Committee : L. Chiche (CBS), O. Gascuel (LIRMM), M.-P. Lefranc (IGH)

And : CIRAD, CRBM, GPI, IBP, IGMM, ISEM, LDCC

Montpellier has an high research potential in Bioinformatics:

More than 50 researchers, PhDs and post-doctoral students

Internationally recognized programs, databases and servers: BIONJ, PHYLOWIN, IMGT, ESTHER, DOMO, BIOSERV, STAR …

National and international responsibilities, e.g. Chair of ACI IMPBio.Thanks to the Genopole:

10 within Genopole collaborations supported by French programs

A master (DESS) in Bioinformatics

Bioinformatics seminars (2/month) and events (eg, Transcriptome Statistical Analysis, 110 attendees, 2002).

Bioinformatics Montpellier GenopoleJournées "Bioinformatique des Génopoles"

Lyon, 22-23 octobre 2003

Three main axes

IMGT

Structural Bioinformatics (protein structure prediction, structural domain clustering, NMR spectra analysis, Knottin database)

Comparative genomics (phylogeny, sequence analysis, alignment)

Perspectives:

Developing IMGT and structural servers and databases

Spreading our software

Designing new dedicated servers (e.g., transcriptome interpretation)

Providing courses on software

Incentive policy towards “young teams”

Bioinformatics Montpellier Genopole

IMGT, the international reference

in Immunogenetics and Immunoinformatics

IMGT,a CNRS registered trademark

EU, Canada, USA

RIO Platform 2001

NetWatch of Science 2002

IMGT,an European flagship

(BIOMED1, BIOTECH, 5th PCRDT)

IMGT, a common access

to standardized, expertly annotated

and integrated data

IMGT, uniqueNo equivalent in Japan

and in USA

IMGT, the international ImMunoGeneTics information system ® http://imgt.cines.fr

Coordinator: Marie-Paule LEFRANC

IMGT specialized in

Immunoglobulins (IG) (antibodies)

T cell receptors (TR)

Major histocompatibility

complex (MHC)

The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

IMGT domain of research: the adaptive immune system

Immunoglobulin

B cellT cell

T cell Receptor MHC

peptide

Trimolecular complex

Immunoglobulin and T cell receptor synthesis

2 x 10 12

5' 3'

V D J C

39- 46 x 23 x 6 34 - 37 x 5 Kappa 30- 33 x 4 -5 Lambda

5' 3'

V J C

250HEAVY CHAIN LIGHT CHAIN

5' 5'3' 3'x 1000

6300 POTENTIAL RECOMBINATIONS POTENTIAL RECOMBINATIONS

N REGIONS AND SOMATIC MUTATIONS

ABOUT POSSIBILITIES3.5 x 10 5ABOUT POSSIBILITIES6.3 x 10 6

185 +165

FUNCTIONAL GENES

DIFFERENT ANTIBODIES

The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

5 Databases

Sequence databases

IMGT/LIGM-DB 77,463 IGand TR nucleotide sequences fromhuman and 150 other vertebrate species, on the Web since July 1995

IMGT/PRIMER-DB on theWeb since 2000

IMGT/MHC-DB hosted at EBI

Genome database

IMGT/GENE-DB1375 IG and TR genes and 2201alleles from human and mouse, on

the Web since February 2003

3Dstructure database

IMGT/3Dstructure-DB634 structures of IG, TR and MHC

Web Resources

Sequences

Alignments of alleles

Tables of alleles

Protein displays, etc.

Genome

Chromosomal localizations Locus representationsGene tables, etc.

2D and 3D structures

2D Colliers de Perles3D representations, etc.

Sequence analysis

• IMGT/V-QUEST

• IMGT/JunctionAnalysis

• IMGT/PhyloGene

• IMGT/Allele-Align

Genome analysis

• IMGT/GeneSearch• IMGT/GeneView• IMGT/LocusView

3D structure analysis

• IMGT/StructuralQuery

8 Tools on line

IMGT Repertoire

8000 HTML pages!

http://imgt.cines.fr

IMGT-ONTOLOGY has been developedto share, reuse and represent knowledge in immunogenetics

IMGT-ONTOLOGY covers five main concepts:

IMGT-ONTOLOGY

IDENTIFICATION

DESCRIPTION

CLASSIFICATION

OBTENTION

http://imgt.cines.fr

NUMEROTATION

 "CLASSIFICATION" concept

The "CLASSIFICATION" concept organizes the immunogenetics knowledge useful to name and classify IG and TR genes in IMGT. (A) Concepts of classification and their

relations. (B) Examples of instances: for each concept of classification is shown the instance which allows the classification of the human IGLV2-11*02 allele.

group

subgroup

allele

locus

is a member of an instance of

is a member of an instance of

is a variant of an instance of

is ordered in an instance

of

IGLV

IGLV2

IGLV2-11

IGLV2-11*02

human IGL(22q11.1-q11.2)

is ordered in

is a member of

is a variant of

is a member of

A B

gene

http://imgt.cines.fr

The international ImMunoGeneTics databaseCoordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

V-GENE

V-EXON

FR1-IMGT FR2-IMGT FR3-IMGT

L-PART1

V-REGION

CC5 ’UTR 3 ’UTR

CD

R3

-IMG

T

DONOR-SPLICE

W

V-GENE V-EXON

FR3-IMGT CDR3-IMGT

L-PART1 DONOR-SPLICE

V-REGION FR1-IMGT

Label 1 Label 2

V-REGION CDR3-IMGT

Label relations

  "DESCRIPTION" concept

http://imgt.cines.fr

  "NUMEROTATION" concepthttp://imgt.cines.fr

Alignmentof alleles

ProteinDisplay

Collier de Perles

http://imgt.cines.fr

Collier de Perles:

3D representation: Human V-DOMAINS from TcR ab A6 (PDB: 1ao7 )

The "OBTENTION" concept specifies the origin and methodology

  "OBTENTION" concept

libraries- genomic- cDNA-combinatorial

origin methodology

transgenic- animal- plant

PCR

cell, tissue, organ- PBL- liver

autoimmune diseases- autoantibody- rheumatoid factor

clonal expansion diseases- leukemia- lymphoma- myeloma

hybridoma- monoclonal antibody

http://imgt.cines.fr

IMGT-ML Schema

IMGTOntologyIMGTOntology

IdentificationIdentification

imgtimgt

NumerotationNumerotation

ObtentionObtention

ClassificationClassification

IMGTDataIMGTData

knowledgeknowledge

seqDataseqData

DescriptionDescriptionExternal schemaExternal schema

http://imgt.cines.fr

IMGT-ML Architecture

XML SchemaXML Schema

IMGT-ONTOLOGY

Documentation

DatabasemodellingDatabasemodelling

ControlledvocabularyControlledvocabulary

Data distribution

format

Data distribution

formatBiologicalexpertize

Biologicalexpertize

http://imgt.cines.fr

2. Services

• WWW at Montpellier: 180,000 sites since January 2000 140,000 requests per month• Data distribution by FTP: CINES, IGH, INFOBIOGEN, EBI• Many sites SRS: INFOBIOGEN, EBI, Institut Pasteur, ... and EMBnet nods• Search by BLAST and FASTA: on different servers (INFOBIOGEN, EBI, etc.)• IMGT Bloc-notes: IMGT Immunoinformatics page, numerous hyperlinks to external sites

The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

1. Research and development

52 publications 1 chapter "Consanguinity" in Encyclopedia of Genetics 20012 books: The Immunoglobulin FactsBook, Academic Press, 2001

The T cell receptor FactsBook, Academic Press, 200147 communications27 invited conferences (China, Japan, USA, Belgium, Italia, The Netherlands, UK)2 PhD theses (1 tenure job at CIRAD, 1 postdoctorate at Princeton, USA)

collaborations USA, Canada, China, Russia, Lebanon, UK, Belgium (EUROGENTEC)

2000-2003 IMGT Platform

IMGT platform

3. Education Participation to the creation of the:• DESS Bioinformatics: Université Montpellier II, 2001• Bioinformatics modules: Doctoral School CBS2, Montpellier, 2001 Doctoral School Univ. St-Joseph, Beirut, Lebanon, 2002 University of Monastir, Tunisia, 2003

4. Innovations, normes et standards

IMGT-ONTOLOGY, the first and only ontology in immunogenetics and immunoinformaticsIMGT Scientific chart provides the controlled vocabulary and the annotation rules• IMGT nomenclature approved by the Human Genome Organization (HUGO) Nomenclature Committee (HGNC) in 1999, 673 human genes and 1206 alleles. The only example of delegation by HGNC. • direct links from LocusLink NCBI to IMGT. The only example of direct links from NCBI to an external site • In development: XML and IMGT-ML, Web-Services, Data integration in medical informatics.

The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr

.

Genome diversity developmental and comparative immunology, evolution of the

adaptive immune system

Biotechnology and antibody engineering

chimeric, humanized, human antibodiesin transgenic mice, scFv combina-

torial libraries, intrabodies

Veterinary researchrepertoire in farm

and wild animal species

Medical researchrepertoire in normal and pathological

situations, autoimmune diseases, AIDS, leukemias, lymphomas, myelomas,

residual diseases, etc.

Therapeutical approaches immunotherapy, grafts,

immunomodulation, immunosppression

IMGT, the international ImMunoGeneTics information system® http://imgt.cines.fr

Coordinator : Marie-Paule LEFRANC

IMGT, a team of

21 persons:

8 CDD annotators

(5 EU, 1 EUROGENTEC

1 Genopole, 1 PPF)

4 Permanent staff

(UM2: 1.5 PU, 0.5 IE

CNRS: 1 IE, 1 ITA)

9 Students (3 PhD,

6 for 4 months/a year)