Class Notes
The Homework page will contain all mandatory readings. Watch past guest lecturers: Samuel Broder and Jonathan Yewdell
Note: Some documents are only accessible from within the campus network.
Scribe template and LaTeX tutorials
| Lecture/Date | Topic | Slides and Notes | Suggested Readings |
|---|---|---|---|
| Thursday 09/02/10 | An introduction to key biological concepts and disease associations | SNPs and the Human Genome[PPT] Genetic Variation in the Human Genome[PPT] Human Genome to Clinical Therapy[PPT] | |
| Tuesday 09/07/10 | Haplotype Blocks, Tagging SNPs, Immunology Intro | Immunogenomics[PPT] Haplotype Blocks and Tagging SNPs[PPT] | Guilt by Association[PDF] Viruses in the Sea[PDF] |
| Thursday 09/09/10 | GWAS Caveats and Protein Folding Introduction | Protein Folding Introduction[PPT] GWAS Caveats[PPT] | Drinking from the Fire Hose -- Statistical Issues in GWAS[PDF] |
| Tuesday 09/14/10 | Population Genetics Models | Population Genetics and Hardy Weinberg[PDF] |
|
| Thursday 09/16/10 | Hardy-Weinberg for Two Alleles and D | Hardy Weinberg[PDF] | |
| Tuesday 09/21/10 | Linkage Disequilibrium, D', and r-squared | LD, D' and r^2[PDF] | A haplotype map of the human genome [PDF] |
| Thursday 09/23/10 | LD, r-squared, HapMap, and GWAS |
LD and Recombination [PDF] r^2 [PDF] GWAS [PDF] HapMap Intro [PPT] |
Linkage disequilibrium and the mapping of complex human traits [PDF] |
| Tuesday 09/28/10 | Tagging SNPs and Haplotype Blocks |
The Architecture of Linkage Disequilibrium Blocks Across Chromosomes 6, 21, & 22 [PPT] |
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21 [PDF] |
| Thursday 09/30/10 | Tag SNPs, Hap Blocks, and Min Informative Subset |
The Minimum Informative Subset [PPT] Importance of Studying Haplotypes [PPT] |
Efficiency and power in genetic association studies [PDF] |
| Tuesday 10/05/10 | Haplotype Phasing -- Clark and EM methods |
Computing Haplotype Frequencies and Haplotype Phasing via the Expectation Maximization (EM) Algorithm [PDF] |
Papers to read for Sam Broder (in November) Bayesian clinical trials [PDF] The Neurobiology of Decision: Consensus and Controversy [PDF] Decisions, Decisions, Decisions: Choosing a Biological Science of Choice [PDF] Papers handed out in class Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study [PDF] Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies [PDF] Supplemental 1 (Proof) [PDF] Supplemental 2 (Informativeness) [PDF] |
| Thursday 10/07/10 | EM Phasing | Continued from previous lecture |
Inference of Haplotypes from PCR-amplified Samples of Diploid Populations [PDF] Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population [PDF] |
| Tuesday 10/12/10 | Yewdell Lecture |
Everything you wanted to know about viral immunology...No Holds Barred [PPT] [PDF] |
Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project" [PDF] |
| Thursday 10/14/10 | MS GWAS Paper and Intro to Wright-Fisher |
MS GWAS Case Study [PPT] MS GWAS Case Study [PDF] |
|
| Tuesday 10/19/10 | Wright-Fisher and Infinite Allele Models |
Wright-Fisher and the Infinite Allele Models: Two Urns Models [PDF] |
Genetic Mapping in Human Disease [PDF] Supporting Material [HTML] |
| Thursday 10/21/10 | Urn Models and Intro to Phasing Complexity |
Midterm Review Document [PDF] |
|
| Tuesday 10/26/10 | Haplotype Phasing Complexity |
Complexity of Pure Parsimony and Maximum Likelihood Haplotype Phasing [PDF] |
|
| Thursday 10/28/10 | Hypothesis Testing |
Classical Hypothesis Testing and GWAS [PDF] Midterm handed out. Due Tuesday November 2. |
|
| Tuesday 11/2/10 | Genetics of Complex Disease |
Genetics of Complex Disease: Heritability [PDF] |
|
| Thursday 11/4/10 | Sam Broder Guest Lecture |
Towards Evidence Based Medicine [PPT] Sam Broder Class Lecture [WVX] [Streaming] Sam Broder Sweatbox [WVX] [Streaming] |
|
| Tuesday 11/9/10 | Hypothesis Testing |
Genetic Heterogeneity in Human Disease [PDF] Missing Heritability and Strategies for Finding the Underlying Causes of Complex Disease [PDF] Finding the missing heritability of complex diseases [PDF] |
|
| Thursday 11/11/10 | Hypothesis Testing |
Transmission Disequilibrium Test in GWAS [PDF] |
|
| Tuesday 11/16/10 | Coalescent and more statistics |
How to Interpret a Genome-wide Association Study [HTML] Chapter 18 from Handbook of Statistical Genetics |
|
| Thursday 11/18/10 | NO CLASS. Make-up to be announced; with pizza! |