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Title: Population-wide linkage disequilibrium and its uses in QTL mapping and estimation of ancestral population size
Author: Tenesa-Prunyonosa, Albert
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2003
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The extent of LD was studied in two population, a dairy cattle population from the United Kingdom (UK) and a human isolated Sardinian population. For the dairy cattle population, data from 50 young bulls were available. These bulls were typed at 6 markers on chromosome 2 and 7 markers on chromosome 6, spanning 38 and 20 cM, respectively. LD extended to about 10 cM between pairs of loci in syntenic groups. Given the observed level of LD, mapping methods based upon population-wide association might provide better resolution than linkage methods in the UK dairy cattle population, as well as reduce the required sample sizes of the experiments. For the human population, 381 individuals typed at 22 markers on chromosome 19 were studied. High levels of disequilibrium were found that extended to 8 cM, when based on the LD measure D’, and 11 cM when based on the significance level of the allelic association. It was also shown, using bootstrapping, that small sample sizes can overestimate both the mean value of D’ and its variance by up to factors of about 3 and 23, respectively, when the sample size decreases from 381 to 25 individuals. Due to the high sampling variance of LD measures, the use of at least 200 unrelated individuals when characterizing the extent of LD is recommended. Three different strategies and study designs to map quantitative trait loci (QTL) using LD were studied using analytical methods and computer simulation. Finally, published data from human chromosomes 22 and 19 was used to infer past effective population size in a population of European ancestry. To do so, the extent of LD was first estimated using a multilocus measure of LD, the chromosome segment homozygosity (CSH). Results suggest that this population has had an average effective population size of around 4500 breeding individuals for approximately the last 4500 generations. This population had a relatively constant size (of between 3000 and 5000 individuals) from about 130000 years ago to about 2000 years ago, when it expanded to more than 10000 individuals.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available