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Analysis Name and Accession
Name: Tier1 Genome Association of Parkinson's Disease Using Discordant Sib-Pairs
Accession: pha002840.1

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Analysis Description
This genome-wide association scan (tier 1) between genotype and the Parkinson 's disease status was computed by the dbGaP group at NCBI. Samples were 443 sibling pairs that were discordant for Parkinson disease. They had been recruited from the clinical practice of the Department of Neurology of the Mayo Clinic in Rochester, MN, between June 1996 through May 2004. Genotype data were provided by Drs. Maraganore and Rocca using Perlegen DNA chip (85k SNP markers) and three chips per individual.
Analysis Methods
The statistical procedure used follows that of the original publication ( Drs. Maraganore et al., 2005 ). To compare the minor allele frequency of a specific SNP marker between affected and unaffected offspring, we performed a sibling transmission/disequilibrium test (S-TDT) using plink v1.00, which is being developed by Shaun Purcell's group ( reference ). Only SNP markers in autosomal regions were involved in computation. The resulting p-values were not adjusted to account for multiple testing as part of this method. SNP makers were removed if their minor allele frequencies were less than 1% and genotype call rates below 90%. No SNP markers were filtered out based on deviation from (HWE) expectation.
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