Transcript RTI ppt template - NCSU Bioinformatics Research Center

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
Phone 919-541-6631
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P.O. Box 12194
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Research Triangle Park, North Carolina, USA 27709
e-mail [email protected]
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
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
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
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
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
Partnerships for Genomics and Molecular
Epidemiology (PGME)
 Bioinformatics
 Statistical Genetics
 Proteomics
 Public understanding of genetics/genomics
 Epidemiology
Epidemiology: a Core Competency that Binds
Disciplines
Laboratory
Molecular Sciences
Health Sciences
Epidemiology
Biostatistics;
Informatics
Social and
Behavioral Sciences
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
PGME: Bioinformatics
http://gdbwww.gdb.org/
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
Proteomics
 Methodologies:
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Tissue Protein Isolations
2-D Gel Separations
Quantitative Image Analysis
Immunological analyses
 Technologies:
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Instrument development
Alternative separations
Protein characterization
Quantitative analysis
Proteomics
 Equipment:
 TOF-TOF
 2 Ion Traps (Linear and 3-D)
 2-D gel electrophoresis platform
 Technology Development:
 Shot-gun proteomics
RTI Shotgun Proteomics
IPG Strip Peptide Work Flow
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K
K
R
R
K
Enzymatic Digest of
Protein MIxture
Load and Focus Peptides
on IEF Strip
Database Searching and
pI Based Data Filtering
Cut IEF Strip
Into Fractions
Extract Peptides from IEF
Fractions
Data-Dependent LC-MS/MS
Analysis
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
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.
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RTI International
Institute of Molecular Medicine
National Institute of Cholera and Enteric Diseases
Duke University
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;
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
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)
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
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
Partnerships for Genomics and Molecular
Epidemiology
Partnership contacts:
Judy Lessler:
[email protected] -- 919-541-6631
Joe Pratt:
[email protected] – 919-541-6463