title: Association assessment of copy number polymorphism and risk of age-related macular degeneration.
abstract: OBJECTIVE
  We previously identified a genetic copy number polymorphism (CNP147) that was statistically associated with age-related macular degeneration (AMD) and that resides downstream of the complement factor H (CFH) gene. Factor H protein is polymorphic at amino acid 402, in which the resulting histidine containing moiety has been established to impart significant risk of AMD. We present a method to precisely determine the exact copy number of CNP147 and examine in more detail the association with AMD.
  
  
  METHODS
  Case-control study.
  
  
  METHODS
  A total of 421 Age-Related Eye Disease Study (AREDS) subjects, of whom approximately 35% were diagnosed with neovascular disease, 19% were diagnosed with geographic atrophy, 16% were diagnosed with both, 30% were diagnosed with large drusen, and 215 were controls.
  
  
  METHODS
  By using copy number assays available from Applied Biosystems Inc. (Carlsbad, CA), we examined 4 loci spanning CNP147 and neighboring CNP148 in an AREDS matched case-control sample set. We analyzed these data by copy number while controlling for 2 high-risk CFH variants, rs1061170 (Y402H) and rs1410996. We phased the high-risk CFH variants with CNP147 and analyzed haplotype frequencies in cases and controls. To further validate copy numbers, 6 Utah Centre D'etude du Polymorphism Humaine (CEPH) families were typed for CNP147, and the segregation was assessed.
  
  
  METHODS
  Increased or decreased risk of AMD from genetic loci.
  
  
  RESULTS
  Having fewer than 2 copies of CNP147 was associated with an estimated 43% reduction in odds of having AMD in this sample set (adjusted odds ratio [OR] = 0.57, P=0.006). CNP148 variation is rare in Caucasians and was not statistically significant. Common haplotypes reveal that the risk alleles for rs1061170 and rs1410996 most frequently segregate with higher copy numbers for CNP147, but not exclusively, and that 1 haplotype that carried a deletion of CNP147 was highly protective (OR = 0.25 P=1.3×10(-13)) when compared with the reference.
  
  
  CONCLUSIONS
  In this matched subset of AREDS subjects, after adjusting for 2 known risk variants in CFH, CNP147 deletion statistically associates with diminished risk for AMD.
  
  
  BACKGROUND
  The author(s) have no proprietary or commercial interest in any materials discussed in this article.
authors.affiliation: SAIC-Frederick, Inc, Frederick, Maryland, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Sawitzke
authors.forename: Kate M
authors.initials: KM
authors.lastname: Im
authors.forename: Brittany
authors.initials: B
authors.lastname: Kostiha
authors.forename: Michael
authors.initials: M
authors.lastname: Dean
authors.forename: Bert
authors.initials: B
authors.lastname: Gold
mesh_terms: D001798:Blood Proteins / Q000235:genetics*; D016022:Case-Control Studies; D003180:Complement C3b Inactivator Proteins / Q000235:genetics*; D017242:Complement Factor H / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D005500:Follow-Up Studies; D020022:Genetic Predisposition to Disease; D005838:Genotype; D057092:Geographic Atrophy / Q000175:diagnosis / Q000235:genetics; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D012307:Risk Factors; D057135:Wet Macular Degeneration / Q000175:diagnosis / Q000235:genetics*
chemical_list: D001798:Blood Proteins; C493495:CFH protein, human; C517621:CFHR1 protein, human; C105970:CFHR3 protein, human; D003180:Complement C3b Inactivator Proteins; D017242:Complement Factor H