Genetic epidemiology and genome-wide association analyses
Dates: 6th-10th June 2016
Location: University of Bergen
Lecturers: Håkon K. Gjessing, Rolv Terje Lie, Anil Jugessur
Course code: GENESTAT
Credits: 3 ECTS
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The first part of the course will provide a broad overview of genetic epidemiology and statistical genetics, including biometrical genetics such as twin studies, population genetics, Hardy-Weinberg equilibrium, population structure, complex diseases, “missing heritability,” attributable fractions, and polygenic risk score. Family design versus case-control design, linkage versus linkage disequilibrium. Gene-environment interactions, case-only designs, Mendelian randomization. Phenotypes measured as continuous, dichotomous, or time-to-event data. Relative risk and penetrance models.
The second part will cover genetic association analyses in detail: Data handling and basic quality control for candidate genes and genome-wide association analyses (GWAS). Data imputation, selection of informative (tagging) SNPs. Power simulations. Analyses: Basic associations analyses, control for population structure, haplotype reconstruction, risk response models; estimation of maternal gene effects and parent-of-origin effects; X-chromosome models. Testing and measuring gene-environment interactions (GxE). Post-processing of results, regional association plots, assessing haplotype blocks, control for multiple testing, False Discovery Rate (FDR), q-values.
The course will use freely available software, including PLINK, GenABEL (in R), HapMap/HaploView, and Haplin (in R).
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