Experimental design For sensitivity and efficiency

analysis, we tested each fungal genomic DNA in three 10-fold serial dilutions in triplicate reactions using the optimized 18S qPCR conditions as described above. Using the Ct-value results, we calculated FungiQuant’s reaction efficiency and correlation coefficient for each species tested. Limit of detection (LOD) validation Y27632 Experimental design To determine the LOD of FungiQuant for detecting low concentration fungal DNA, we analyzed no-template controls (i.e., molecular grade H2O), background control (i.e., 10 ng, 50ng, and 150ng human DNA), as well as three low concentration of fungal DNA: a) 1.8 copies, b) 5 copies, and c) 10 copies of fungal 18S rRNA gene. Each template was analyzed in 96 replicates in 10 μl and 5 μl reactions using conditions as described above. Data Analysis Experimental results using all templates were assessed for: a) the proportion of determined and undetermined values and b) the Ct-value distribution among those replicates with determined values. Using the specificity associated with the background controls, which provides the most likely source of contamination and signal noise, the probability of each triplicate results was calculated under the null hypothesis that

the sample contained no positive selleck kinase inhibitor target. The analysis was performed separately

Selleck Bortezomib for each reaction volume using an alpha level of 0.05 to determine results inconsistent with the null. Analysis using the Ct-value from samples with positive amplification was also performed using a non-parametric median test to determine if 1.8 copies, 5 copies, or 10 copies templates could be differentiated from the no-template and background controls. The Ct-value data was further assessed to determine if the average Ct-value is an appropriate estimate of the true Ct-value in low concentration samples for reporting and analysis. FungiQuant laboratory quantitative validation Experimental design We followed the Minimum Information for publication of Quantitative real-time PCR Experiments, or the MIQE guidelines, whenever applicable [31]. We performed additional Dynein tests to evaluate FungiQuant performance when background human DNA is present. We included seven template conditions: plasmid standards alone and plasmid standards with 0.5 ng, 1 ng, 5 ng, and 10 ng of human DNA per reaction in 10 μl reactions, as well as plasmid standards alone and plasmid standards with 1 ng human DNA in 5 μl reactions. For each condition assessed, we performed three qPCR runs to assess reproducibility. In each run, three replicate standard curves were tested across the 384-well plate to assess repeatability.