Figures & data
Table 1. Summary of results from the initial test application of the immunoglobulin recombination search algorithm applied to TCGA DLBL files: Unique recombinations detected.
Table 2. Summary of results from application of the immunoglobulin recombination search algorithm applied to TCGA WXS files: Unique recombinations detected.
Table 3. Summary of results from application of the immunoglobulin recombination search algorithm applied to Moffitt Cancer Center bladder cancer patient exomes: Unique recombinations detected.
Figure 1. Total number of productive and unproductive Ig recombinations detected for the indicated cancer datasets, with each data set represented by 100 barcodes. BRCA represents the largest number of Ig recombinations, but the only the comparison of BRCA and KIRP represents a statistical significance, with a p value < 0.02 (t-test).
Figure 2. Number of barcodes for the indicated datasets, out of a total of 100 barcodes each, representing either a productive or unproductive Ig gene recombination. BRCA represents the highest number, however, only the difference between BRCA and KIRP represents a statistically significant difference, with a p value < 0.044 (t-test).
Figure 3. Example immunoglobulin recombinations with V-, J-, and N-region nucleotides indicated. The recombinations indicated are taken from the Moffitt BLCA reads, , bottom 3 barcodes, in order in this figure as they appear in .
Table 4. Summary of results from application of the immunoglobulin recombination search algorithm applied to TCGA WXS files: Barcodes with immunoglobulin recombinations.
Table 5. Example IGH recombinations detected in TCGA WXS files. (All VJ usage in this table was verified using the web tool at https://www.ncbi.nlm.nih.gov/igblast/). Reads indicated by nucleotide number for TCGA samples to meet publication standards.
Table 6. Example IGK recombinations detected in TCGA WXS files.
Table 7. Example IGL recombinations detected in TCGA WXS files.