Genetics and Genomics at the Channing Laboratory: How Bioinformatics Will Change the Future of Epidemiology
Outline
Growth in genomic data (not knowledge)
What is Bioinformatics
Glossary
Innate Immunity
Immunity at the Host/Environment Interface
Scope of Work for the PGA
Task
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Lab Information Management System (LIMS)
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SNPper (SNP Explorer)
SNPper: First Page
SNPper: Gene Display
SNPper: Sequence Display
SNPper: SNP View
IL10
TLR4
Slide 24
SNP Output Table
Slide 26
IL10 Frequencies
Haplotype Frequencies at IL10 SNPs: Asthmatic (Caucasians)
Slide 29
IL-10 SNP with > 5% RAF Separate Populations
IL10 Genotypes From Case Control Study African American & European American Cases & Controls
Exploring the Framework with Relevance Networks
Construction of Relevance Networks 1
Construction of Relevance Networks 2
Construction of Relevance Networks 3
Construction of Relevance Networks 4
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How Does This Apply to Epidemiology
The Future
Faculty of BWH Innate Immunity PGA
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Innate Immunity in Diseases of Heart, Lung and Blood
Slide 47
Faculty of U of Arizona/BWH Innate Immunity PGA
PGA University of Arizona & Brigham and Women’s Hospital
Analytical Strategy
Case Control Selection for Association Studies
Association of IL10 SNP Genotypes with Case-Control Status
Educational Activities
Usage Stats
Slide 55
IL-10 SNP with > 5% RAF ALL Samples Combined (not a good idea; n=90)
TLR4 SNP (all - no minimum RAF)
This is more easily viewed in the innateimmunity.net website ! This huge sequence surrounding TLR4 - most of the SNP are between exons outside transcribed areas of the gene.These areas may be important in regulation.
TLR4 SNP (5% minimum RAF)
TLR2 SNP (5% minimum RAF)
TLR9 SNP (5% minimum RAF)
Program in Genomic Applications (PGA)
Linkage Analysis
The New Pharmacology
Genes and Anti-Cancer Agents
Slide 66
Distribution of r^2
Author: Scott T. Weiss, M.D., M.S.
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