Statistical models for multilocus structures
Christopher E. Aston · ANU Open Research (Australian National University) · 1985
In this thesis methods are considered for analysing relationships between genetic systems, usually loci, in an organisms genome.In particular, the genome of the individuals are typed at several sites.Chapter 1 provides an introduction to and motivation for the areas covered in this thesis.The remaining chapters are divided into two parts.Part I, comprising chapters 2 and 3, deals with the analysis of multilocus data in population genetics, and in particular, plant genetics.Chapters 4, 5 and 6 form Part II which looks at the analysis of multilocus data in the context of medical studies.Summary measures of pairwise nonrandom allelic association are studied in chapter 2.An alternate form of an existing summary measure is proposed.The sampling properties of both these measures, and of tests for detecting nonrandom allelic association based on these measures, are studied using computer simulations.The application of log-linear model analysis to data on multiple sites is outlined in chapter 3. Frequently such data necessitate the construction of large sparse contingency tables.To accommodate these iv.large tables a modification of the usual test procedures utilised in log-linear model analysis is proposed.A stepwise procedure for detecting nonrandom allelic associations is described and applied to wild barley data.Turning to more medically orientated problems chapter 4 considers genotypic data for diploid organisms in which the constituent gametes are not identified.A composite link function is used to adapt log-linear model analysis to these data.Application to artificial data sets is used to justify this computationally more complex approach.In chapter 5 attention is turned to linkage analysis of family data where individuals have been typed for multiple markers/loci (usually referred to, in this context, as multipoint data).A multipoint linkage analysis is proposed and applied to artificial family data.Extensions of this multipoint linkage analysis and its role in general linkage analysis are discussed.The thesis concludes with chapter 6.This chapter describes the implementation of the multipoint linkage analysis given in chapter 5. Some of the results in chapter 5 have been published in Aston and Wilson (1985) and Aston (in press).A modified version of chapter 4 is to be published (Aston and Wilson: Log-linear model analysis of allelic associations).It is intended to submit the results of chapter 2 for publication in the near future.