The Importance Of260/230Ratio To DNA Quality Control In GWAS

BackgroundA genome-wide association study (GWAS) has been an important tool toidentify the causal variants with a certain disease. In our lab, we selected Infinium ofIllumina to genotyping in GWAS.In the results, the Call Rate is on behalf of theDetection rate of the DNA samples. To achieve good call rates and reliable data forthe following analysis, the quality control steps for DNA samples is really vital. As acommon protocol, we initially used NanoDrop and PicoGreen as the method forquality control But we often have some samples passing QC,while the Call Rates ofthose samples are lower than0.6,By reviewing the specification of these failedsamples in quality control process, in this study, we trying to find the threshold forQC test to get good genotyping call rates and test more samples with this criteria.MethodInitially, DNA samples with concentration greater than50ng/ul by PicoGreenfrom our laboratory stock were sent to PCR test. Some samples were chosen fromthe whole collection randomly for genotyping.All the samples were divided into two groups according to their PCRperformance. Then the receiver operating curve (Receiver operating characteristic,the ROC) analysis were used to evaluate the threshold of260/230which has thestrongest power to predict the PCR results and determine the best diagnostic point,the points of specificity90%,95%.Data was processed by the statistical softwareSPSS13.0.Result1. PCR results are completely consistent with the data quality of Illuminagenotyping.compared with the classic quantitative means of nucleic acids,PCRmethod offers more reliability to ensure the the success rate of genotyping.2. The ratio of260/230has enough power to predict the PCR results(AUC=0.727); the best diagnostic point and the points of specificity90%,95%were as follows:0.895(specificity0.61, sensitivity0.815),2.175(sensitivity0.21),2.305(sensitivity0.16).ConclusionsBased on this study, the ratio of260/230is correlated with the success ofgenotyping. For the samples which has lower ratio of260/230, PCR test should beperformed to ensure the good call rate of genotyping. A high degree of specificity (260/230=2.305, specificity:0.95), lower sensitivity (0.16) can avoid theunnecessary waste of genotyping chips, and improve the efficiency of the qualitycontrol.