Technological and Biological Studies of Human Structural Variation

Extensive regions of copy number variation (CNV) located throughout the genome play a significant role in common disease. This thesis describes the study of a structural variation on chromosome 12p13.31, and its involvement in susceptibility to complex disease, specifically the autoimmune disorder rheumatoid arthritis (RA). Methods of studying CNV include oligo-array Comparative Genomic Hybridisation (oaCGH), for which we developed a relatively optimised protocol on an in-house customisable microarray platform. In parallel, studies of the 12p13.31 locus using PCR-based methods revealed a large novel tandem duplication. Using quantitative assays we detected copy number variation within this duplication which occurs at a frequency of ~4% in European populations. At least two distinct points of recombination have been identified, supporting our theory that CNV in this region initiated from NAHR between the two units of the tandem duplication. We assessed copy number of sequences within the tandem duplication in a Swedish RA cohort, and revealed that a low copy number within this region occurs at a significantly higher rate in control samples compared to cases (p=0.001, OR=2.3 (95% CI 1.4-3.9)), suggesting a protective role for this variant. This was replicated in a UK cohort (p=0.036, OR=1.90 (95% CI 0.93-3.82)). We believe that the size of this effect is as large as any previously reported impact of CNV on common disease. An association was also detected in a Swedish psoriasis cohort (p=0.013, OR=2.16 (95% CI 1.2-4.1)). Future investigations into the effect of CNV at 12p13.31 on gene and protein expression may provide an insight into mechanisms of RA susceptibility and development. Given the tendency for autoimmune disease loci to share susceptibility regions, as well as the biological importance of genes located with the tandem duplication, we consider it likely that this region may also play a role in other complex disorders.