Imputation aided analysis of the association between autoimmune diseases and the MHC

Thesis

The Major Histocompatibility Complex (MHC) is a genomic region in chromosome 6 which has been consistently found to be associated with the risk of developing virtually all common autoimmune diseases. Although its importance in disease pathogenesis has been known for decades, efforts to disentangle the roles of the classical human leukocyte antigens (HLA) and other variants responsible for the susceptibility to disease have often met with limited success, owing to the complex structure and extreme heterogeneity of the region.

In this thesis, I interrogate the MHC for association with three common autoimmune diseases, ankylosing spondylitis, psoriasis and multiple sclerosis, with the aim of confirming the previously-reported associations and of identifying novel ones. To do so, I employ a systematic, joint analysis of single nucleotide polymorphism (SNP) and HLA allele data, in a logistic regression framework, using a recently developed algorithm to predict the HLA alleles for samples where such information is unavailable. To ensure the reliability of the analysis, I apply stringent quality control procedures and integrate over the uncertainty of the HLA allele predictions. Moreover, I resolve the haplotype phase of individuals from the HapMap project to create reliable reference panels, used in both HLA prediction and in quality control procedures.

By directly testing HLA subtypes for association with the disease, the power to detect such associations is increased. I present the results of the analysis on the three disease phenotypes and discuss the evidence for important novel findings amongst both SNPs and HLA alleles in two of the diseases.

In the final part of this thesis, I introduce a novel, model-based approach to detect inconsistencies in the data and show how it can be used to flag problematic SNPs which conventional quality control procedures may fail to identify.

Authors: Moutsianas, L

• Publication date: 2011
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: Oxford University, UK
• Language: English
• Keywords: multiple sclerosis; HLA; Li & Stephens model; ankylosing spondylitis; association studies; autoimmune diseases; statistical genetics; psoriasis; GWAS; MHC
• Subjects: Genetics (life sciences); Multiple Sclerosis; Mathematical genetics and bioinformatics (statistics)