1 Genetic and Human Phenotype Data Support in the Immunology Database and Analysis Portal ImmPort www.immport.org www.immport.org Richard H. Scheuermann,

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  • *Genetic and Human Phenotype Data Support in the Immunology Database and Analysis PortalImmPortwww.immport.org Richard H. Scheuermann, Ph.D.Department of PathologyU.T. Southwestern Medical Center

    19 JAN 2011

  • OutlineSummary of project data in ImmPortFirst complete dataset available ITN CasaleCollaborative ImmPort development projectsHLA Genetics Consortium and HLA typing dataPopGen and genetic analysisSpecial Pops and FCM analysisData from previous PopGen projectsData submission support

  • ImmPort Purpose and History NIH/NIAID/DAIT would like to:maximize the return on the public investment in basic, translational and clinical researchallow investigators to more effectively extract meaningful information from the vast amounts of data generated from advanced research technologies=> data sharing policy

    Bioinformatics Integration Support Contract (BISC) to support data sharing for all DAIT-funded programs - basic, translational and clinical research

    Immunology Database and Analysis Portal (ImmPort) - www.ImmPort.org Archive and manage basic and clinical research dataIntegrate these research data with extensive biological knowledgeSupport analysis of these integrated data

  • 5+ DAIT-funded ProgramsImmune Function and Biodefense in Children, Elderly, and Immunocompromised Populations ProgramPopulation Genetics Analysis Program: Immunity to Vaccines/Infections ProgramHLA Region Genetics in Immune-Mediated Diseases ProgramOther Consortium ProjectsImmune Modeling CentersImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported ProgramsReagent Development for Toll-like and other Innate Immune Receptors

    DMID-funded Centers of Excellence for Influenza Research and Surveillance

    GlaxoSmithKline COPD trial

    Human Immune Phenotyping Centers34 Projects, >100,000 subjects, terabytes of FCM, microarray, SNP genotype, ELISA, ELISPOT, etc. data

  • PopGenGrants/Contracts/Projects:Population Genetics Analysis Program: Immunity to Vaccines/Infections ProgramImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project Title Institute Principle Investigator Objective Number of Subjects Mechanistic Assays StatusImmunity to Vaccinia Virus Infection Mayo Clinic Gregory A. Poland, M.D .To correlate variability in humoral and cell-mediated immune responses to vaccinia virus immunization with genetic variation in the HLA, cytokine and cytokine receptor genes and the broader genome. 1,076ELISA, ELISPOT, HLA genotype, GWAS, Microarray, Flow Cytometry Completely loaded in PPWPopulation Genetics Program on West Nile Virus Project McMaster University Mark Loeb, Ph.D. Gene analysis using Illumina Human NS-12 and Omni 1, single nucleotide polymorphisms (SNPs) to compare gene frequencies between individuals with meningoencephalitis and those with West Nile Fever using a case-control study design. 1,346Infinium assay, sequenom, whole-genome expression Completely loaded in PPW

    Immunity to Vaccines/Infections Immune Response Polymorphisms: Smallpox, Tuberculosis, Influenza and Common Encapsulated Bacteria Infections deCODE Genetics Jeffrey Gulcher, M.D., Ph.D. To map, isolate and validate human host genes that confer risk of either adverse reactions to smallpox vaccination or lack of specific immune response to the vaccine. 90,037genotyping, mRNA expression, GWAS Partially loaded in PPW

    Immune Response Polymorphisms: Typhoid/Cholera Vaccines RTI International Diane Wagener, Ph.D. To understand role of polymorphisms in genes of innate and adaptive immunity in modulating the response to typhoid vaccine. 2000Sequencing , ELISA, Mass spectrometry, multiplex bead assay, gel electrophoresis, shotgun proteomics, vibriocidal assay Completely loaded in PPW

    Genetic Risk for Smallpox Vaccine Related to Myocarditis University of Washington Christopher B. Wilson, M.D. To identify genetic differences that increase the risk for a major adverse event associated with smallpox vaccination - myocarditis - and to determine the mechanism by which these genetic differences confer risk Unknown? SNP Array Genotyping, HLA genotyping Completely loaded in PPW

    Genetic Factors and Immune Response to Anthrax Vaccine Univerity of Alabama at Birmingham, Birmingham AL Richard Kaslow, M.D. To investigate variability in host genes predicting variation in antibody responses and adverse reactions to Anthrax Vaccine Adsorbed (AVA). 1453ELISA, Flow Cytometry, Pyrosequencing, Gene expression Completely loaded in PPW

  • Special PopsGrants/Contracts/Projects:Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations ProgramImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutionPrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssaysStatusAn Improved Influenza A Vaccine for Rapid Protection of the ElderlyThe Wistar InstituteHildegund C. J. Ertl, M.D.To conduct pre-clinical studies needed to develop a vaccine for the elderly that would provide protection in the event of a bioterror attack with influenza A virus.600ELISA, ELISPOT, Flow CytometryPartially loaded in PPWProtective Immunity in Transplant RecipientsEmory Transplant CenterLarsen, Christian, Ph.D.To determine the effects of chronic immunosuppressive therapies on adaptive, innate and specific immunity90ELISA, ELISPOT, Microarry, RT - PCRPartially loaded in PPWKinetic analysis of immunologic repletion and influenza vaccine responsivenessChildrens Hospital of PhiladelphiaSullivan, Kathleen, Ph.D.To propose a comprehensive analysis of the immunologic response to killed trivalent influenza vaccine in different immunocompromised populations in order to understand how to improve vaccine responses54ELISPOT, Sequencing, Flow CytometryPartially loaded in PPWImmune Function and Biodefense in Children, Elderly, and Immunocompromised Populations: TLRs in Innate Immunity and the Induction of Adaptive Immunity in the Neonate and InfantUniversity of WashingtonHajjar, Lynn, M.D.To define comprehensively and in molecular and cellular detail differences in recognition and response to microbe-derived danger signals between adults, neonates and infants, and how these, in turn, contribute to differences in innate immunity and the induction of antigen-specific (adaptive) immunity17 adults, 17 neonatesRT-PCR, ELISA, Flow Cytometry, MicroarrayPartially loaded in PPWResponses to Influenza Vaccination in Systemic LupusOklahoma Medical Research Foundation (OMRF)Thompson, Linda, Ph.D.To understand why many patients with systemic lupus erythematosus (SLE) fail to make adequate responses to immunization with the influenza vaccine.60ELISPOT, ELISA, multiplex RT-PCRPartially loaded in PPWImmune function and Biodefense in Children, Elderly and Immunocompromised PopulationsOregon Health and Science UniversityNikolich-Zugich, Janko, M.D., Ph.D.To characterize immune markers and mechanisms in the elderly that determine their vulnerability to infectious and bioterrorism agents in categories A-C.130Flow Cytometry, ELISA, RT-PCR, Gene expression, Partially loaded in PPWImmune Response to Virus Infection During PregnancyMt. Sinai School of MedicineMoran, Thomas, Ph.D.To determine whether the different trimesters of pregnancy, characterized by unique hormonal environments, are associated with (a) identifiable, discrete changes in maternal systemic immunity and/or (b) recognizable alterations in susceptibility to select bio-defense pathogens and/or (c) differential responses to influenza vaccination75Flow Cytometry, multiplex ELISA, RT-PCRPartially loaded in PPWRochester BiodefenseUniversity of RochesterSanz, Ignacio, M.D.To identify the specific immune defects that make immunocomprised populations specially susceptible at bioterrorists attack.280Flow CytometryPartially loaded in PPWInnate Immune Responsiveness in the Elderly and the Immunosuppressed Yale School of MedicineMontgomery, Ruth, M.D.,Erol Fikrig, MDThis proposal will explore the hypothesis that altered innate immune responsiveness in the elderly and the immunosuppressed contributes to vaccine unresponsiveness or disease susceptibility.1160SNP genotyping, Flow Cytometry, ELISAPartially loaded in PPW

  • Immune Modeling CentersGrants/Contracts/Projects:Immune Modeling CentersImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutePrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssayStatusModeling Immunity for BiodefenseMount Sinai School of MedicineStuart C. Sealfon, M.D.The main research goal of this project is to develop experimental data-based mathematical models of human myeloid dendritic cell signaling responses to viral infection.N.A.Flow cytometry, ELISA, Luminex, qPCRPartially loaded in PPWModeling Immunity for BiodefenseDuke UniversityThomas Kepler, Ph.D.Development of computational tools for application in the rational design of vaccine adjuvants.~500 miceFlow cytometry, qPCR, ELISA, Luminex, Microarray Gene Expression, ImmunohistochemistryPartially loaded in PPWModeling Infection by and the Immune Responses to Pulmonary PathogensUniversity of PittsburghPenelope A. Morel, M.D. Modeling Immunity for Biodefense: Modeling Infection by and Immune Responses to Pulmonary Pathogens.N.A.Flow cytometry, qPCR, ELISPOT, ELISA, Luminex, Microarray Gene Expression, ImmunohistochemistryPartially loaded in PPWModeling Immunity for BiodefenseUniversity of RochesterHulin Wu, Ph.D.To develop comprehensive, computational models of the human immune response to unmodified and genetically engineered influenza A.N.A.Flow cytometry, FLORISPOT, qPCR, ELISPOT, Hemaglutination assayPartially loaded in PPWModeling Immunity to Enteric Pathogens (MIEP)Virginia Bioinformatics Institute (Virginia Tech)Josep Bassaganya-Riera, Ph.D.N.A.N.A.N.A.Nothing loaded yet

  • HLA Genetics ConsortiumGrants/Contracts/Projects:HLA Region Genetics in Immune-Mediated Diseases ProgramImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutePrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssaysStatusHLA Region Genetics and SLE in U.S. Black WomenBoston U-Slone EpidemiologyRosenberg, LynnTo survey the HLA region for genetic associations with SLE in 400 African American women with SLE and 800 matched African-American controls from the BWHS1200 Microarray, Genotype, SequencingNothing loaded yet

    HLA Region Genetics in Immune Mediated Disease: HLA/KIR Region Genetics in Pediatric ArthritisCincinnati Childrens HospitalGlass, DavidTo construct high throughput SNP maps in a family based Juvenile Rheumatoid Arthritis study.900 families HLA genotyping, SNP genotyping, Sequencing, Wide Genome Association, Nothing loaded yet

    Epigenomics of Hematopoietic Cell TransplantationFred Hutchinson Cancer Research CenterPetersdorf, EffieTo define the genetic barriers to successful allogeneic hematopoietic cell transplantation (HCT).15,548 HLA geneotypingPartially loaded in PPWThe Role of HLA and KIR in Rheumatoid Arthritis and Crohns DiseaseChildrens Hospital Oakland Research Institute (CHORI)Erlich, HenryTo carry out case/control association analyses for Crohn's Disease and Rheumatoid Arthritis using our high resolution HLA and KIR(Killer Immunoglobulin-like Receptors) genotyping methods.94 GenotypingPartially loaded in PPWMolecular Genetics of HLA and DiseaseUniversity of California, San FranciscoHauser, SteveTo identify and characterize the complete repertoire of genes encoded in the MHC region that predispose and/or modulate the expression of autoimmune disease.14,700 SNP genotyping, SequencingNothing loaded yet

  • Consortium ProjectsGrants/Contracts/Projects:Other Consortium ProjectsImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutePrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssayStatusAllergen immunotherapy Co-administered with Omalizumab shared to Semi-Public Workspace (SPW) ProjectImmune Tolerance Network Group (ITN)Thomas CasaleTo determine whether taking a drug called omalizumab (also known as Xolair) before getting the allergy shots is more effective than allergy shots alone or other treatments, such as prescription antihistamines. 159Flow cytometry, ELISACompletely available in SPWAtopic Dermatitis and Vaccinia Network (ADVN )manyDonald Leungmany2761Flow cytometry, ELISA, ELISPOT, RT-PCR, Microarry gene expression, GenotypingPartially loaded in PPW

  • ADVNAtopic Dermatitis and Vaccinia Network (ADVN ):Other Consortium ProjectsImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutePrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssayStatus Immune Response to Varicella Vaccination in Subjects with Atopic Dermatitis Compared to Nonatopic Controls (Varicella) Childrens Hospital, BostonLynda Schneider, M.D.To determine if children with AD have VZV-specific cell mediated immune (CMI) responses to varicella vaccination that differ from those of nonatopic controls60 ELISA, ELISPOT, Flow CytometryCompletely loaded in PPWResponses to Immunization with Keyhole Limpet Hemocyanin (KLH)National Jewish Medical and Research CenterHenry Milgrom, M.D.To determine whether two administrations of KLH by the scarification route (15 jabs, 20 mg/mL) induce an anti-KLH IgG antibody response to KLH in nonatopic subjects25 ELISACompletely loaded in PPWAnalysis and Correlation of Cathelicidin Expression in Skin andSaliva of Subjects with Atopic Dermatitis and Psoriasis (CATH 02)University of. California, San DiegoRichard Gallo, M.D., Ph.D.To measure the local and systemic expression of cathelicidin (hCAP18/LL-37) in subjectswith ADEH-, ADEH+, psoriasis, and in non-atopic controls80 ELISACompletely loaded in PPWAnalysis of the Response of Subjects with Atopic Dermatitis to Oral Vitamin D3 by Measurement of Antimicrobial Peptide Expression in Skin and Saliva (CATH 03)University of. California, San DiegoRichard Gallo, M.D., Ph.D.To examine the effect of oral administration of Vitamin D3 on AMP (hCAP18/LL-37, HBD3) expression in AD subjects' skin as compared to change in AMP expression in lesional and non-lesional skin of subjects who receive the Vitamin D3 placebo.80 RT-PCR, ELISACompletely loaded in PPWRole of Antimicrobial Peptides in Host Defense Against Vaccinia Virus ( AMP 01)National Jewish HealthDonald Leung, M.D., Ph.D.Recent studies have demonstrated that the T-Helper 2 cell (Th2) phenotype of AD skin suppresses antimicrobial peptides (AMP).296 RT-PCR, Gene expression, MicroarrayCompletely loaded in PPWRisk Factors in Atopic Dermatitis for the Development of Eczema Herpeticum (ADEH)University of Bonn, GermanyThomas Bieber, M.D., Ph.D.Phenotypical, qualitative, and quantitative analysis of myeloid and plasmacytoid DCs of the different subgroups240 Flow Cytometry, ELISA, ELISPOT, RT- PCRCompletely loaded in PPWA study of the Systemic and Cutaneous Immune Responses to Yellow Fever Vaccination in Atopic Dermatitis Subjects (Yellow Fever)Oregon Health Sciences UniversityJon Hanifin, M.D.To gain greater insight into the immunological parameters that distinguish AD subjects from controls. 80 RT-PCR, ELISA, Radioimmunoassay, Partially loaded in PPW

    Genetics of Atopic Dermatitis Eczema Herpeticum (Genetics)University of RochesterLisa A. Beck, M.D.To identify candidate genes relevant in AD subjects with a history of EH (ADEH+) and to characterize the frequency of minor allele variants in candidate genes according to African American and Caucasian race.900 Genotyping, Expression profilingCompletely loaded in PPWADVN Biomarker Registry Study (Biomarker)University of RochesterSusan Lieff, Ph.D.;Lisa A. Beck, M.D.To facilitate ADVN clinical research designed to reduce the risk of eczema vaccinatum (EV), a complication of vaccinia immunization that occurs in patients with AD1000 ELISAPartially loaded in PPW

  • Human Immune PhenotypeDependent on:age, race gender, genetic backgrounddisease status, therapeutic and vaccine interventionsGenetic predispositionsSNP, CNV, HLA typeCellular componentsFCM, ELISPOT, CyTOFSerum antibodyELISA, HAI, and neutraliz.Serum cytokine/chemokineELISA, CBA, MSAntigen receptor repertoireSequencing, spectrotypingGene expressionMicroarray, QPCR, RNASeq

  • Complete representation of ITN CasaleComplete support for ITN CasaleGrants/Contracts/Projects:Other Consortium ProjectsImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    Project TitleInstitutePrinciple InvestigatorObjectiveNumber of SubjectsMechanistic AssayStatusAllergen immunotherapy Co-administered with Omalizumab shared to Semi-Public Workspace (SPW) ProjectImmune Tolerance Network Group (ITN)Thomas CasaleTo determine whether taking a drug called omalizumab (also known as Xolair) before getting the allergy shots is more effective than allergy shots alone or other treatments, such as prescription antihistamines. 159Flow cytometry, ELISACompletely available in SPWAtopic Dermatitis and Vaccinia Network (ADVN )manyDonald Leungmany2761Flow cytometry, ELISA, ELISPOT, RT-PCR, Microarry gene expression, GenotypingPartially loaded in PPW

  • ImmPort home page login

  • Semi-public workspace projects

  • Study summary

  • Study schematic

  • Additional study summary contents

  • Study endpoints

  • Study download packages

  • Summary of records for download

  • Download folder of data

  • Links to external resources

  • ClinicalTrials.gov record

  • Data sets - Demographics

  • ImmPort-calculated summary statistics

  • Data sets - Assessments

  • Assessment summaries and links to complete results sets

  • Assessment results details - Wheal

  • Data sets Adverse events

  • Adverse events broken down by study arm

  • Data sets Lab tests

  • Lab test summaries and links to complete results sets

  • Hematocrit

  • Data sets Mechanistic assays

  • ELISA and FCM

  • Experiment samples

  • Results, protocols, reagents, biological samples

  • Download of FCM sample sets

  • Complete representation of a clinical trial in ImmPortAccess data through advanced query interface as well

  • Collaborative ImmPort Development ProjectsHLA Region Genetics ConsortiumHLA typing ambiguity reduction pipelineHLA sequence feature definition and variant type analysis and visualizationPyPop-based genetic analysisPopulation Genetics ProgramHaploview implementationPed file generationLD Select implementationSpecial Populations Program Novel methods and infrastructure for flow cytometry analysis FLOCK

  • *Summary of SFVT approachTraditional HLA allele association analysis treats entire allele as a single unit and does not capture the structural relationships between allelesSequence Feature Variant Type (SFVT) approach Define individual sequence features (SF) in HLA proteins (genes)Determine the extent of polymorphism for each sequence feature by defining the observed variant types (VT)Re-annotate HLA typing information with complete list of VT for each SFExamine the association between every sequence feature variant type and disease or other phenotype

  • Representative Sequence Features

  • *A*0201 - CD8 binding &TCR binding SF

  • Summary of SFs defined1775 total

  • Variant Types for Hsa_HLA-DRB1_beta-strand 2_peptide antigen binding

  • Publicationprotective risk

  • *ImmPort HLA SFVT Workflow

  • HLA Typing Platforms and AmbiguityHLA Typing PlatformsSSOP single-stranded oligonucleotide probeSSP sequence-specific primingSBT sequence-based typingSSCP single-stranded conformation polymorphismAllelic AmbiguityTyping methodology cannot distinguish between sets of allelesPolymorphisms that distinguish these alleles are not interrogated by the method Outside of exon 2 (class II) or exons 2 and 3 (class I) Sections of these exons not covered by the probes/primersGenotypic AmbiguityInability to determine phase in heterozygous samples

  • Ambiguity in HLA Typing Data

  • Allelic Ambiguity ReductionEliminate othersAre any of the alleles reg-CWD?Elimination of less-probable alleles by CWD statusReduction of multiple alleles to G- or P-codesyesnoEliminate othersAre any of the alleles CWD?yesnoEliminate othersAre any of the alleles reg-Rare?yes

  • Outcome of HLA Ambiguity ReductionAllelic Ambiguity ReductionGenotypic Ambiguity Reduction

  • ImmPort HLA Tools

  • Ambiguity Reduction Output

  • Collaborative ImmPort Development ProjectsHLA Region Genetics ConsortiumHLA typing ambiguity reduction pipelineHLA sequence feature definition and variant type analysis and visualizationPyPop-based genetic analysisPopulation Genetics ProgramHaploview implementationPed file generationLD Select implementationSpecial Populations Program Novel methods and infrastructure for flow cytometry analysis FLOCK

  • ImmPort Genetic Analysis Tools

  • Haploview Implementation

  • Browse/Download Results

  • Ped File Generation

  • LD Select Implementation

  • Collaborative ImmPort Development ProjectsHLA Region Genetics ConsortiumHLA typing ambiguity reduction pipelineHLA sequence feature definition and variant type analysis and visualizationPyPop-based genetic analysisPopulation Genetics ProgramHaploview implementationPed file generationLD Select implementationSpecial Populations Program Novel methods and infrastructure for flow cytometry analysis FLOCK

  • Traditional Flow Cytometry AnalysisSubjectiveTime-consumingDoesnt handle overlapping distributions wellSensitive to slight difference in fluorescence intensity distributions between samples Requires at least one 2D plot that clearly segregates populations in questionGoal - group together cells with similar characteristicsTraditional approach - manual gating 2D at a time

  • FLOCKFLOCK is an algorithmic application for the identification of unique cell populations in multi-dimensional flow cytometry dataN1-3UM1-2UM3-4PBGSMGNSMDNMCD27IgDA

  • FLOCK in ImmPort

  • 2D Plot Overview

  • Population Plots

  • Cross Sample Plots

  • Population Statistics

  • FlowCAP

  • FlowCAP-I Data Sets

    Dataset# Samples# Events# ColorsAnalyte-ReporterProviderGvHD1214,0004CD4-FITC;CD8b-PE; CD8-APC;CD3-PerCPBCCRC & TreeStarDLBCL305,0003CD5-FITC;CD19-PE; CD3-Cy5BCCRCHSCT3010,0004CD45.2-APC;CD45.1-FITC;Ly65/Mac1-PE;Dead cells-PIBCCRCWNV13100,0006CD3-PECy5; CD4-PECy7;CD8-AF700;IFNg-PEA;IL17-APC;Free amine-CFSEMcMasterND3017,00010CD56-Q605;CD8-AF700;CD45-PECy5;CD3/CD14-PECy7;Proprietary-FITC, PerCPCy5, PacificBlue, PacificOrange, APC, PEAmgen

  • FlowCAP-I ResultsAutomatically Predict Cluster Membership of Each Event (Cell)

  • POPGEN SUBMISSION STATUS

  • PopGenGrants/Contracts/Projects:Population Genetics Analysis Program: Immunity to Vaccines/Infections ProgramImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    PI NamePI Organization Project Title Keywords Data AvailabilityDate-Final Public ReleaseAmount of Data AvailableTotal Number of SubjectsTotal # of Subjects Characteristics CollectedTotal Number of Result Files or RecordsTotal Amount of Data Gregory A. Poland, M.D .Mayo Clinic Immunity to Vaccinia Virus Infection smallpox, immunogentics, genetic association, elispot, elisa, cytokines, neutralizing antibody9/30/201110634ELISPOT1275650 MB (BISC will load additional 22 GB of GE, Flow, GT data)

    HLA Typing1071Viral Neutralization Assay1071Genotyping other1056Mark Loeb, Ph.D. McMaster University Population Genetics Program on West Nile Virus Project West-Nile Virus, Population genetics, genotyping, polymorphism, candidate genes9/30/201116599Genotyping Illumina1699 1.37 GB (BISC will load additional 27 GB of GT data)Jeffrey Gulcher, M.D., Ph.D. deCODE Genetics Immunity to Vaccines/Infections Immune Response Polymorphisms: Smallpox, Tuberculosis, Influenza and Common Encapsulated Bacteria Infections smallpox, polymorphism9/30/20110000300 MB (BISC is building summarized data sets with deCode)

  • PopGenGrants/Contracts/Projects:Population Genetics Analysis Program: Immunity to Vaccines/Infections ProgramImmPort Research Data | My Work BenchBrowse Data/ ImmPort Research Data/ ImmPort Supported Programs

    PI NamePI Organization Project Title Keywords Data AvailabilityDate-Final Public ReleaseAmount of Data AvailableTotal Number of SubjectsTotal # of Subjects Characteristics CollectedTotal Number of Result Files or RecordsTotal Amount of Data Diane Wagener, Ph.D.RTI International Immune Response Polymorphisms: Typhoid/Cholera VaccinesPolymorphism, typhoid, cholera9/30/201120974Mass Spectrometry35370.5 GBELISA6001Genotyping other2085DIGE Assay4386Vibriocidal Assay2000Multiplex Bead Assay7394Christopher B. Wilson, M.D. ,Debbie Nickerson, Ph.D.University of Washington Genetic Risk for Smallpox Vaccine Related to Myocarditis smallpox vaccine, myopericarditis, risk, genetic9/30/20114134HLA Typing31263 GBGenotyping other331Genotyping Illumina76Richard Kaslow, M.D. University of Alabama at Birmingham, Birmingham AL Genetic Factors and Immune Response to Anthrax Vaccine Anthrax, variation9/30/201126415HLA Typing9490.8 GBGenotyping other1365ELISA375

  • SUBMISSION SUPPORT

  • User SupportBISC Contacts for PopGenrichard.scheuermann@utsouthwestern.edu; 214-648-4115

    PIInstitutionScientific ContactTechnical ContactDr. Gregory PolandMayo ClinicPaula GuidryPatrick DunnDr. Mark LoebMcMaster University Nishanth MarthandanPatrick DunnDr. Richard Kaslow/Dr. Robert KimberlyUniversity of Alabama at BirminghamJie HuangPatrick DunnDr. Deborah Nickerson/ Dr. Chris CarlsonUniversity of WashingtonNishanth MarthandanPatrick DunnDr. Pardis SabetiBroad InstituteJie HuangPatrick Dunn

  • Data SubmissionMechanistic assays (online or hard drive)Metadata (.xls or .xml) experiment, experiment sample, biological sample, subject, reagent, protocolResults (native results formats) FCM, HLA typing, microarray or RT-PCR for expression, ELISA for serum antibody or cytokine, ELISPOT, SNP genotypingClinical dataStudy design timeline and clinical phenotypes from CRFs collected separatelyNo PHI

  • Metadata

  • Suggested Flow of Filling TemplatesImmPort Data Submission Fields and Relations

    subjectAnimalSubject User-Defined ID*Species name*Subject Treatment Protocol User-Defined ID*Subject Treatment Protocol ImmPort Accession*Enrollment AgeAge UnitGenderStrain NameStrain CharacteristicsFamily Pedigree IDSubject's Pedigree IDFather's Pedigree IDMother's Pedigree IDAffection StatusAffection Phenotypetreatment agent 1 nametreatment agent 1 concentrationtreatment agent 1 volumetreatment agent 1 weighttreatment 1 durationtreatment 1 temperature

    bioSampleBiological Sample User-Defined ID*Biological Sample Type*Biological Sample Protocol User-Defined ID*Biological Sample Protocol ImmPort Accession*Biological Sample NameBiological Sample DescriptionBiological Sample sub-typeSource Biological Sample User-Defined IDSource Biological Sample ImmPort AccessionSource Subject User-Defined IDSource Subject ImmPort AccessionPooled SampleBiological Sample PurityBiological Sample ConcentrationBiological Sample VolumeBiological Sample Weighttreatment agent 1 nametreatment agent 1 concentrationtreatment agent 1 volumetreatment agent 1 weighttreatment 1 timetreatment 1 temperature

    experimentExperiment User-Defined ID*Experiment Type*Measurement technique*Protocol User-Defined ID*Protocol ImmPort Accession*Experiment NameDescriptionHypothesisRationaleKeywordsQuality Control MeasuresExperimentersLinks to PublicationsConstantsConditional VariablesResponding Variables

    experimentSampleGE or GT or FCM or Other Experiment Sample User-Defined ID*Experiment User-Defined ID*Experiment ImmPort Accession*Protocol User-Defined ID*Protocol ImmPort AccessionReagent User-Defined ID*Reagent ImmPort Accession*Experiment Sample NameExperiment Sample DescriptionResult File or Folder NameReplicate Group IDBiological Sample User-Defined IDBiological Sample ImmPort Accession

    reagentArray Reagent User-Defined ID*Array Platform Name*Manufacturer*Catalog Number*Array Platform DescriptionArray Platform Annotation File NameLot NumberContactWeb Link

    protocolProtocol User-Defined ID*Protocol File Name*

  • BlueprintsWe have started to use study blueprints to help coordinate data submission.Summarizes overall structural relationships among data components.Helps projects teams keep track of data for submission.Helps BISC team ensure that the correct links between data components are in place.Helps DAIT program officers keep track of submission status.

  • BlueprintsInitial drafts prepared by BISC team based on project documentation proposals, SOWs, study protocolsNeed to be reviewed, revised and returned by project personnel.Blueprints should be considered to be living documents subject to revision.

  • High-level relationships

  • Project description

  • Specific project

  • Study description

  • Genotyping experiment

  • FCM experiment

  • SummaryImmPort is starting to accumulate a lot of interesting immunology research dataFirst completed project dataset (ITN Casale) made available in semi-public workspace in Oct 2010All of this data is now readily accessible by both the immunology research community and the study team itselfBISC team available to provide submission supportRequestFor previous projects, allow BISC team access to PPW to validate accuracy and consistency data and representations before migration to semi-public workspaceFor new/renewed projects, provide proposals, protocols, SOW and/or other documentation for blueprint draftingReview blueprints when providedSuggestion for future ImmPort enhancements

  • UT SouthwesternDavid KarpMegan KongDiane XiangYu (Max) QianJie HuangNishanth MarthandanYoung Bun KimPaula GuidryDavid Dougall

    CollaboratorsKaren Kessler (Rho)Keith Boyce (ITN)Dave Parrish (ITN)Ignacio Sanz (Rochester)Michael Feolo (NCBI)Glenys Thomson (UC Berkeley)Steven G. E. Marsh (ANRI)Bjoern Peters (LIAI)Effie Petersdorf (FHCRC)Steve Mack (CHORI)DAIT-funded programs

    Supported by NIH N01AI40076Northrop GrummanCarl DahlkeVincent DesboroughJohn CampbellYue LiuPatrick DunnLiz ThompsonTom SmithJeff WiserMike Attasi

    AcknowledgmentsDedicated to Carl Dahlke In Memorium

    *Matthew Fenton building a skyscraper*Archive support for 5 DAIT-funded programs and 2 consortium projectsRequested to support completed clinical trial from Glaxo Smith KlineRequested to support immunology experiment data from the DMID-supported Centers of Excellence for Influenza Research and SurveillanceRequested to support Human Immune Phenotyping Centers

    *6 projects focused on the identification of genetic pre-dispositions to adverse responses to infection and variable responses to vaccination.Projects are completed and data is loaded in the investigators private project workspace, for the most part.Schedule for release into semi-public area in 2011.*Program investigating variation in immune responses in special human population subsets.All groups have loaded some data into ImmPort; will review in more detail later.*Modeling of immune responses to infection and vaccination*HLA associations with autoimmune disease development.Data still being generated.BISC team has collaborated with this consortium on the development of novel methods for analyzing HLA typing data the Sequence Feature Variant Type approach and automated methods for allelic and genotypic ambiguity reduction.**Consortium of project investigating immune response variations in patients with atopic dermatitis.Most of the project data are completely loaded in ImmPort.Scheduled for release into semi-public workspace in 2011.In summary, comprehensive data from 34 different projects are in various stages of loading into and release through ImmPort, with many more scheduled for support in the coming years.*Use the term semi-public because access still requires user to login and agree to the terms of use in order to see these data. However, any registered ImmPort user will have access once logged in.**My workspace.The one semi-public study we refer to as Casale.**Browse through all of the data.Start at the study level with basic administrative and study design information.**Overall study design schematic with study arms, timeline and kinds of events represented.**Primary and secondary endpoints in free text.**Download capabilities.**Number of data records of various sorts available.Click here and download a folder with all of the information.**Download folder contents, mainly in the form of tab-delimited text files for easy incorporation into spreadsheets for further analysis.**Links to external resources**ClinicalTrial.gov record**Blocks of study data sets**In addition to the primary data, ImmPort also calculates useful summary statistics. In this case, summary of demographics distributions broken down by study arms.**Results from physical exam assessments.**Again, summaries and individual assessment components.Select an individual assessment e.g. Wheal measurement**Table of results, with individual results broken down by subject and study day.Additional useful demographic information about the subjects and study arms is also provided.**Adverse events summaries and specifics again broken down by study arm.**In some cases, clinical lab tests are accompanied by reference ranges provided by the testing labs.**Finally, the mechanistic assays being performed on specimens isolated from the study participants.**FCM and ELISA**Experiment descriptions listing all experiment samples.In this case 14,462 FCM samples analyzed, derived from 1718 biological samples isolated from 158 study participants.**Drill into further details about the results, samples, protocols and reagents used.**Provide option to download various packages of FCM data broken down by study Arm, Visits, and Staining Panel.Over 2 Gigabytes of FCM data from this one study.**Example of a complete representation of a clinical trial and its resulting data in ImmPort.In addition to the representation shown here for browsing, the data can be queries and filtered using any of the criteria shown.********Allelic true of 4 and 6-digit level unless sequencing entire cDNAtrue of 8-digit level unless sequencing the entire locus

    Genotypic true of all platforms ******Allelic and genotypic ambiguity reduction results for every subject at each locus

    Note location of logic document and flow chart

    Sow the results for the example file

    ***These are primary B cells stained with CD19-APC-Cy7; CD21-FITC; CD24-PE; IgD-PerCP, AA4.1-APC; CD40-PE-Cy5; IgM-PE-Cy5.59 parameters total; 6 evaluated so far in this depiction to a subset of cellsDiffuse Large B-cell Lymphoma (DLBCL); WNV (West Nile Virus); ND (Normal Donors)Graft versus Host disease (GvHD)Hematopoetic Stell Cell Transplant (HSCT)Normal Donors (ND)Symptomatic West Nile Virus (WNV)*6 projects focused on the identification of genetic pre-dispositions to adverse responses to infection and variable responses to vaccination.Projects are completed and data is loaded in the investigators private project workspace, for the most part.Schedule for release into semi-public area in 2011.*6 projects focused on the identification of genetic pre-dispositions to adverse responses to infection and variable responses to vaccination.Projects are completed and data is loaded in the investigators private project workspace, for the most part.Schedule for release into semi-public area in 2011.*These research studies are very complex, making submission somewhat challenging.Dont go it alone!!We are here to help. Each project has been assigned a team of BISC liaisons who can help with reformatting and mapping local data structures into the ImmPort schema.Local data managers should have heard from them.Also, do not hesitate to contact me personally if you have any questions or problems.**Data about mechanistic assays include the metadata and primary results from the platforms listed.Clinical data includes the study design timelines and clinical phenotypes from CRFs.No protected health information supported.**Experiment sample is the key lynchpin between the experiment metadata and the results.**Key project personnel and overall project abstract**Study-experiment schematic**Study timeline with sequence of events very useful to convey temporal relationships **Type of experiment and number of samples expected to be analyzed***I want to thank the dedicated BISC team at UT Southwestern and Northrop Grumman for all of their hard work developing the ImmPort system.Id also like to acknowledge the help we have received for several people from Rho, ITN and Inaki Sanz group at U. Rochester.And finally, Id like to dedicate my presentation to a friend and colleague, Carl Dahlke, who passed away last month from an unexpected illness.

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