"bridging the gap between bioinformatics and medical informatics"

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INBIOMEDvision workshop at MIE2012 - XXIV Conference of the European Federation for Medical informatics. August 2629, 2012. Pisa, Italy. Presentations: M.A. Mayer, V. Lpez Alonso, N.Shublaq.

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  • 1. Bridging the gap betweenBioinformatics and MedicalInformaticsINBIOMEDvisionhttp://www.inbiomedvision.eu/ Workshop MIE 20122nd Consortium Meeting, Barcelona 16th May, 2011

2. MIE 2012 Workshop :Why defining the Biomedical Informatics Field is so importantDrMiguelAngelMayer PompeuFabraUniversityFIMIM Joint Research Programme on Biomedical Informatics (GRIB)Prospective analysis on Biomedical Informatics enablingpersonalised medicineDraVictoriaLpez-Alonso InstituteofHealthCarlosIII Medical Bioinformatics DepartmentPersonalised medicine: a legacy of promises without delivery can we get it right today?DraNourShublaq UniversityCollegeLondon Centre for Computational Science2nd Consortium Meeting, Barcelona 16th May, 2011 3. INBIOMEDvision: Promoting & monitoring BMI in Europe Partners: Universitat Pompeu Fabra (Coordination) Fundaci IMIM (Managing) Danish Technical University Erasmus University Medical Center Universidad Politecnica de Madrid Instituto de Salud Calos III University College London + 40 additional experts participants Overseas scientific advisory boardhttp://www.inbiomedvision.eu/2nd Consortium Meeting, Barcelona 16th May, 2011 4. INBIOMEDvision: Promoting & monitoring BMI in EuropeINBIOMEDvision provides overviewson the state-of-the-art, methods and models that connect biological systems described at the molecular levelwith clinical physiopathology and compiles the existing knowledge on genotype-phenotype data resources.http://www.inbiomedvision.eu/2nd Consortium Meeting, Barcelona 16th May, 2011 5. Operational Objectives INBIOMEDvision To consolidate a BMI community of researchers by congregating and promoting the interaction between scientists from a wide range of relatedfields. To develop and facilitate training activitiespromoting new generations of scientists and professionals having the BMI perspective. To widely disseminate the BMI knowledge and resources.2nd Consortium Meeting, Barcelona 16th May, 2011 6. Community building activitiesResearcher DirectoryConsolidation of a Biomedical InformaticsCommunityTraining Activities Training ChallengeTo promote cross-talk between disciplinesto tackle a specific case study, byengagement of complementary expertiseScientific EventsTo provide and facilitate interaction andcollaboration between EU & internationalresearchers from different relateddisciplines2nd Consortium Meeting, Barcelona 16th May, 2011 7. Think Tanks Reports &Summary and international experts, leaders in their own fields,Different Europeanparticipated in three Think Tanks, in order to identify opportunities for futurecollaborative work, and making recommendations for the wider scientific community. 2nd Consortium Meeting, Barcelona 16th May, 2011 8. MIE 2012 Workshop :Why defining the Biomedical Informatics Field is so importantDrMiguelAngelMayer PompeuFabraUniversityFIMIM Joint Research Programme on Biomedical Informatics (GRIB)Prospective analysis on Biomedical Informatics enablingpersonalised medicineDraVictoriaLpez-Alonso InstituteofHealthCarlosIII Medical Bioinformatics DepartmentPersonalised medicine: a legacy of promises without delivery can we get it right today?DraNourShublaq UniversityCollegeLondon Centre for Computational Science2nd Consortium Meeting, Barcelona 16th May, 2011 9. Prospective analysis onBiomedical Informaticsenabling personalised medicineVictoria Lpez Alonso PhDBioinformtics UnitInstituto de Salud Carlos III SpainWorkshop INBIOMEDvision, MIE 20122nd Consortium Meeting, Barcelona 16th May, 2011 10. OverviewPersonalised medicineBiomedical Informatics (BMI) enabling personalisedmedicine:2nd Consortium Meeting, Barcelona 16th May, 2011 11. Personalised medicine in current practiceChemotherapymedicationstrastuzumab Incidenceofadverseeventsfordrugs andImatinib Abacavir,CarbamazepineandClozapine (Dettling et al., 2007; Ferrell and McLeod, 2008). (Gambacorti-Passerini, 2008;Hudis, 2007) Targetedpharmacogeneticdosingalgorithmisusedforwarfarin(International Warfarin Pharmacogenetics Consortium et al., 2009) 2nd Consortium Meeting, Barcelona 16th May, 2011 12. Personalised medicine and BMI Advancing biomedical research requires an overlap of genomic and clinical research. The assimilation of information at the molecular, cellular, tissue, organ, and personal level leads to the development of innovative BMI tools and technologies. High throughput biological measurementsInformationPersonalisedMedicine DNA, RNA, proteins, small molecules, and lipidsDiagnosis Genomics Individual genomics (SNPs, CNVs), Functional genomics,Disease ReclassificationProteomicsPharmacogenomics BIOMEDICALINFORMATICS patients, diseases, symptoms, laboratory tests, pathology Clinicalreports, clinical images, and drugs Population-based health data&EHR 2nd Consortium Meeting, Barcelona 16th May, 2011 13. Powerful Network of data resourcesData sources coupled with clinical decision supportsystems(CDS), should become readily available at the bedside tosupport informed decision making and to improve patient safety.Clinical Bioinformatics Molecular&Clinical ElectronicMedicalRecords DatabasesGenbank, Pubmed,Standardsfor:GEO, PDBDiseases:UMLS, MESH, UCSC, EnsemblSNOMED Human Genome Adverseevents:MedDRA Nomenclature Drugs:RXNorm Veterans CommitteeAffairs National Drug HumanCyc and KEGG,The Adverse EventReferenceLaboratorytests:Reactome Reporting System (AERS)LOINCHealthinformation:HL 7, The Standards:Anatomical TherapeuticGene OntologyNetworkclassificationresourcesChemical of data2nd Consortium Meeting, Barcelona 16th May, 2011 14. BMI for Health-Related Genomics Bentley D. Genomes for Medicine. (2004). Nature Insight 429, p440-446 2nd Consortium Meeting, Barcelona 16th May, 2011 15. Personalised medicine in current practiceToday patients genetics are consulted only for few diagnosesand treatments and only in certain medical centers(cystic fibrosis , breast cancer) Clinical assessment incorporating a personal genome.Ashley et al. Lancet (2010)They assessed his risk for common diseases and his response to hundred of drugs based oninformation about the presence of certain genetic alleles2nd Consortium Meeting, Barcelona 16th May, 2011 16. BMI for Health-Related Genomics The ability to measure human genetic information creates opportunities for translational bioinformatics. Sequence of entire genomes and exomes, measures of genetic variations 1,63 millionSNPs shared by twins that differ from reference human genome 9,531 Variants that code for proteins4,605 Variants thatchange aa seq 77 Rare variants 3 Candidate genes BMI structure to1 gen linked to disorder store and process genomic data 2nd Consortium Meeting, Barcelona 16th May, 2011 17. BMI for Health-Related GenomicsEvaluation of biomarkers for Molecular Diagnostics and PrognosisDiagnostic classifiers thatcan identify subclasses ofdisease with differentprognoses or therapeuticsensitivities. (i.e. expressiondata clustering). 2nd Consortium Meeting, Barcelona 16th May, 2011 18. BMI for Health-Related GenomicsEvaluation of biomarkers for Molecular Diagnostics andPrognosticsGenome wide association studies(GWAS) for discovering geneticassociation between a disease anda biomarker (case-control design).The most basic analyses includecharacterizing cellular populationsand clustering them on the basisof similar profiles.It is important to collect data onexposure to potential non-genetic(environmental) risk factors.2nd Consortium Meeting, Barcelona 16th May, 2011 19. BMI for Health-Related Genomics The Wellcome Trust Consortium published a landmark paper: 14,000 cases & 3,000 controls in a GWAS analysis of seven common diseases using 500,000 SNPs. They found 24 independent associations, and made the data available for the development of additional methods for GWAS analysis 2nd Consortium Meeting, Barcelona 16th May, 2011 20. BMI for Health-Related GenomicsModel Selection Methods havebeen successful with disease and traitGWAS studies using selectiontechniques to choose multifactorialmodels that balance the false positiverate, statisticalpowerandcomputational requirements of thesearchDimensionality reduction methodsPrincipal Components AnalysisInformation GainMultifactor Dimensionality Reduction(ie. hypertension and familial amyloid polyneuropathytype I) Ritchie and Monsimger, 20102nd Consortium Meeting, Barcelona 16th May, 2011 21. BMI for Health-Related Genomics Methodstobeable 20millionofreferencestoextractLiteratureminingcould innaturallenguage informationfrombeusedtocreateaset naturaltextand representitformallyof candidate genes: indatabasesthatmethodsthatuse allowautomated search,indexingandsentence syntax andinferencenatural languageprocessing to establishthelink betweenmolecular and clinicalentities and derivedrug-gene and gene-gene interactions fromscientific literature.2nd Consortium Meeting, Barcelona 16th May, 2011 22. Informatics for Health-Related Genomics A key obstacle in the use of genome data for decision making in the clinic is the billions of features that are contained in a single human genome. Difficulty to discriminate between causal variation that has predictive value in the clinic and the substantial amount of passenger variation that travels along in an uncorrelated manner. Systems-level analyses can drastically reduce the combinatorial problem: grouping individual genetic variants that affect the samemolecular machineryturning EHR data into valuable clinical markers relative togene approaches 2nd Consortium Meeting, Barcelona 16th May, 2011 23. BMI for Network-based decision support Systems biology and network approaches: integration of molecular data at multiple levels (genomes, transcriptomes, metabolomes, proteomes and functional and regulatory networks 2nd Consortium Meeting, Barcelona 16th May, 2011 24. BMI for Network-based decision support Systemsmedicine: characterizing disease states at the molecular level. Systemspharmacology: