Figure 2

The use of standards demonstrates the semi-quantitative range of ligation-mediated PCR to detect transposon insertions in a complex sample. (A) A set of 10 plasmid standards were added to eight DNA samples from SB-induced tumors. These tumors were generated using either a high-copy (HC1-4) [5] or low-copy (LC1-4) transposon donor [8]. The standards were split into three groups and spiked into each tumor DNA sample to mimic insertion events present in 1 copy per cell (1X), 0.5 copies per cell (0.5X), or 0.125 copies per cell (0.125X). The maximum read value obtained for each standard was then expressed as a percentage of the most abundant standard identified in each sample. The indicated values represent the average value for each standard obtained from three independent sequence runs for each sample. (B) Insertion sites in each sample were grouped according to the normalized read value (% of maximum signal). The false discovery rate was estimated for each group of insertions (see Methods).