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Dense Deposit Disease (DDD) causes chronic renal dysfunction which progresses to end-stage renal disease in about half of patients within 10 years of diagnosis. Deficiency of and mutations in complement Factor H (CFH) are associated with the development of DDD, suggesting that dysregulation of the alternative pathway (AP) of the complement cascade is important in disease pathophysiology. Patients with DDD are studied to determine whether specific allele variants of the genes of the alternative pathway of the complement system segregate preferentially with the DDD. We have screened coding and intronic regions of genes of the complement system in DDD cases and controls using PCR, restriction digest and bidirectional sequencing. We have been able to identify novel mutations, allele variants and haplotypes in several genes of the complement system which are associated with the DDD phenotype based on statistical analyses. Since we have identified several genes associated with DDD, we have determined possible gene-gene interactions using computational analyses. We have found a strong synergistic interaction between polymorphisms in CFH and C3. To ascertain if the associated allele variants had a functional impact in the complement activity of an individual, we have obtained blood samples from normal individuals and measured AP complement activity and genotyped CFH and C3 for these samples. Association between AP activity and genotypes is analyzed using statistical methods. Significant association of CFH and C3 variants with AP complement activity has been observed. We also have generated a mice deficient of CFH and Factor D (CFD). CFH deficient mice develop renal pathology similar to DDD in humans. Renal function and complement activity have been determined in the double knockout in comparison to CFH deficient and CFD deficient mice. Results have shown that absence of Factor D can inhibit complement activation in CFH mice. Our data imply that DDD is a complex genetic disease and that genes of the AP complement system contribute to level of complement activity and the pathogenesis of DDD. With this study, we hope to develop an effective diagnosis and treatment plan for DDD patients.