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Linkage studies have defined susceptibility regions for late‐onset Parkinson disease (PD) on chromosomes 1 and 2, but specific genetic variants have not been definitively identified. Here we report the results of a case‐control study to identify disease‐associated single nucleotide polymorphisms (SNPs) in these loci. In the initial phase of our study, we genotyped two putative functional SNPs in ubiquitin‐specific protease 24 (USP24), a biological candidate gene within the chromosome 1 linkage region, and scanned the chromosome 2 linkage peak with 43 SNPs in a sample set of 224 PD cases and 186 matched controls. Both USP24 SNPs were significantly associated with disease risk (p = 0.0037 for rs1165222:T>C, p.Thr195ILe, and p = 0.037 for rs13312:C>G, a SNP in the 3′‐untranslated region), and one marker, rs1048603:C>T, p.Arg1123Cys, in USP40 was significant from the chromosome 2 scan (p …