RTI International is a trade name of Research Triangle Institute

1. Incorporating Genomics in Epidemiological Research: Examples from the Partnerships for Genomics and Molecular Epidemiology Judith T. Lessler March 18, 2005 RTI International is a trade name of Research Triangle Institute 3040 Cornwallis Road ■ P.O. Box 12194 ■ Research Triangle Park, North Carolina, USA 27709 Phone 919-541-6631 e-mail lessler@rti.org

4. NIH Research “Solving the puzzle of complex diseases, from obesity to cancer, will require a holistic understanding of the interplay between factors such as genetics, diet, infectious agents, environment, behavior, and social structures.” Zerhouni SCIENCE VOL 302 October 3, 2003

5. NIH Directions • Focus on interdisciplinary teams to solve large scientific problems • Provide a seed mechanism for high-risk research • Create programs to forge public-private partnerships • NIH Institutes focus on • Genomics and gene-environment interactions • Sharing of data; public data resources

6. NIMH and Mood Disorders • Mood disorders (depression and bipolar disorder) are highly heritable • Non-genetic factors, particularly stress are significant in triggering episodes of mood disorders Breaking Ground, Breaking Through: The Strategic Plan for Mood Disorders Research, National Institutes of Mental Health, July 2002

7. Influence of Life Stress on Depression (Caspi, et. al, 2003) • Prospective-longitudinal cohort study of stress and depression • Functional polymorphism in the promoter region of the serotonin transporter (5-HTT) gene • Individuals with the short allele of the 5-HTT promoter polymorphism exhibited more depressive symptoms, diagnosable depression, and suicidality in response to stress Caspi, A, et. al (2003) Influence of Life Stress on Depression, Science, Vol. 301, July 18, 2003

8. Partnerships for Genomics and Molecular Epidemiology (PGME) • Goal: Build a research program that would allow us to conduct complex research that illuminates the interaction between genetics and the environment • Took a building block approach • Development of internal capabilities and experience • Partnering with universities and other organizations that have complementary capabilities

9. Partnerships for Genomics and Molecular Epidemiology (PGME) • Bioinformatics • Statistical Genetics • Proteomics • Public understanding of genetics/genomics • Epidemiology

10. Epidemiology: a Core Competency that Binds Disciplines Laboratory Molecular Sciences Health Sciences Epidemiology Biostatistics; Informatics Social and Behavioral Sciences

11. PGME: Bioinformatics • Data management and data integration • Data types: clinical, biological assays, sequence data, gene expression, and protein expression • Integration of external data sets on genes, proteins, biological pathways • High performance computing • 64-cpu Linux Cluster

12. PGME: Bioinformatics http://gdbwww.gdb.org/

13. Statistical Genetics • Data mining • Mathematical modeling • Statistical Genetics: genetic linkage analysis, genetic association mapping, gene-environment interactions • Analysis of microarray and proteomic data • Statistical and data coordinating centers

14. Proteomics • Methodologies: • Tissue Protein Isolations • 2-D Gel Separations • Quantitative Image Analysis • Immunological analyses • Technologies: • Instrument development • Alternative separations • Protein characterization • Quantitative analysis

15. Proteomics • Equipment: • TOF-TOF • 2 Ion Traps (Linear and 3-D) • 2-D gel electrophoresis platform • Technology Development: • Shot-gun proteomics

16. RTI Shotgun Proteomics

17. Partnerships • Expertise in sequencing and gene expression • Clinical expertise: immunology, vaccine response, drug and alcohol abuse, heart disease, pre-term labor, microbial systems, pulmonology, etc., high performance computing, software development • Duke, UNC, NC State, East Carolina, IBM, SAS, Alpha-Gamma Inc, Virginia Commonwealth University, and from India: Institute of Statistical Sciences, National Institute of Cholera and Enteric Diseases [NICED] and Institute of Molecular Medicine

18. NIAID Program on Immunity to Vaccines/Infections The objective is to understand role of polymorphisms in genes of innate and adaptive immunity in modulating the response to vaccines for two gastrointestinal tract infections: typhoid and cholera. • RTI International • Institute of Molecular Medicine • National Institute of Cholera and Enteric Diseases • Duke University

19. Immunity to Vaccines/Infections • Collect blood and saliva from 1000 participants for each vaccine in Kolkata, India, at days 0, 3, and 28 • Perform vaccine related immunological assays on all biospecimens and classify subjects as non-, poor-, and good responders using ELISA and vibrocidal antibody assays • Discover and validate SNP polymorphisms and screen all participants’ DNA for SNPs to 14 innate immunity genes and genome scans for adaptive immunity genes;

20. Immunity to Vaccines/Infections • Protein/peptide expression of 11 protein mediators of innate/adaptive immunity and 22 proteins involved in cell stimulation and signal transduction. Using LC/MS, immunoassay, and flow cytometry • Also using 2-D gel MS/MS on 100-200 proteins, protein isoforms and protein fragments to determine more generalized effects of immune activation, signal transduction and general response to vaccination, • Analysis if association between vaccine response and SNPs, haplotypes, or protein expression

21. Immunity to Vaccines/Infections • Data will be included in a NIAID sponsored data system that will integrate data from 5 other similar trials • Bioinformatics Integration Support System (BISS)

22. Opportunities Abound • NC has many resources that can be used to develop partnerships • Appreciate work that Donna Spoon and others have done to create opportunities for sharing information and developing partnerships

23. PGME Team (partial) • Diane Wagener, PhD, Director of Genetic Epidemiology and project director for the vaccine research project • Jim Stephenson, PhD, Director of Proteomics Group • Jamie Cuticchia, PhD, Director of Bioinformatics • Georgiy Bobashev, PhD, Director of Statistical Genetics

24. Partnerships for Genomics and Molecular Epidemiology Partnership contacts: Judy Lessler: lessler@rti.org -- 919-541-6631 Joe Pratt: jpratt@rti.org – 919-541-6463