakker*, Leiden
United Kingdom Ms Su Stenhouse* Newcastle
Warsaw, Upon
18-19 Tyne.
June 2002
 Summary of Results HD EQA
• Genotyping: outside error limit
– 1997: 9/146 (6.2%)
– 1998: 24/251 (9.6%)
– 1999: 13/184 (8.7%) STANDARDISATION
– 2000: 16/111(7.7% NEEDED !!
– 2001: 22/144(7.8%)
• Diagnostic errors
– 1997: 1/78 cases (1.3%)
– 1998: 2/126 cases (1.6%) QUALITY CONTROLE
– 1999: 1/93 cases (1.1%) NEEDED!!
– 2000: 4/111 cases (4.5%)
– 2001: 2/144 cases (2.1%) ACCREDITATION?

EMQN EQA studies Scheme Organiser

Warsaw, 18-19 June 2002 dr M. Losekoot (Leiden)
 New developments
Increasing diagnostic resolution:
- High throughput sequencing
- Mutation detection methods, scanning or screening
- SNP, mbv Chips, Arrays, Pyrosequencer, Mass-
spectrometer
- Realtime PCR, Quantification
- Expression studies, Chips
Bioinformatics: Databases, Internet, Automation (lab robotics),

Warsaw, 18-19 June 2002

 Hereditary Colorectal Cancer
1%
2%
Sporadic FAP
50% - 90% ? HNPCC
Hereditary/Familial
Clustering Familial Colorectal
10-50% ?? Cancer

Warsaw, 18-19 June 2002

Future of molecular genetic testing
Genetic tests either molecular genetic tests or
functional tests will be available for:
Monogenetic diseases
Also for: (rare disorders)
Complex gene-environment interactions like for
cardiovascular disease, cancer,
hypertension, arthritis,
migraine, epilepsy,
Parkinson and Alzheimer.
genetic-factors for drug and nutrient metabolism
Eventually for:
Infectious disease control , Improvement
of wound healing after surgery or trauma.
Warsaw, 18-19 June 2002
 Future of molecular genetic testing
Needed:
Laboratory accreditation for all diagnotic labs
Training programm’s for staff members
Clossely related to research groups/academic and/or
industry
Innovation within the clinical molecular genetic labs
Implementation of new genetic tests
(disorders/ risk factors)
Automation:- Robotics, sample-handling
- Informatics, data handling,
- Software
Warsaw, 18-19 June 2002
Application-oriented genomic approaches to medical knowledge

Clinical molecular genetics is an (fast) expanding field

Many genes to be tested
More demanding clinicians and patients
Many new technologies emerging
Proper implementation/ validation needed
Increasing standard of testing (need for QC/QA)
No certified reference materials available
Present molecular diagnostic situation is far from ideal
Difficult to get additional funds for
implementation of
diagnostics or new technologies, etc ( FP6 ?)
Warsaw, 18-19 June 2002
 6TH Framework Programme
Area 1.1.1: Genomics and Biotechnology for health
Expression of Interest - network of excellence
- EUROGENETEST - Technol dev
Academia/Industry
Genetic Research
Academia/Industry

Genetic Testing in Europe Genetic Test Analytical

Validation
Development
EQA: Best

-Integrated Network Practice

Guidelines
Patient
Organisations

for test development Reference

Routine Performance
of Genetic Testing
Materials Clinical Hosp / Private
Application Laboratories
and harmonisation
Accreditation
Quality manag. Clin. Validation
of quality ofgenetic & Utility

Patient

testing services
Warsaw, 18-19 June 2002
prepared by ITPS-JRC, EC with 28 participants
 Acknowledgements:
Dolores Ibarreta, AK Bock, IPTS-Joint Research Center (Spain) EC

Jean Jaques Cassiman, Els Dequeker , Center for Human Genetics , Belgium
European Thematic Network on Cystic Fibrosis (EQA scheme for cystic fibrosis, funded by the EU)

Rob Elles, Simon Patton, Central Manchester and Manchester Children's University Hospitals
NHS Trust, UK
European Molecular Genetics Quality Network) EU funding. collection to reporting the results.
Best practice guidelines are agreed for each inherited disease after a workshop and these guidelines ar
posted on the web (www.emqn.org).

David Barton, National Centre for Medical Genetics, Ireland

Currently participating in a EU-funded project “Quality in Molecular Genetic Testing: Development of
Certified Reference Materials (CRMGEN)”.

Christof Klein, IRMM-Joint Research Center, Belgium, EC

Largest supplier of genetic reference materials in the EU and partner in the CRMGEN project

ClemensR Müller, Department of Human Genetics, Germany

The German QA schemes for genetic testing services (Berufsverband Medizinische Genetik)

Warsaw, 18-19 June 2002