1. 1 Immunology Database and Analysis Portal ImmPort www.immport.org www.immport.org Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center 16 DEC 2010

2. ImmPort Purpose and History NIH/NIAID/DAIT would like to: –maximize the return on the public investment in basic, translational and clinical research –allow 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 www.ImmPort.org –Archive and manage basic and clinical research data –Integrate these research data with extensive biological knowledge –Support analysis of these integrated data

3. Take-home messages ImmPort has been tailored to support the needs of the immunology research community Comprehensive integrated resource for the capture, support and analysis of a wide range of basic, translational and clinical research data Compliant with established and emerging data standards, e.g. MIAME, MIFlowCyt, Cell Ontology Work collaboratively with system users to develop and implement novel data processing and analysis methods

4. Built by Immunologists Bioinformaticians Computational Biologists Biostatisticians Professional Software Developers for Immunologists Tailored for immunology Built by Immunologists for Immunologists

5. Vignettes HLA Region Genetics Consortium –HLA typing ambiguity reduction pipeline –HLA sequence feature definition and variant type analysis and visualization –PyPop-based genetic analysis Novel methods and infrastructure for flow cytometry analysis – FLOCK Comprehensive support for clinical and translational research design and results data – Casale/ITN

6. www.immport.org

7. Reference and research data

8. Visualization tools

9. Analysis tools

10. Workspaces Public –Reference data –Accessible without registration or log in “Semi-public” –Research data released after publication –Access to analytical tools –Registration and log in required for access –Accessible to all registered users Private –Pre-publication research data –Access controlled by P.I. (or P.M.) Collaborative –Controlled sharing of research data

11. Vignettes HLA Region Genetics Consortium –HLA typing ambiguity reduction pipeline –HLA sequence feature definition and variant type analysis and visualization –PyPop-based genetic analysis Novel methods and infrastructure for flow cytometry analysis – FLOCK Comprehensive support for clinical and translational research design and results data – Casale/ITN

12. 12 Summary of SFVT approach Traditional HLA allele association analysis treats entire allele as a single unit and does not capture the structural relationships between alleles Sequence 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 SF –Examine the association between every sequence feature variant type and disease or other phenotype

13. Representative Sequence Features

14. 14 A*0201 - ‘CD8 binding’ & ‘TCR binding’ SF CD8 Binding TCR Binding

15. Summary of SFs defined 1775 total

16. Variant Types for Hsa_HLA-DRB1_beta-strand 2_peptide antigen binding

17. Publication 67F 70D 71R 86V 26F 37Y 30Y 28D 67I 70D 71R 86G 26F 37F 30L 28E protectiverisk

18. 18 ImmPort HLA SFVT Workflow Table of subject vs. HLA 4-digit typing data Table of subject vs. SFVT feature vector Table of p-values, adj. p-values, odds ratio, confidence intervals CD8 Binding TCR Binding

19. HLA Typing Platforms and Ambiguity HLA Typing Platforms –SSOP – single-stranded oligonucleotide probe –SSP – sequence-specific priming –SBT – sequence-based typing –SSCP – single-stranded conformation polymorphism Allelic Ambiguity –Typing methodology cannot distinguish between sets of alleles –Polymorphisms 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/primers Genotypic Ambiguity –Inability to determine phase in heterozygous samples

20. Ambiguity in HLA Typing Data

21. Allelic Ambiguity Reduction Eliminate others Are any of the alleles reg-CWD? Elimination of less-probable alleles by CWD status Reduction of multiple alleles to G- or P-codes yes no Eliminate others Are any of the alleles CWD? yes no Eliminate others Are any of the alleles reg-Rare? yes Combine to G- code Do any alleles belong to a common G- code? yes no Combine to P- code Do any alleles or G-codes belong to a common P- code? yes Eliminate rare alleles Do the alleles contain any G- or P-codes? yes no

22. Outcome of HLA Ambiguity Reduction Allelic Ambiguity Reduction Genotypic Ambiguity Reduction

25. Vignettes HLA Region Genetics Consortium –HLA typing ambiguity reduction pipeline –HLA sequence feature definition and variant type analysis and visualization –PyPop-based genetic analysis Novel methods and infrastructure for flow cytometry analysis – FLOCK Comprehensive support for clinical and translational research design and results data – Casale/ITN

26. Flow Cytometry Analysis FLOCK is an algorithmic application for the identification of unique cell populations in multi-dimensional flow cytometry data N1-3 UM1-2 UM3-4 PB GSM GNSM DNM CD27 IgD A

31. Population statistics

32. Summary Statistics

33. B cell component of the Cell Ontology http://www.obofoundry.org/

34. FlowCAP

35. Vignettes HLA Region Genetics Consortium –HLA typing ambiguity reduction pipeline –HLA sequence feature definition and variant type analysis and visualization –PyPop-based genetic analysis Novel methods and infrastructure for flow cytometry analysis – FLOCK Comprehensive support for clinical and translational research design and results data – Casale/ITN

36. 5+ DAIT-funded Programs Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program Population Genetics Analysis Program: Immunity to Vaccines/Infections Program HLA Region Genetics in Immune-Mediated Diseases Program Other Consortium Projects Immune Modeling Centers ImmPort Research Data | My Work Bench Browse Data/ ImmPort Research Data/ ImmPort Supported Programs Reagent Development for Toll-like and other Innate Immune Receptors DMID-funded Centers of Excellence for Influenza Research and Surveillance GlaxoSmithKline – COPD trial 34 Projects, >100,000 subjects, terabytes of FCM, microarray, SNP genotype, ELISA, ELISPOT, etc. data

37. PopGen Grants/Contracts/Projects: Population Genetics Analysis Program: Immunity to Vaccines/Infections Program Project TitleInstitute Principle InvestigatorObjective Number of SubjectsMechanistic AssaysStatus Immunity to Vaccinia Virus InfectionMayo 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. 1,076 ELISA, ELISPOT, HLA genotype, GWAS, Microarray, Flow Cytometry Completely loaded in PPW Population Genetics Program on West Nile Virus Project McMaster UniversityMark 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. 1,346 Infinium 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. 90,037 genotyping, 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. 2000 Sequencing, 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). 1453 ELISA, Flow Cytometry, Pyrosequencing, Gene expression Completely loaded in PPW ImmPort Research Data | My Work Bench Browse Data/ ImmPort Research Data/ ImmPort Supported Programs

38. Special Pops Grants/Contracts/Projects: Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program Project TitleInstitution Principle InvestigatorObjective Number of SubjectsMechanistic AssaysStatus An Improved Influenza A Vaccine for Rapid Protection of the Elderly The Wistar Institute Hildegund 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. 600 ELISA, ELISPOT, Flow Cytometry Partially loaded in PPW Protective Immunity in Transplant Recipients Emory Transplant Center Larsen, Christian, Ph.D. To determine the effects of chronic immunosuppressive therapies on adaptive, innate and specific immunity 90 ELISA, ELISPOT, Microarry, RT - PCR Partially loaded in PPW Kinetic analysis of immunologic repletion and influenza vaccine responsiveness Children´s Hospital of Philadelphia Sullivan, 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 responses 54 ELISPOT, Sequencing, Flow Cytometry Partially loaded in PPW Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations: TLRs in Innate Immunity and the Induction of Adaptive Immunity in the Neonate and Infant University of Washington Hajjar, 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) immunity 17 adults, 17 neonates RT-PCR, ELISA, Flow Cytometry, Microarray Partially loaded in PPW Responses to Influenza Vaccination in Systemic Lupus Oklahoma 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. 60 ELISPOT, ELISA, multiplex RT-PCR Partially loaded in PPW Immune function and Biodefense in Children, Elderly and Immunocompromised Populations Oregon Health and Science University Nikolich-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. 130 Flow Cytometry, ELISA, RT- PCR, Gene expression, Partially loaded in PPW Immune Response to Virus Infection During Pregnancy Mt. Sinai School of Medicine Moran, 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 vaccination 75 Flow Cytometry, multiplex ELISA, RT-PCR Partially loaded in PPW Rochester BiodefenseUniversity of RochesterSanz, Ignacio, M.D. To identify the specific immune defects that make immunocomprised populations specially susceptible at bioterrorists attack. 280Flow Cytometry Partially loaded in PPW Innate Immune Responsiveness in the Elderly and the Immunosuppressed Yale School of Medicine Montgomery, Ruth, M.D., Erol Fikrig, MD This proposal will explore the hypothesis that altered innate immune responsiveness in the elderly and the immunosuppressed contributes to vaccine unresponsiveness or disease susceptibility. 1160 SNP genotyping, Flow Cytometry, ELISA Partially loaded in PPW ImmPort Research Data | My Work Bench Browse Data/ ImmPort Research Data/ ImmPort Supported Programs

39. Consortium Projects Grants/Contracts/Projects: Other Consortium Projects ImmPort Research Data | My Work Bench Browse Data/ ImmPort Research Data/ ImmPort Supported Programs Project TitleInstitute Principle InvestigatorObjective Number of SubjectsMechanistic AssayStatus Allergen immunotherapy Co-administered with Omalizumab shared to Semi-Public Workspace (SPW) Project Immune Tolerance Network Group (ITN) Thomas Casale To 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, ELISA Completely available in SPW Atopic Dermatitis and Vaccinia Network (ADVN ) many Donald Leungmany2761 Flow cytometry, ELISA, ELISPOT, RT-PCR, Microarry gene expression, Genotyping Partially loaded in PPW

40. Study summary

41. Study schematic

42. Study download packages

43. Summary of records for download

44. Download folder of data

45. Links to external resources

46. Data sets - Demographics

47. ImmPort-calculated summary statistics

48. D ata sets - Assessments

49. Assessment summaries and links to complete results sets

50. Diastolic Blood Pressure

51. Data sets – Adverse events

52. ELISA and FCM

53. Results, protocols, reagents, biological samples

54. Download of FCM sample sets

55. Complete representation of a clinical trial in ImmPort Access data through advanced query interface as well

56. Take-home message ImmPort has been tailored to support the needs of the immunology research community Comprehensive integrated resource for the capture, support and analysis of a wide range of basic, translational and clinical research data Compliant with established and emerging data standards, e.g. MIAME, MIFlowCyt, Cell Ontology Work collaboratively with system users to develop and implement novel data processing and analysis methods

57. Human Immune Phenotype Dependent on: age, race gender, genetic background disease status, therapeutic and vaccine interventions Genetic predispositions SNP, CNV, HLA type Genetic predispositions SNP, CNV, HLA type Cellular components FCM, ELISPOT, CyTOF Cellular components FCM, ELISPOT, CyTOF Serum antibody ELISA, HAI Serum antibody ELISA, HAI Serum cytokine/chemokine ELISA, CBA, MS Serum cytokine/chemokine ELISA, CBA, MS Antigen receptor repertoire Sequencing, spectrotyping Antigen receptor repertoire Sequencing, spectrotyping Gene expression Microarray, QPCR, RNASeq Gene expression Microarray, QPCR, RNASeq

58. UT Southwestern David Karp Megan Kong Diane Xiang Yu (Max) Qian Jie Huang Nishanth Marthandan Young Bun Kim Paula Guidry David Dougall Collaborators Karen 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 N01AI40076 Northrop Grumman Carl Dahlke Vincent Desborough John Campbell Yue Liu Patrick Dunn Liz Thompson Tom Smith Jeff Wiser Mike Attasi Acknowledgments Dedicated to Carl Dahlke In Memorium