Analyse des génomes. Fatena Bellahcene, Xavier Brochet, Laetitia Régnier, Marie-Paule Lefranc. M2 Bioinformatique

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1 Analyse des génomes Fatena Bellahcene, Xavier Brochet, Laetitia Régnier, Marie-Paule Lefranc M2 Bioinformatique Montpellier, 13,14 et 16 janvier 2009

2 Plan Analyse de génomes (en immunogénétique) Axiomes et concepts d IMGT-ONTOLOGY Un outil que vous utiliserez: IMGT/V-QUEST Notions requises et à redécouvrir: Locus, gènes, allèles Orientation et localisation Description Classification Fonctionalité Relations séquences-structures-fonctions

3 IMGT, the international ImMunoGeneTics information system Pourquoi IMGT a-t-il été créé?

4 IMGT domain: the adaptive immune response Vertebrates Immunoglobulin (IG) T lymphocyte B lymphocyte peptide T cell receptor (TR) MHC Trimolecular complex

5 Bone marrow Blood Lymph nodes, spleen V-D-J and V-J rearrangements Hypermutations, selection

6 Spacefill 3D representation of an IgG The Immunoglobulin FactsBook, 2001

7 Structural domains IG and TR MHC V-DOMAIN C-DOMAIN G-DOMAINs

8 Immunoglobulin (IG) T cell receptor (TR) V-DOMAIN V-J-REGION Light chain Contribution of the 2 V-DOMAINs to the antigen binding site V-DOMAIN V-D-J-REGION Alpha - Beta Gamma - Delta Heavy chain V-J-REGION V-DJ-REGION Membrane IgM T cell receptor The Immunoglobulin FactsBook, 2001

9 Immunoglobulin IgG IMGT Repertoire,

10 genomic DNA (IGH Locus 14q32) Immunoglobulin (IG) synthesis V D J C 5 3' rearranged DNA mrna 5 3' 2 x different IG per individual IMGT Repertoire,

11 Immunoglobulin (IG) synthesis 150 FUNCTIONAL IG GENES HEAVY CHAIN V D J C 5' 3 ' V J C 5' 3' LIGHT CHAIN x 2 3 x x 5 Kappa x 4-5 Lambda 6300 POTENTIAL RECOMBINATIONS POTENTIAL RECOMBINATIONS N-DIVERSITY SOMATIC MUTATIONS x ' 3' 5' 3' ABOUT 6.3 x 10 6 POSSIBILITIES ABOUT 3.5 x 10 5 POSSIBILITIES 2 x DIFFERENT ANTIBODIES IMGT Repertoire,

12 IMGT 6 Bases de données 15 outils pages de ressources Web

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14 IMGT Ressources Web IMGT Repertoire Chromosomal localizations Locus representations Gene tables Alignments of alleles Protein displays... IMGT Bloc-notes Interesting links The IMGT Immunoinformatics page Resources The IMGT Biotechnology page Clinical monoclonal antibodies IMGT Education Tutorials, IMGT Lexique pages HTML

15 Axiomes et concepts d IMGT-ONTOLOGY

16 IMGT-ONTOLOGY IMGT-ONTOLOGY seven axioms: To share, reuse and represent knowledge in Immunogenetics and Life Sciences IDENTIFICATION OBTENTION CLASSIFICATION ORIENTATION DESCRIPTION LOCALIZATION NUMEROTATION Giudicelli and Lefranc, Bioinformatics 1999

17 CLASSIFICATION axiom group is a member of an instance of locus IGLV is a member of human IGL (22q11.2) subgroup is a member of an instance of is ordered in an instance of IGLV2 is a member of is ordered in gene IGLV2-11 is a variant of an instance of is a variant of allele IGLV2-11*02 «Concepts» «Instances»

18 Human IGH locus Chromosome 14q32.33

19 IG and TR: 1512 genes and 2461 alleles from human and mouse

20 CLASSIFICATION axiom The IMGT-ONTOLOGY main concepts of classification include group, subgroup, gene, allele. They allowed to set up the nomenclature for IG and TR genes (V, D, J, C genes). IMGT gene names were approved by HGNC in 1999 and entered in GDB, LocusLink and Entrez Gene (NCBI). IMGT/GENE-DB is the international reference database for IG and TR genes (direct links from Entrez Gene NCBI). WHO-IUIS/IMGT 2007 report (Dev. Comp. Immunol., Immunogenetics).

21 DESCRIPTION axiom PROTOTYPE for a V-GENE L-PART1 V-GENE V-EXON 5 UTR FR1-IMGT FR2-IMGT FR3-IMGT C W C CDR3 -IMGT 3 UTR DONOR-SPLICE V-REGION Label 1 Label 2 V-GENE V-EXON Relations entre Labels FR3-IMGT L-PART1 V-REGION V-REGION CDR3-IMGT DONOR-SPLICE FR1-IMGT CDR3-IMGT

22 An example of V-GENE >X HSVI2 Homo sapiens VI-2 gene for immunoglobulin heavy chain tgagagctcc gttcctcacc atggactgga cctggaggat cctcttcttg gtggcagcag 60 ccacaggtaa aa gaggctccct agtcccagtg atgagaaaga gattgagtcc agtccaggga 120 gatctcatcc acttctgtgt tctctccaca ggagcccact cccaggtgca gctggtgcag 180 tctggggctg aggtgaagaa gcctggggcc tcagtgaagg tctcctgcaa ggcttctgga 240 tacaccttca ccggctacta tatgcactgg gtgcgacagg cccctggaca agggcttgag 300 tggatgggat ggatcaaccc taacagtggt ggcacaaact atgcacagaa gtttcagggc 360 agggtcacca tgaccaggga cacgtccatc agcacagcct acatggagct gagcaggctg 420 agatctgacg acacggccgt gtattactgt gcgagagaca cagtgtgaaa tgaaa acccacatcc 480 tgagggtgtc agaaacccaa gggaggaggc ag L-PART1 V-INTRON L-PART2 V-REGION V-RS 5' 5'UTR 3'UTR 3' V-HEPTAMER 1st-CYS 2nd-CYS DONOR ACCEPTOR V-SPACER SPLICE -SPLICE V-NONAMER

23 An example of D-GENE >J00256 IGHD7-27*01 Homo sapiens D-GENE ccagccgcag ggtttttggcc tgagctgaga accactgtgc taactgggga cacagtgattatt 60 ggcagctcta caaaaaccat gctcccccgg g 5 D-RS D-REGION 3 D-RS 5'UTR 3'UTR 5' 3' 5 D-NONAMER 5 D-SPACER 5 D-HEPTAMER 3 D-HEPTAMER 3 D-SPACER 3 D-NONAMER

24 An example of J-GENE >J00256 IGHJ1*01 Homo sapiens J-GENE accccgggct gtgggtttct gtgcccctgggcccctgg ctcagggctg actcaccgtg gctgaatact 60 tccagcactg gggccagggc accctggtca ccgtctcctc aggtgagtct gctgtactgg 120 ggatagcggg gagccatgtg tactgggcca agcaagggct ttggcttcag 170 J-RS J-REGION 5'UTR 3'UTR 5' 3' J-NONAMER J-TRP DONOR J-SPACER 118 -SPLICE J-HEPTAMER Heavy chain Light chain WGXG (J-TRP) FGXG (J-PHE)

25 IMGT/LIGM-DB D E S C R I P T I O N Avril 2007: sequences from 150 species Mars 2008: sequences from 221 species Janv. 2009: sequences from 229 species IMGT-ONTOLOGY: 277 IMGT labels for sequences 285 IMGT labels for 3D structures SO (Sequence ontology): 67 IMGT labels

26 DESCRIPTION axiom The IMGT-ONTOLOGY concepts of description comprise the standardized IMGT labels and relations. They have allowed to describe the IG, TR and MHC sequences and 3D structures, whatever the receptor type, the chain type, or the species. They are particularly useful to describe IG, TR, and MHC and their complexes (IG/antigen, TR/pMHC). It is possible to query the IMGT databases (IMGT/LIGM- DB for sequences, IMGT/3Dstructure-DB for 3D structures) with IMGT labels. Sequence Ontology (SO) includes IMGT labels.

27 IMGT/V-QUEST

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29 Analysis by batches of up to 50 sequences in a single run

30 Selection of ouput parameters

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34 V-DOMAINs: VH and V-KAPPA VH V-D-J junction V-KAPPA V-J junction VH V-KAPPA Side view of the V-DOMAINs View from above the CDRs Mouse(Mus musculus) E5.2Fv CDR-IMGT= Complementarity determining region (en couleurs) FR-IMGT= Framework region (en gris)

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