Craig E. Pennell, Felipe Vadillo-Ortega, David M. Olson, Eun-Hee Ha, Scott Williams, Tim M. Frayling, Siobhan Dolan, Michael Katz, Mario Merialdi, Preterm Birth Genome Project (PGP) Consortium, Ramkumar Menon
August 18, 2012
We determined a series of quality control (QC) analyses to assess the usability of DNA collected and processed from different countries utilizing different DNA extraction techniques prior to genome-wide association studies (GWAS). The quality of DNA collected utilizing four different DNA extraction techniques and the impact of shipping DNA at different temperatures on array performance were evaluated. Fifteen maternal-fetal pairs were used from four countries. DNA was extracted using four approaches: whole blood, blood spots with whole genome amplification (WGA), saliva and buccal swab. Samples were sent to a genotyping facility, either on dry ice or at room temperature and genotyped using Affymetrix SNP array 6.0. QC measured included extraction techniques, effect of shipping temperatures, accuracy and Mendelian concordance. Significantly fewer (50%) single nucleotide polymorphisms (SNPs) passed QC metrics for buccal swab DNA (P<0.0001) due to missing genotype data (P<0.0001). Whole blood or saliva DNA had the highest call rates (99.2 0.4% and 99.3 0.2%, respectively) and Mendelian concordance. Shipment temperature had no effect. DNA from blood or saliva had the highest call rate accuracy, and buccal swabs had the lowest. DNA extracted from blood, saliva and blood spots were found suitable for GWAS in our study.