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Analysis Name and Accession

Note: This analysis was released as part of the study entitled NINDS- Genome-Wide Genotyping in Parkinson's Disease

Name: Genome-wide Association of Parkinson Disease in Samples Sharing Common Caucasian Ancestry
Accession: pha002868.1

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Analysis Description
This analysis is for stage I of a designed two-stage GWAS. The genotyping was performed using HumanHap550 BeadChips (Illumina, Inc.). Following quality control filtering a final dataset of 463,185 SNPs was analyzed in 1,713 PD cases and 3,978 controls from the United States and Germany.

To assess the homogeneity of our cohort, pair-wise Identity by State distances were calculated using HapMap data as a reference. The results of these analyses reveal that our samples share common Caucasian ancestry. Power calculations showed that our sample had 80% power to detect variants conferring an odds ratio (OR) of 1.3 with an allele frequency of 10%. Each SNP was tested for association using a trend model.

The genotype data being made available within the dbGaP Study Accession phs000089.v3.p2, consist of cases and controls from the United States from the stage I analysis that are eligible for inclusion in dbGap. Samples for this study are available through Coriell under the NINDS Repository Collection.
Analysis Methods

All statistical analyses were performed using PLINK toolset.

Low quality genotyping: Samples with call rates below 95% were repeated using fresh DNA aliquots and if the call rate persisted below this level, the samples were excluded from the analysis. Low-quality genotyping led us to repeat 57 individual samples, of which 40 were ultimately excluded from the analysis, including 16 cases and 25 controls.

Gender ambiguity: Individuals with gender ambiguity were flagged based on heterozygosity on chromosome X genotypes (inbreeding coefficient [F] in this chromosome). A male call is made if F is more than 0.8 and a female call if F is less than 0.2. Samples with an ambiguous F score or discrepancies between genotyped and reported sex, were considered as problematic. These samples were analyzed by visual examination of log R ratio and B allele frequency metrics with the Illumina Genome Viewer (IGV) tool within BeadStudio to rule out whether this discrepancy was caused because of copy number variation or extended homozygosity in chromosome X. These analyses led to the exclusion of 15 samples, including 11 cases and 4 controls.

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