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WP 6.3 Genomics and chronic inflammation

WP 6.3 Genomics and chronic inflammation. Final results of Pilot 6-3 Genomics and chronic inflammation Periodontitis as case study. 11 th Consortium Meeting, Barcelona , 27-28 June 2007. Environmental life habits. Genomic data. Phenomic data. Microbiology data. Intermediate

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WP 6.3 Genomics and chronic inflammation

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  1. WP 6.3 Genomics and chronic inflammation Final results of Pilot 6-3 Genomics and chronic inflammation Periodontitis as case study 11th Consortium Meeting, Barcelona, 27-28 June 2007

  2. Environmental life habits Genomic data Phenomic data Microbiology data Intermediate phenotype Age Gender BMI CRP, ……… WP 6.3 Genomics and chronic inflammation Assessment / Annotation External DBs Programs Periodontitis Data Warehouse (PDW) 11th Consortium Meeting, Barcelona, 27-28 June 2007

  3. Environmental life habits Genomic data Phenomic data Microbiology data Intermediate phenotype Tooth 41 Age Gender BMI CRP, ……… CEJ BL Apex distal mesial WP 6.3 Genomics and chronic inflammation Assessment / Annotation External DBs Programs Periodontitis Data Warehouse (PDW) 11th Consortium Meeting, Barcelona, 27-28 June 2007

  4. WP 6.3 Genomics and chronic inflammation DIA tool (dental image analysis): ACTA & AVEIRO & UPM Tooth 41 Tooth 35 CEJ CEJ BL BL Apex Apex distal mesial 11th Consortium Meeting, Barcelona, 27-28 June 2007

  5. WP 6.3 Genomics and chronic inflammation Conventional “hand” measurements using a Schei ruler CEJ BL Apex 11th Consortium Meeting, Barcelona, 27-28 June 2007

  6. WP 6.3 Genomics and chronic inflammation Clinical validation of a dental image analysis (DIA) tool to measure alveolar bone loss in periodontitis patients. 11th Consortium Meeting, Barcelona, 27-28 June 2007

  7. WP 6.3 Genomics and chronic inflammation • Conclusions: • DIA-tool works as good as traditional hand measurements ! • However, DIA tool has 2 main advantages: • Circumstances: easier, less fatigue, larger view • Data generation: direct input in data-base, no paper intermediate step 11th Consortium Meeting, Barcelona, 27-28 June 2007

  8. WP 6.3 Genomics and chronic inflammation Manuscripts: Coelho et al. (2007) Measurement of alveolar bone loss using a newly developed dental image analysis (DIA) tool on dental X-ray images. Teeuw et al. (2007) Clinical validation of a dental image analysis (DIA) tool to measure alveolar bone loss in periodontitis patients. 11th Consortium Meeting, Barcelona, 27-28 June 2007

  9. WP 6.3 Genomics and chronic inflammation INFOBIOMED network WP-1 WP-2 WP-3 WP-4 WP-5 WP-6 Pilot applications WP6-1 WP6-2 WP6-3 WP6-4 Genomics and chronic inflammation Pharma informatics Cross pilot interaction 11th Consortium Meeting, Barcelona, 27-28 June 2007

  10. WP 6.3 Genomics and chronic inflammation Finding Links between Periodontitis and Atherosclerosis in the Literature: a Combination of Co-Occurrence and Natural Language Processing Techniques Cross pilot interaction 11th Consortium Meeting, Barcelona, 27-28 June 2007

  11. Relation atherosclerosis and periodontitis Dental plaque Fibrous plaques Chronic inflammation in coronary arteries Chronic inflammation in periodontium • Bacteraemia • Increased inflammatory • activity Atherosclerotic lesion Periodontitis WP 6.3 Genomics and chronic inflammation HYPOTHESIS 11th Consortium Meeting, Barcelona, 27-28 June 2007

  12. WP 6.3 Genomics and chronic inflammation What could be the possible biological pathways in the relation between atherosclerosis and periodontitis? • TextBlast: identification of potential genes • PathwayAssist: interactions of gene products with LPS 11th Consortium Meeting, Barcelona, 27-28 June 2007

  13. Gene Symbol Gene Full Name % Similarity PON1 Paraoxonase 1 100 CD14 CD14 antigen 85 TLR2 Toll-like receptor 2 71 ADIPOQ Adiponectin, C1Q and collagen domain containing 66 PON2 Paraoxonase 2 56 TLR4 Toll-like receptor 4 48 OLR1 Oxidised low density lipoprotein (lectin-like) receptor 1 48 MTHFR 5,10-methylenetetrahydrofolate reductase (NADPH) 47 CXCL16 Chemokine (C-X-C motif) ligand 16 45 SCARB1 Scavenger receptor class B, member 1 43 TNFRSF11B Tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) 40 FCGR2A Fc fragment of IgG, low affinity IIa, receptor (CD32) 40 CXCL10 Chemokine (C-X-C motif) ligand 10 36 ADD1 Adducin 1 alpha 32 CCR2 Chemokine (C-C motif) receptor 2 32 APOE Apolipoprotein E 30 WP 6.3 Genomics and chronic inflammation TextBLAST Results 11th Consortium Meeting, Barcelona, 27-28 June 2007

  14. WP 6.3 Genomics and chronic inflammation PathwayAssist • Database of interactions between entities (e.g. proteins, small molecules) derived from literature • Visualisation of the interactions • Pathways 11th Consortium Meeting, Barcelona, 27-28 June 2007

  15. WP 6.3 Genomics and chronic inflammation Direct Interactions Network 11th Consortium Meeting, Barcelona, 27-28 June 2007

  16. WP 6.3 Genomics and chronic inflammation Direct Interactions, Including Intermediate Nodes 11th Consortium Meeting, Barcelona, 27-28 June 2007

  17. WP 6.3 Genomics and chronic inflammation PathwayAssist Results Summary • LPS and non-LPS dependent pathways. 11th Consortium Meeting, Barcelona, 27-28 June 2007

  18. WP 6.3 Genomics and chronic inflammation Manuscript submitted Finding Links between Periodontitis and Atherosclerosis in the Literature: a Combination of Co-Occurrence and Natural Language Processing Techniques. Hettne et al. (2007) 11th Consortium Meeting, Barcelona, 27-28 June 2007

  19. WP 6.3 Genomics and chronic inflammation 2007 2004 2005 2006 ACTA, KI, UAVR and ISCIII • Insight in the complex pathophysiology • Clear disease classification schemes • Risk profiling and possibilities for screening ACTA, Custodix, ISCIII, UPM and FORTH June 2007 11th Consortium Meeting, Barcelona, 27-28 June 2007

  20. WP 6.3 Genomics and chronic inflammation Manuscripts (all): Loos, B.G. et al. (2005) Identification of genetic risk factors for periodontitis and possible mechanisms of action. Journal of Clinical Periodontology, 32 (Suppl. 6): 159-179. Eich HP et al. (2005) Practical Approaches to the Development of Biomedical Informatics: the INFOBIOMED Network of Excellence. Studies in Health Technology and Informatics. 116; 39-44. Loos et al. (2007) Biomedical Informatics in Chronic Infectious and Inflammatory Disease Research: Periodontitis as a Case Study. Journal of Oral Sciences, in preparation Laine et al. (2007) The relative importance of IL-1 gene polymorphisms in periodontitis in relation to microbiological and environmental factors. Journal of Clinical Periodontology, in preparation. Laine et al. (2007) The role of TLR-5 gene polymorphisms in chronic inflammatory diseases: Crohn’s disease and periodontitis. Frontiers in Biosciences, in preparation. Crusius et al. (2007) TNF gene polymorphisms in periodontitis. Genes and Immunity, in preparation. Moustakis et al. (2007) Modeling genetic susceptibility: a case study in periodontitis. Proceedings, in press. Laine et al. (2007) Genetic susceptibility index for periodontitis. Genes and Immunity. in preparation. Hettne et al (2007) Finding Links between Periodontitis and Atherosclerosis in the Literature: a Combination of Co-Occurrence and Natural Language Processing Techniques. Journal of Clinical Periodontology, submitted. Coelho et al. (2007) Bone loss measurement with Digital Image Analysis (DIA) of dental radiographs. Journal of xxxxxx, in preparation Teeuw et al. (2007) Clinical validation of a dental image analysis (DIA) tool to measure alveolar bone loss in periodontitis patients. Journal of Clinical Periodontology, in submission. 11th Consortium Meeting, Barcelona, 27-28 June 2007

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