GENE 3200 Lecture Notes - Lecture 1: Quantitative Trait Locus, Linkage Disequilibrium, Allele Frequency
Document Summary
Genome-wide association studies (gwas: gwas uses indirect associations- gene mapping method based on population. This is a way to do qtl mapping without doing a testcross. You can get differences in allele frequencies by: gwas scans the entire genome for associations, create associations and then break them up via recombination"s. Id significant snps- these differ in allele frequency between groups. If there is no association, you don"t expect a difference. There is lots of recombination: casual genes- depending on what allele you have, you will either get the disease or not. Indirect association with snp- very close association but doesn"t cause the phenotype. The allele is still associated with the phenotype it just does not cause it: not causal gene, this is due to linkage disequilibrium. Gwas: why do non-causal markers associate with phenotypes: linkage disequlibrium (ld)- alleles of closely linked genetic markers tend to display it. How does ld arise: closer sites/loci show higher levels of association.
