jump to content past intro images and navigation barFrom Genome to Disease II
A Symposium of
High Throughput Biology
July 19 - 20, 2005
Natcher Conference Center
National Institutes of Health
Bethesda, Maryland
Berkeley PGA

PhysGen PGA BayGenomics PGA
SeattleSNPs PGA

PGA Symposium Home Page


Tutorials Caution: Registrants should not pick more than 4 tutorials.
Seattle SNPs PGA

Title: SNP Discovery and Analysis: Application to Association Studies

Instructors: Deborah Nickerson, Mark J. Rieder and Dana Crawford

This presentation will feature the application of SNPs for genetic association studies. Specifically, we will highlight an example where we have used all facets of SNP discovery and analysis to carry out an association study related to the clinical pharmacogenetics of warfarin dosing. In this study, we have found a set of SNPs and haplotypes that separate patients on warfarin therapy into low, medium and high dose categories. We will also show that haplotype distributions can vary between different populations. Following this, we will present methods for the preliminary work needed to carry out this study. This will include extraction of SNP data from public resources, approaches for SNP discovery by re-sequencing, software tools for SNP analysis, inference of haplotypes, and rational selection of optimal SNP marker sets (using linkage disequilibrium), and their application to different genotyping platforms.

PhysGen PGA

Title: Building a Phenome Project: A Physiological Genomics Approach to NHLBI Disorders in the Rat

Instructors: Melinda Dwinell & Howard Jacob

This tutorial will provide an overview of the tools and resources being generated by PhysGen PGA ( http://pga.mcw.edu/) to map physiological traits to individual chromosomes and/or genes. The first part of the tutorial will review the animal models and the phenotyping strategies currently being used. Strategies and advice on how to use high-throughput phenotyping in individual research labs will be presented. The second part of the tutorial will focus on the available bioinformatics tools being used to visualize and analyze the vast database. This portion will focus on a disease or pathway being characterized in our phenotyping component (heart, lung, kidney, vasculature, and blood function in response to environmental stressors). Integration with the Rat Genome Database ( http://rgd.mcw.edu/) as well as other PGA and non-PGA websites will be used to link the rat phenotyping data with other animal and human models as well as genomic resources for connecting biology to the genome.

Baygenomics PGA

Title: The Baygenomics Mouse Knockout Project

Instructor: Alex Nord

This tutorial will include an introduction to mouse models and the value of gene knockouts followed by a description of gene trap technology at Baygenomics, genome coverage with Baygenomics cell lines and how to make mice from those cell lines.

Also included will be an overview of other resources from Baygenomics including in situ images, GenMAPP and how to navigate the Baygenomics website. Finally, annotation of cell lines and localization on the genome will be covered as well as relevant educational information and Bioinformatics tutorials available through Baygenomics. The International Gene Trap Consortium will also be introduced.

Berkeley PGA

Title: Comparative Genomics in Biomedical Research

Instructors: Dario Boffelli, Jan-Fang Cheng

The completion of the Human Genome Project and the availability of sequences of the genomes of species ranging from fish to primates have revolutionized biomedical research. This massive availability of comparative sequence data enables biomedical researchers to efficiently sift through large genomic regions to develop and test hypothesis about the function and regulation of genes. The purpose of this tutorial is to bridge the gap between the bench biomedical scientist and the computational and experimental tools that have been developed to use the data generated by the Human Genome Project and other sequencing programs. This tutorial provides a detailed introduction to using genome sequences and comparative genomics to solve problems of interest to biomedical investigators. The practical use of software tools will be illustrated through numerous examples will be drawn from heart, lung and blood disorders. By the end of the tutorial, students should be familiar with 1) principles of experimental design using genomic resources, 2) navigating genome browsers and retrieving data from genome databases, 3) using comparative genomic tools for sifting through large genomic intervals to identify novel genes and gene regulatory elements and 4) experimental approaches to verify computational analyses.


Title: Mouse Mutant Resources for Studying Human Heart, Lung, Blood and Sleep Disorders.

Instructor: Carol Bult

This tutorial will enable researchers to utilize existing resources of the JAX PGA to link both quantitative trait loci (QTL) and single-gene mutations to gene function and disease and to dissect the genetic variation underlying complex cardiovascular, lung, hematopoietic, and sleep dysfunction. Included will be a demonstration of how to access and use all resources generated by this PGA as well as other relevant tools, how to access mutant mouse resources, phenotypic and genotypic data, and educational and training opportunities offered by The Jax-PGA.


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