Figure 3

Performance evaluation of DEEPER-Library. (A) Incorporation ratios of single stranded DNA in DEEPER-Library pipeline. The fractions of DNA molecules that were incorporated into DEEPER-Library construction from different amounts of starting DNA (500 ng, 20 ng, 1 ng, 100 pg, 20 pg and 10 pg genomic DNA) were plotted. Ratios were measured by Qubit® ssDNA Assay Kit on a Qubit unit (ThermoFisher Scientific). (B) Genomic locations of 298 cancer related genes on human chromosomes (indicated by red arrows). (C) Six ΔC t values for each of the 298 genes were calculated by real-time PCR assays detecting gene abundance difference between 500 ng original genomic DNA input and 500 ng DEEPER-Library final products created from six different amounts (500 ng, 20 ng, 1 ng, 100 pg, 20 pg and 10 pg) of input genomic DNA. The 298 genes were ranked by the GC% of their amplicons and gene names were shown on the x-axis from low GC% (left) to high GC% (right).