Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center 19 JAN 2011

1. Genetic and Human Phenotype Data Support in the Immunology Database and Analysis PortalImmPortwww.immport.org Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center 19 JAN 2011

2. Outline • Summary of project data in ImmPort • First complete dataset available – ITN Casale • Collaborative ImmPort development projects • HLA Genetics Consortium and HLA typing data • PopGen and genetic analysis • Special Pops and FCM analysis • Data from previous PopGen projects • Data submission support

3. 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 • Archive and manage basic and clinical research data • Integrate these research data with extensive biological knowledge • Support analysis of these integrated data

4. 5+ DAIT-funded Programs Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Population Genetics Analysis Program: Immunity to Vaccines/Infections Program HLA Region Genetics in Immune-Mediated Diseases Program Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program Immune Modeling Centers Other Consortium Projects Reagent 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 Centers 34 Projects, >100,000 subjects, terabytes of FCM, microarray, SNP genotype, ELISA, ELISPOT, etc. data

5. PopGen Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Population Genetics Analysis Program: Immunity to Vaccines/Infections Program Grants/Contracts/Projects:

6. Special Pops Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program Grants/Contracts/Projects:

7. Immune Modeling Centers Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Immune Modeling Centers Grants/Contracts/Projects:

8. HLA Genetics Consortium Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench HLA Region Genetics in Immune-Mediated Diseases Program Grants/Contracts/Projects:

9. Consortium Projects Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Other Consortium Projects Grants/Contracts/Projects:

10. ADVN Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Other Consortium Projects Atopic Dermatitis and Vaccinia Network (ADVN ):

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

12. Complete representation of ITN Casale Complete support for ITN Casale Browse Data/ ImmPort Research Data/ ImmPort Supported Programs ImmPort Research Data | My Work Bench Other Consortium Projects Grants/Contracts/Projects:

13. ImmPort home page login

14. Semi-public workspace projects

15. Study summary

16. Study schematic

17. Additional study summary contents

18. Study endpoints

19. Study download packages

20. Summary of records for download

21. Download folder of data

22. Links to external resources

23. ClinicalTrials.gov record

24. Data sets - Demographics

25. ImmPort-calculated summary statistics

26. Data sets - Assessments

27. Assessment summaries and links to complete results sets

28. Assessment results details - Wheal

29. Data sets – Adverse events

30. Adverse events broken down by study arm

31. Data sets – Lab tests

32. Lab test summaries and links to complete results sets

33. Hematocrit

34. Data sets – Mechanistic assays

35. ELISA and FCM

36. Experiment samples

37. Results, protocols, reagents, biological samples

38. Download of FCM sample sets

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

40. Collaborative ImmPort Development Projects • HLA Region Genetics Consortium • HLA typing ambiguity reduction pipeline • HLA sequence feature definition and variant type analysis and visualization • PyPop-based genetic analysis • Population Genetics Program • Haploview implementation • Ped file generation • LD Select implementation • Special Populations Program • Novel methods and infrastructure for flow cytometry analysis – FLOCK

41. 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

42. Representative Sequence Features

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

44. Summary of SFs defined 1775 total

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

46. Publication 67F 67I 70D 70D 71R 71R protective risk 28D 28E 26F 26F 30Y 30L 37Y 37F 86V 86G

47. 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 TCR Binding CD8 Binding ImmPort HLA SFVT Workflow

48. 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

49. Ambiguity in HLA Typing Data

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