Class Notes

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Date	Scribe	Topic
Thursday 6 September 2007	Lecture Slides	SNPs, Haplotypes, and Disease Association
Thursday 6 September 2007	Notes from Fall 2006	Population Genetics Introduction
Tuesday 11 September 2007	Dong Wook Kim	Statistical Testing
Tuesday 18 September 2007	Ryan Tarpine	The International HAPMAP Project
Tuesday 18 September 2007 and Thursday 20 September 2007	Eric Ruggieri	Introduction to Linkage Disequilibrium
Tuesday 25 September 2007	Yongxing Guo	Hardy Weinberg Principle
Thursday 27 September and Tuesday 2 October 2007	David Moskowitz	LD and Recombination, Tests of Association
Thursday 4 October 2007	David Moskowitz	Population Methods and Haplotype Phasing
Tuesday 9 October 2007 and Thursday 11 October 2007	Eric Ruggieri	Haplotype Phasing and Clark's Algorithm
Thursday 18 October 2007	Fumei Lam	Introduction to Maximum Likelihood
Thursday 25 October 2007	Kimberley Burchett (Notes from Fall 2006)	Complexity of Haplotype Phasing
Tuesday 30 October 2007	Student Presentations	Presentation of Four Papers on Genetic Variation
Thursday 1 November, Tuesday 6 November, and Thursday 8 November 2007	Eric Ruggieri	Complexity of Parsimony Phasing and Maximum Likelihood
Tuesday 6 November 2007	Professor Ryan	Association Study on Diabetes
Thurday 15 November 2007	Professor Ryan	Summary of "Mapping Using Inferred ARGs" (Minichiello & Durbin)
Thurday 13 December 2007 Friday 14 December 2007	Sorin Istrail	Genomewide Association Studies
Tuesday 18 December 2007	Student Presentations Genomewide association studies	Presentation agenda Type II diabetes (Eric) Multiple Sclerosis (Yongxing) Prostate Cancer (David)
Thursday 20 December 2007	Student Presentations Special Topics	Tagging SNPs (Eric) Bayesian methods for phasing (Yongxing)

Association Study	Papers
Prostate Cancer (David)	Multiple prostate cancer risk variants on 8q24, Witte, Nature Genetics 39, 579 - 580 (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24, Yeager et al. Nature Genetics 39, 645 - 649 (2007) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men, Freedman et al. PNAS vol. 103, no. 38, pg 14068-14073 (2006) A common variant associated with prostate cancer in European and African populations, Amundadottir et al. Nature Genetics 38, 652 - 658 (2006)
Heart Disease (Don)	Ruth McPherson et al., Science 8 June 2007, Vol. 316 no. 5830, pp. 1488 - 1491, A Common Allele on Chromosome 9 Associated with Coronary Heart Disease Helgadottir et al., A Common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 2007 Jun 8;316(5830)1491-3. Epub 2007 May 3 Semani et al., Genomewide Association Analysis of Coronary Artery Disease, New England Journal of Medicine, July 2007 (10.1056/NEJMoa072366)
Diabetes (Eric)	Helgason A et al. Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution. Nature Genetics 39, Feb 2007, 218-225 Valeriya Lyssenko et al, Mechanisms by which common variants in the TCF7L2 gene increase risk of type 2 diabetes, J Clin Invest. 2007 August 1; 117(8): 2155-2163
Multiple Sclerosis (Yongxing)	Simon G Gregory et al., Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis Nature Genetics 39, 1083 - 1091 (2007) The International Multiple Sclerosis Genetics Consortium, Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study, Volume 357:851-862, August 30, 2007, Number 9 Leena Peltonen, Old Suspects Found Guilty; The First Genome Profile of Multiple Sclerosis, New England Journal of Medicine, Volume 357:927-929, August 30, 2007, Number 9

Topic	Papers
Coalescent (David)	Mark J. Minichiello and Richard Durbin, Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs, The American Journal of Human Genetics, volume 79 (2006), pages 910-922 Sebastian Zollner and Jonathan Pritchard, Coalescent-based association mapping and fine mapping of complex trait loci, Genetics. 2005 Feb;169(2):1071-92. Epub 2004 Oct 16
Admixture (Don)	Hoggart CJ et al., Design and analysis of admixture mapping studies, Am J Hum Genet. 2004 May;74(5):965-78 David Reich and Nick Patterson, Will admixture mapping work to find disease genes?, Philos Trans R Soc Lond B Biol Sci. 2005 August 29; 360(1460): 1605-1607 Michael W. Smith and Stephen J. O'Brien, Mapping by admixture linkage disequilibrium: advances, limitations and guidelines, Nature Reviews Genetics 6, 623-632 (August 2005) Patterson N et al., Methods for high-density admixture mapping of disease genes, Am J Hum Genet. 2004 May;74(5):979-1000
SNP selection and haplotype blocks (Eric)	V. Bafna, B. V. Halldorsson, R. Schwartz, A. Clark, and S. Istrail, Haplotypes and Informative SNP selection: Don't block out information, RECOMB, 2003 :19-27. Bjarni V. Halldorsson, Vineet Bafna, Ross Lippert, Russell Schwartz, Frasisco M. De La Vega, Andrew G. Clark, and Sorin Istrail, Optimal haplotype block free selection of tagging SNPs for genome-wide association studies, Genome Research, 2004 14:1633-1640 Eran Halperin, Gad Kimmel and Ron Shamir, Tag SNP selection in genotype data for maximizing SNP prediction accuracy, Bioinformatics, conference version in The Annual Meeting of the International Society for Computational Biology (ISMB), 2005
Bayesian Methods for Phasing (Yongxing)	Matthew Stephens and Peter Donnelly, Am J Hum Genet., A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data, 2003 November; 73(5): 1162-1169 P Scheet and M Stephens, A fast and flexible statistical model for large-scale population structure in genetic association studies, Genome Research 2006 vol:16 pg:290 Olle Haggstrom, Finite Markov Chains and Algorithmic Applications (we have a copy available for you)