Topics suggested Fall 2005

We identified three global topics of interest, plus a few less classifiable topics. We decided to start with complex traits - trait models, and then to move to association analyses and linkage disequilibrium. We also to wait on the topics that are more related to classical population genetics topics until winter quarter. A few specific suggested papers related to the topics are given at the end.

Complex traits.
• Covariates
• Age-dependent traits
• Longitudinal data
• Multivariate data
• Missing covariates
• Gene by environment interaction
  • What methods available?
  • What, if any, success is there in detecting G x E interaction in humans?
  • What are the limiting factors?
  • What examples are there from animal model?
• From phenotype to gene: trait models, linkage detection, fine-scale mapping, positional cloning
• Allele-sharing based linkage statistics
• pdf file with an incomplete list of references pulled from ISI web of Science on complex trait model is here.

Association analyses and linkage disequilibrium.
• Affects of linkage disequilibrium on linkage analysis
• Design issues in association studies, e.g., Satagopan et al 2003
• Incorporating LD into fine-scale localization of traits using SNP panels

Population genetics topics.
• There were a few of these, but mostly not turned in on paper, so I only have my memory to go on for these, and not all may be what was intended.
• Fine-scale variation in recombination rates
• Evolution of dominance
• Inferring histories of varying population size and natural selection

Misc
• A topic that crosses multiple topics would be: choose a complex disease and follow the study of the genetics of the disease. This could include all types of linkage and association studies, animal models, etc. (e.g., type II diabetes). Inferences resulting from different methods, populations, genetic data, models, etc. could be compared.

Specific suggested papers:
• Whittemore and Halpern (1994) A class of tests for linkage using affected pedigree members. Biometrics 50:118-127.
• McPeek (1999) Optimal allele-sharing statistics for genetic mapping using affected relatives. Genetic Epidemiology 16:225-249.
• Almasy and Blangero (1998) Multipoint quantitative trait linkage analysis in general pedigrees. American Journal of Human Genetics 62:1198-1211.
• Marth et al (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166:351-372.
• Abecasis & Wigginton (2005) Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-767.
• November issue of Genetics, 2005 (noted by Bertrand - papers not yet checked for actual applicability to our topics):
• Schouten, Michael T., Christopher K. I. Williams and Chris S. Haley The impact of using related individuals for haplotype reconstruction in population studies
• Macgregor, Stuart, Sara A. Knott, Ian White and Peter M. Visscher Quantitative trait locus analysis of longitudinal quantitative trait data in complex pedigrees
• Hammarlund, Marc, M. Wayne Davis, Hung Nguyen, Dustin Dayton and Erik M. Jorgensen Heterozygous insertions alter crossover distribution but allow crossover interference in Caenorhabditis elegans
• Saunders, Matthew A., Montgomery Slatkin, Chad Garner, Michael F. Hammer and Michael W. Nachman The span of linkage disequilibrium caused by selection on G6PD in humans
• Vuylsteke, Marnik, Fred van Eeuwijk, Paul Van Hummelen, Martin Kuiper and Marc Zabeau Genetic analysis of variation in gene expression in Arabidopsis thaliana