Infinium humanhap550 chip

Genome-wide genotyping in the Framingham Offspring cohort was performed on the AffymetrixGeneChip Human Mapping 500k Array Set and the 50K Human Gene Focused Panel. The genotyping of the KORA sample was performed with the Affymetrix Human Mapping 500k Array 2 chip set (Sty I and NSP I). Genotypes were imputed in both samples to the HapMap CEU panel using MACH algorithm. Genotyping in the GHS I and GHS II was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 (http://www.affymetrix.com), as described by the Affymetrix user manual.
The individual studies included in the stroke population of the CHARGE consortium had finalized their genome-wide association scans before forming the consortium. In the ARIC study, genotyping was performed with the GeneChip SNP Array 6.0 (Affymetrix); in the Cardiovascular Health Study, the HumanCNV370-Duo (Illumina) was used and in the Rotterdam Study, version 3.0 of the Infinium HumanHap550 chip (Illumina) was used.
In the Leeds stroke cohort we used a fluorescence-based assay (Applied Biosystems) to directly genotype the SNPs reaching genome-wide significance in the discovery analysis for SDMA. Genotyping in the HVH study was performed using the Illumina 370CNV BeadChip system.
Filtering and imputation methods are detailed in the Supplemental Information File Section 2.