title: Implication of common and disease specific variants in CLU, CR1, and PICALM.
abstract: Two recent genome-wide association studies (GWAS) for late onset Alzheimer's disease (LOAD) revealed 3 new genes: clusterin (CLU), phosphatidylinositol binding clathrin assembly protein (PICALM), and complement receptor 1 (CR1). In order to evaluate association with these genome-wide association study-identified genes and to isolate the variants contributing to the pathogenesis of LOAD, we genotyped the top single nucleotide polymorphisms (SNPs), rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), and sequenced the entire coding regions of these genes in our cohort of 342 LOAD patients and 277 control subjects. We confirmed the association of rs3851179 (PICALM) (p = 7.4 × 10(-3)) with the disease status. Through sequencing we identified 18 variants in CLU, 3 of which were found exclusively in patients; 8 variants (out of 65) in CR1 gene were only found in patients and the 16 variants identified in PICALM gene were present in both patients and controls. In silico analysis of the variants in PICALM did not predict any damaging effect on the protein. The haplotype analysis of the variants in each gene predicted a common haplotype when the 3 single nucleotide polymorphisms rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), respectively, were included. For each gene the haplotype structure and size differed between patients and controls. In conclusion, we confirmed association of CLU, CR1, and PICALM genes with the disease status in our cohort through identification of a number of disease-specific variants among patients through the sequencing of the coding region of these genes.
authors.affiliation: Laboratory of Neurogenetics, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Ferrari
authors.forename: Jorge H
authors.initials: JH
authors.lastname: Moreno
authors.forename: Abu T
authors.initials: AT
authors.lastname: Minhajuddin
authors.forename: Sid E
authors.initials: SE
authors.lastname: O'Bryant
authors.forename: Joan S
authors.initials: JS
authors.lastname: Reisch
authors.forename: Robert C
authors.initials: RC
authors.lastname: Barber
authors.forename: Parastoo
authors.initials: P
authors.lastname: Momeni
mesh_terms: D000368:Aged; D000544:Alzheimer Disease / Q000453:epidemiology* / Q000235:genetics*; D051152:Clusterin / Q000235:genetics*; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D006801:Humans; D008297:Male; D034041:Monomeric Clathrin Assembly Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015995:Prevalence; D017463:Receptors, Complement 3b / Q000235:genetics*; D012307:Risk Factors; D013781:Texas / Q000453:epidemiology
chemical_list: C495242:CLU protein, human; C509991:CR1 protein, human; D051152:Clusterin; D005819:Genetic Markers; D034041:Monomeric Clathrin Assembly Proteins; C439003:PICALM protein, human; D017463:Receptors, Complement 3b