Genomics Research

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 T

a

T*

probe

T 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

Cystic fibrosis

1: 4,000

CFTR

98%

Duchenne Muscular Dystrophy

1: 4,000*

DMD

70-80%

Fragile X syndrome 100%

1: 4,000*

FMR1

Huntington’s disease 100%

1: 5-10,000

HD

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 100%

1-2 :100,000 Warsaw, 18-19 June 2002

FGFR3

Mutation

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 Warsaw, 18-19 June 2002on BRCA1/2 Additional info eg. Patent discussion

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

Thanatophore dysplasie

3,4,6,8

nee

-

ja

3 mnd

Acute intermitterende porfyrie

5

nee

-

ja

6 mnd

-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,

1

ja

3-5 mnd

nee

-

4

ja

3 mnd

soms

-

Achondro-/Hypochondroplasie

ADCA:

X-linked (OAI)

Alport Syndroom6

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 PCR

Warsaw, 18-19 June 2002

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 [email protected] 44 161 276 6129 fax 44 161 276 6606 email [email protected]

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 Upon Tyne. Warsaw, 18-19 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%) – 2000: 16/111(7.7% – 2001: 22/144(7.8%) Diagnostic errors – 1997: 1/78 cases (1.3%) – 1998: 2/126 cases (1.6%) – 1999: 1/93 cases (1.1%) – 2000: 4/111 cases (4.5%) – 2001: 2/144 cases (2.1%)

STANDARDISATION NEEDED !!

QUALITY CONTROLE NEEDED!! 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, Massspectrometer - Realtime PCR, Quantification - Expression studies, Chips Bioinformatics: Databases, Internet, Automation (lab robotics),

Warsaw, 18-19 June 2002

Hereditary Colorectal Cancer 1% Sporadic 50% - 90% ?

FAP

Hereditary/Familial Clustering 10-50% ??

Warsaw, 18-19 June 2002

2% HNPCC

Familial Colorectal Cancer

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 Warsaw, 18-19 June 2002 diagnostics or new technologies, etc ( FP6 ?)

6TH Framework Programme Area 1.1.1: Genomics and Biotechnology for health Expression of Interest

- network of excellence

- EUROGENETEST Genetic Testing in Europe -Integrated Network for test development and harmonisation of quality ofgenetic

Genetic Research Academia/Industry

Technol dev Academia/Industry

Genetic Test EQA: Best Practice Guidelines

Reference Materials

Development

Analytical Validation

Patient Organisations

Routine Performance of Genetic Testing Clinical Application

Accreditation Quality manag.

Hosp / Private Laboratories

Clin. Validation & 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