Fig. 4: Sequencing depth and tumor purity requirements for IgCaller. | Nature Communications

Fig. 4: Sequencing depth and tumor purity requirements for IgCaller.

From: IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms

Fig. 4

a Sensitivity of IgCaller to detect a complete and productive IGH or IGK/L rearrangement at different ranges of coverage for CLL and MCL cases. b Downsampling experiment with 29 tumor samples. The sensitivity of IgCaller is shown for each specific mean coverage analyzed. c Identity for IGH (top) and IGK/L (bottom) gene rearrangements for each case at different downsampling conditions. d Sensitivity of IgCaller at distinct tumor cell contents after mixing tumor/normal (T/N) pairs at different ratios. The mean depth was set to 30×. e Similar to d but with a mean depth of 60×. Note that only purities of 50%, 35%, 20%, and 5% were analyzed. f Ig gene identity according to tumor cell content in different T/N mixing conditions. g Sensitivity of IgCaller when tumor samples are mixed with a polyclonal-like population. h Oligoclonal situation created in silico by mixing at different ratios two tumor samples carrying two IGH rearrangements each; one productive (Prod.) and one unproductive (Unprod.). The score of each rearrangement according to IgCaller is shown. A score of 0 is used for illustrative purposes for rearrangements not identified in a specific mixing condition. The score is calculated based on the number of reads supporting each rearrangement (“Methods”). Source data are provided as a Source data file.

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