Quality requirements for genomic DNA preparations and storage conditions for a high-density oligonucleotide microarray.

High-density oligonucleotide microarrays are widely used in genome-wide association studies. The purpose of this study was to assess the influence of various factors during the preparation of DNA on genotype calling for the Affymetrix high-density oligonucleotide microarray 250K GeneChip. DNA was extracted from peripheral whole blood by solution-based and silica-membrane-based methods. Blood was stored at 4°C or 25°C for 4 or 24 h, followed by DNA extraction. To examine the effects of freeze-thaw cycles, blood and DNA were also subjected to 5 and 10 or 20 of freeze-thaw cycles, respectively. The suitability of variously DNA preparations for the array was assessed by the call rate resulting from genotyping. All DNA samples showed mean call rates of more than 0.99, which passed the quality criteria for genotyping (greater than 0.95). The results indicated that the solution-based method and the silica-membrane-based DNA extraction method could provide DNA of sufficient quality for genotyping. In addition, DNA quality suitable for high-density oligonucleotide microarrays is not strongly dependent on the preparation conditions under standard procedures.