Computational protocol: Genome-wide meta-analysis of cerebral white matter hyperintensities in patients with stroke

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Protocol publication

[…] Genotyping of all cohorts was performed on commercially available arrays from Affymetrix (Santa Clara, CA) or Illumina (San Diego, CA) (table e-2). All cohorts performed extensive quality control steps prior to imputation, removing SNPs showing significant departure from Hardy-Weinberg equilibrium, high levels of missingness, or low minor allele frequency. Individuals were removed who did not segregate with Hapmap II European populations based on ancestry informative principal component analysis using EIGENSTRAT or multidimensional scaling in PLINK., Additionally, individuals showing cryptic relatedness or having high levels of missingness or heterozygosity were excluded. All datasets were imputed to 1000 Genomes integrated variant set (March 2012) using IMPUTE v2. […]

Pipeline specifications

Software tools PLINK, IMPUTE
Application GWAS
Organisms Homo sapiens
Diseases Stroke, Leukoencephalopathies, Cerebral Small Vessel Diseases
Chemicals Nucleotides