Cross-Platform Quality Control

Genotyping error can be influential in the validity of the association results.
In order to estimate the size of this technical error we re-genotyped 20% of 
GWAS samples for 20 random SNPs. From a total of 3,160 genotypes, 25 (0.7%) 
were called as missing with Illumina BeadArray technology and 42 (1.3%) were 
called as missing in the Sequenom platform. In the remaining genotypes, we 
found only 11 (0.3%) to be discordant between platforms.