Assessing the Genotyping Quality of Different SNP-Chips and Imputed Data Using Family-Data

Genotyping quality is one of the key properties that defines the success chances of any genome-wide association studies. Data cleaning of the genotype data is therefore an important part of the statistical analysis. With family-data the genotype quality of each study subject can be assessed globally, using genome-wide family-based association test. We applied the approach to different, commonly used SNP-Chips and imputed data and assessed the genotype quality of all study subjects. Based on the two pairs of datasets available, we observed that the overall data quality varies greatly with the SNP-Chips used and the Minor Allele Frequency (MAF) is a more influential factor comparing to other Quality-Control (QC) filtering parameters, especially for certain SNP-Chips.