The HLA Community s Success in Combining Clinical & Genomic Data

Transcription

1 The HLA Community s Success in Combining Clinical & Genomic Data Elizabeth Trachtenberg MS, PhD, DABHI Director, Center for Applied Genomics HLA/Immunogenetics Laboratory Children s Hospital & Research Center Oakland Associate Research Scientist Children s Hospital Oakland Research Institute

2 INTEGRATED CLINICAL / RESEARCH LAB at CHRCO c IMMUNOGENETIC RESEARCH & Methods Development Transplantation Disease Association Population Genetics CLINICAL Immunogenetics Histocompatibility Post-Transplant Chimerism Molecular Diagnostics Molecular Clinical Laboratory & GENOMICS CORE c. 2009

3 CHRCO GENOMIC LABORATORIES CERTIFICATIONS State of California Clinical Laboratory Dept. of Health & Human Services, CLIA American Society for Histocompatibility and Immunogenetics(ASHI) College of American Pathologists (CAP) Joint Commission American Hospital Organization (JCHAO) National Referee Lab &/or Clinical Proficiency Committee (>10 yrs) National Marrow Donor Program Research Laboratory (>12 yrs) NIH funded disease association research (7 grants in 2009)

4 Human Leukocyte Antigen Complex 4 MB within the MHC Chromosome 6p21.3 The HLA Genes exhibit extreme polymorphism, complex to type (htz ambiguity) transplantation histocompatibility stem cell and organ identification: paternity, forensics disease association studies (autoimmunity, infectious, cancer ) population genetics, evolution of the immune system

5 Rate of Discovery of HLA Alleles: Advent of Molecular HLA

6 DEVELOPMENT OF GUIDELINES, STANDARDS & DATABASES IN THE FIELD OF HLA IMMUNOGENETICS Development of Int l Community of Immunogeneticists International Workshops: IHWC Development of Societies, Guidelines and Standards International Societies: ASHI, EFI Development of curated Databases and Tools IMGT, IPD, NMDP, BMDW Development of other databases dbmhc, AlleleFreq, NIAIDS/BISC What Still Needs to be Done

7 Development of International Community of Cooperative Immunogeneticists Int l Histocompatibility Workshop & Conference (IHWC) c.1964 Reference: Histocompatibility Testing: Report of a Conference and Workshop. Amos et al., Washington DC: National Academy of Sciences - National Research Council, yrs between meetings 15 th IHWC, Rio de Janeiro & Buzios, Brazil 2008 >300 labs worldwide participated Now >40 years of international cooperative analyses of HLA: cellular & genetic components reagents & methods/technology outcomes analyses for transplantation population genetics, disease associations

8

9 From IHWC: Development of Societies To Further Establish Guidelines & Standards American Society of Histocompatibility & Immunogenetics c ASHI = Gold Standard Clinical Accreditation Research & Clinical components to meetings, publications American Board of Histocompatibility & Immunogenetics c ABHI - Clinical Board Certification (Directors, Techs) Internationally (e.g.): European Federation of Immunogeneticists (EFI) British Society for Histocompatibility & Immunogenetics, many others

10

11 Development of Curated Sequence Databases, Nomenclature Guidelines and Tools HLA Informatics Groups Steven Marsh, PhD Anthony Nolan Trust, UK specialist databases for the study of polymorphism in genes of the immune system International ImmunoGenetics Project (IMGT)/HLA Database IMGT/Killer Immunoglobulin-like Receptor (KIR) Database Immuno Polymorphism Databases (IPD)

12

13

14 Other public, useful databases & tools dbmhc (NIH, NCBI, IHWG) AlleleFreq (Ireland, UK) AND NIAIDS-BISC database under development

15 Development of Databases & other Tools for Donor Searches and Research in Stem Cell Transplantation National Marrow Donor Program Donor Search Bioinformatics Databases & Clinical Tools Internationally: Bone Marrow Donors Worldwide, others

16 Clinical Tools Bioinformatics CIBMTR: Clinical Outcome Analyses

17 Patchwork pattern of polymorphism at the DPB1 locus Colored gene-conversion blocks in the exon-2 encoded amino-acid sequences of 17/135 DPB1 alleles are shown.

18

19 Next Generation ROCHE GS FLX 454 Sequencer: Procedure for Clonal Analysis A Add PCR Reagents & emulsion oil Micro-reactors B Amplicon pool Mix amplicons & capture beads PCR in water-in-oil emulsion Isolate DNA containing beads Load beads onto PicoTiter Plate Load Enzyme Beads Load PTP on Sequencer Pyro-sequence DNA Capture Bead APS PPi T Read Flowgram Sulfurylase Luciferase ATP Light + oxyluciferin luciferin cooled 16Mpixel CCD camera

20 We ve come a long way in HLA, but there are still Challenges in Immunogenomic Data Management & Analysis Consistency in Data Management Temporal Nomenclature Allelic & Genotype ambiguities Consistent Application of Analytical Methods High levels of polymorphism, rare alleles, haplotype estimation (no SOP here!) Data Portability and Integration Between Analytical Tools Disparate data formats Various levels of resolution (heterogeneous data elements) Lack of standardized input formats Jill Hollenbach, Steve Mack at CHRCO: RO1 to address these