Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (<i>CFH</i>) gene family.

Abstract

Structural variation and single-nucleotide variation of the complement factor H (<i>CFH</i>) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four <i>CFH</i>-related (<i>CFHR</i>) gene paralogs (<i>CFHR2</i> and <i>CFHR4</i> ∼25-35 Mya and <i>CFHR1</i> and <i>CFHR3</i> ∼7-13 Mya). Remarkably, all evolutionary breakpoints share a common ∼4.8-kbp segment corresponding to an ancestral <i>CFHR</i> gene promoter that has expanded independently throughout primate evolution. This segment is recurrently reused and juxtaposed with a donor duplication containing exons 8 and 9 from ancestral <i>CFH</i>, creating four <i>CFHR</i> fusion genes that include lineage-specific members of the gene family. Combined analysis of >5,000 AMD cases and controls identifies a significant burden of a rare missense mutation that clusters at the N terminus of <i>CFH</i> [<i>P</i> = 5.81 × 10^-8, odds ratio (OR) = 9.8 (3.67-Infinity)]. A bipolar clustering pattern of rare nonsynonymous mutations in patients with AMD (<i>P</i> < 10^-3) and AHUS (<i>P</i> = 0.0079) maps to functional domains that show evidence of positive selection during primate evolution. Our structural variation analysis in >2,400 individuals reveals five recurrent rearrangement breakpoints that show variable frequency among AMD cases and controls. These data suggest a dynamic and recurrent pattern of mutation critical to the emergence of new <i>CFHR</i> genes but also in the predisposition to complex human genetic disease phenotypes.