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Analysis Name and Accession
Name: Genome Wide Association Study in Familial Parkinson Disease
Accession: pha002865.1

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Analysis Description
Unlike previous studies that focused primarily on sporadic Parkinson disease (PD), we have performed the first genome-wide association study (GWAS) in familial PD. Genotyping was performed at the Center for Inherited Disease Research (CIDR) with the Illumina HumanCNV370Duo array in 857 familial PD cases and 867 controls. A logistic model was employed to test for association under additive and recessive modes of inheritance after adjusting for gender and age (age at evaluation for controls and onset for cases). PD cases were selected from two ongoing studies of familial PD: PROGENI and GenePD. On average, each PD participant had an additional 1.8 relatives who were reported to have PD. Only a single individual per family was genotyped ensuring sample independence. PD cases underwent a uniform neurological evaluation that employed PD diagnostic criteria based broadly on the United Kingdom PD Society Brain Bank criteria. Control samples (n = 895) were obtained from the NINDS Human Genetics Resource Center at the Coriell Institute Coriell Cell Repositories. Cases were excluded from analyses if they were known to harbor a causative mutation (i.e. two parkin mutations, one LRRK2 mutation, etc.).
Analysis Methods
PLINK was used to implement the logistic regression models (additive and recessive). Samples were removed based upon call rate (> 98%), DNA source (whole genome amplified samples removed) and self-declared ethnicity (only included Caucasian, non-Hispanic). Cryptic relatives, as well as those cases and controls that were outside the main Caucasian, non-Hispanic cluster when a principal components analysis was performed, were removed prior to final analyses. SNPs were filtered based on call rate (<98%), minor allele frequency (<0.01), differential call rates between cases and controls or males and females (p <1E-5), differential rates of heterozygosity between males and females (>0.10), deviation from Hardy-Weinberg equilibrium within the control sample (p <1E-6), and parent-parent-offspring Mendelian inconsistencies in HapMap controls (more than 1).
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Selected Publications