Objective To investigate the significance of D₂₆₀/D₂₃₀ ratio of NanoDrop detection in quality assay of DNA in genome wide association study (GWAS). Methods Blood samples from 1 494 patients with ankylosing spondylitis (AS) were collected and the DNA was extracted. The concentrations of DNA samples were detected by NanoDrop and PicoGreen methods. In first stage, 24 DNA samples with concentrations>50 ng/μL were detected by Omni ZhongHua-8 microarray. Among the samples, 16 cases of chip reaction were successful and 8 were failure, and then the ratios of D₂₆₀/D₂₈₀ and D₂₆₀/D₂₃₀ were compared between the two groups. In second stage, 1 122 DNA samples with a concentration greater than 50 ng/μL according to NanoDrop and PicoGreen tests were selected for PCR detection of house-keeping genes. Samples with successful PCR reaction were detected by Human Omni ZhongHua-8 microarray. The 1 122 samples are divided into two groups according to the results of PCR (successful and failure groups). Mann-Whitney U test was used to compare the ratio of D₂₆₀/D₂₃₀ between the two groups, and receiver operating characteristic (ROC) curve was used to evaluate the predictive efficiency of D₂₆₀/D₂₃₀ value in PCR results. Results In the first stage, there were no significant differences in D₂₆₀/D₂₃₀ values between DNA samples with successful chip reaction and failure chip reaction (P=0.444), while the D₂₆₀/D₂₃₀ value of the fomer samples was significantly lower than that of the latter (Z=-3.920, P<0.001). In the second stage, the success rate of genotyping of DNA samples with positive PCR results was 100%. There were significant differences in D₂₆₀/D₂₃₀ values between the DNA samples with positive and negative PCR results (Z=-5.983, P<0.01. The area under curve of D₂₆₀/D₂₃₀value predicting the PCR results was 0.727; the D₂₆₀/D₂₃₀ values of the best diagnostic point and the point of specificity 95% were 0.89 and 2.305, respectively. Conclusion In GWAS, when DNA sample has better concentration and D₂₆₀/D₂₈₀ value and has lower D₂₆₀/D₂₃₀ value, PCR test should be performed to ensure the quality of the samples; when D₂₆₀/D₂₃₀ value is higher than 2.305, the samples are pure enough for microarray detection and the PCR detection can be omitted.