Fig. 6. Analysis of 42 human skin samples for KSHV DNA.

(a) The true KSHV DNA concentration of 42 human skin samples (as determined by qPCR), grouped by LAMP result from TINY. Each sample was amplified in TINY twice. Samples with detectable levels of KSHV were those that amplified for both trials with threshold times < 24 minutes. One sample had mixed results for the two trials and was classified as uncertain. Samples reported as 0 copies/reaction by qPCR were below the qPCR limit of detection (shown by the dashed line: about 19 copies/reaction). (b) KSHV DNA quantification by qPCR and LAMP (in TINY) for the 33 detectable samples from (a). The mean from two independent experiments is plotted. Dashed line shows where the two assays match. r² is the ordinary coefficient of determination. (c) The order-of-magnitude difference in KSHV quantification between duplicates for each assay/system. Sample size is 33 patients for each box plot. Maximum whisker length is 1.5 times the interquartile range, and the median of each group is plotted and overlaid. Technical replicates were samples amplified twice on the same qPCR plate, while experimental replicates were samples amplified in different qPCR experiments. (d) A comparison of absorbance and fluorescence threshold times for the 33 detectable samples. LAMP quantification reported in (b) and throughout this manuscript was calculated using fluorescence threshold time. r² is the ordinary coefficient of determination.