This proposal is aimed at continuing our ongoing efforts to identify and characterize novel AD genes involvedin presenilin-related pathways. AD candidate genes implicated in presenilin-related pathways will be derivedfrom three different 'pools': Pool 1. Positional candidate genes mapping to established AD genetic linkagepeaks, including UBQLN1, VPS26A, VPS35, VDAC1, VDAC2, NCSTN, PSEN1 and TFCP2; Pool 2.Candidate genes derived from systematic meta-analyses performed on ourAlzGene.org database, includingCHRNB2, DAPK1, SORCS1, SORL1, TNK1, HMGCS2, CH25H, and SOAT1; and 3. Novel AD candidategenes from our ongoing whole-genome association (WGA) screens of the NIMH AD family sample in which>1400 subjects from 457 uniformly ascertained and evaluated AD families have been genotyped using threedifferent Affymetrix genotyping arrays: 500K genomic single nucleotide polymorphisms (SNPs), 100Kgenomic SNPs, and 20K coding SNPS (cSNPs). Follow-up analyses of presenilin pathway-related ADcandidate genes will include genetic confirmation/replication testing, linkage disequilibrium analyses, andmutation identification. In collaboration with the other P01 projects and cores, we will also carry out biologicaland functional validation studies of specific candidate genes based on our genetic results.
In specific aim 1, genotyping of the NIMH sample will be completed for all genes in all three pools.
In specific aim 2, SNPsexhibiting genome-wide significance for family-based association with AD in the NIMH sample will besubjected to replication testing in four independent AD family samples: CAG (224 families; 505 subjects; AD:245), NIA (353 families; 1117 DNAs; AD: 815), NCRAD (369 families; 1266 DNAs: AD: 895), and NIMHAfrican American (24 families, 58 subjects; AD: 49). For genes exhibiting the strongest association with AD,we will carry out extensive linkage disequilibrium mapping of additional SNPs and re-sequencing in probandsand unaffected individuals of specific associated families for each locus.
In specific aim 3., we will performbioinformatic (in silico) analyses of AD candidate genes to identify which SNPs represent potentiallypathogenic gene mutations/variants for AD. Finally, in specific aim 4., we will collaborate with the other P01projects and cores to carry out biological validation and functional analyses of novel AD candidate genes,including effects of RNAi silencing and overexpression of wild-type and potentially pathogenicmutations/variants on presenilin function, e.g. APP trafficking/processing as well as A(3 and AICD generation,y-secretase activity, APP-PS1 interaction, and PS1 conformation. Lay Summary: The four known AD genes(APP, PSEN1, PSEN2, and APOE) are the subjects of the vast majority of current biological research on AD.Yet, these genes represent only ~30% of the genetic variance of AD. The goal of this project is identify theadditional AD genes implicated in presenilin-related biological pathways to increase our knowledge of thecauses of AD and the role of the presenilins in AD pathogenesis.
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