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Fig. 3 | Genome Medicine

Fig. 3

From: A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing

Fig. 3

cisCton calls. a Log ratio values and segmentation in negative control data for an FFPE sample. Red and blue regions indicate regions called as amplifications and deletions, respectively, despite the data being negative control data. b Normalized numbers of regions called as amplified or deleted out of the target capture regions in the negative control data of two FFPE samples. The normalization was based on target region size (477 k bp) for possible comparison with other gene panels with different sizes. No calls are expected in these negative control data. c Violin plots to show the sizes of consecutive regions in panel b. d Isolated calls, i.e., regions called by each tool, and those not called by the given tool but called by all the other tools, for 75 FFPE samples. The normalization was based on the target region size (477 k bp). e Numbers of SC-FPs and SC-FNs confirmed by qPCR for 65 calls randomly selected from the datasets in panel c. The sample size (n) is indicated below the x-axis

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