Copy Number Variation and Relevance to Disease of the Complement C3b/C4b Receptor 1 (CR1) Gene

The complement 3b/4b receptor 1 (CR1) gene is located at chromosome 1q32.2 in a cluster of complement-related genes. CR1 regulates both classical and alternative pathways of the complement system. CR1 is a major receptor for Plasmodium falciparum, and variation within the gene has been associated with different malarial clinical phenotypes. CR1 shows intragenic copy number variation (CNV) resulting in variation in protein length and number of C3b/C4b binding domains. Previously, CR1 was related to Alzheimer’s disease (AD) via complement system regulation. Furthermore, CR1 variation is responsible for the alleles of the Knops blood group, including McCoy and Swain-Langley. In this thesis, Novel paralogue ratio test (PRT) assays were developed to robustly type CNV of the low-copy repeat (LCR) regions (which defines the common CR1-A and CR1-B alleles, but also rarer alleles) within the gene in large cohorts, and an allele-specific hybridisation assay to genotype alleles of the Knops blood group system. Variation was analysed across global populations, and in the Tori-Bossito cohort (563 infants) from Benin, followed since birth to observe malaria acquisition and treatment. This showed that the Swain-Langley Sl2 polymorphism is not in strong linkage disequilibrium (LD) with the CNV, nor with other Knops blood group alleles. It appears to provide protection against early acquisition of malaria and subsequent number of malarial infections in the Tori-Bossito cohort but these results were not confirmed in an independent cohort (n=276). The association between the CR1-B allele and AD (early-onset (EOAD) and late-onset (LOAD)) was explored, showing that the CR1 risk loci (rs3818361, rs6656401 (only for EOAD) and rs6701713) were in moderate LD with CR1-B, but revealing no association between CR1-B (p=0.755) and EOAD (n=633). However, the CR1-B allele (risk) appears to be associated with LOAD (n=2185) with (p=0.015) and without (p=0.048) use of a junction fragment PCR assay.