Supporting reads for the detected IGHV-IGHJ recombinations in six DLBCL Samples from TCGA.

<p>Subfigure A, B, C, D and E report respectively for Samples I, II, III, IV, V and VI on the number of supporting reads for the detected IGHV-IGHJ recombinations.</p

RPKM-like distance between the main clone and the other most supported clones having different gene segments and subgroups in the five MCL Samples.

<p>Subfigure A, B, C, D and E report respectively for Samples A, B, C, D, and E on the differences in terms of normalized read counts between the main clone detected in the sample and nearest clones characterised by different gene segments and subgroups.</p

Data relative to the main clones detected by VDJSeq-Solver tool in the five MCL Samples.

<p>In each line are reported, respectively for Samples A, B, C, D and E, the V, D and J gene segments involved in the main clone recombination, the relative V(D)J rearranged sequence, the number of mismatches identified in this sequence with respect to the PCR validated sequence and the percentage ratio between the number of mismatches and the sequence length.</p

VJ alleles individuation.

<p>In Figure are detailed the different activities, as well as inputs and outputs, executed during the VJ alleles research. With yellow ellipses are depicted respectively input and output data, with exception of the final result that is highlighted with a dark blue rectangle. With light blue boxes are represented the operations performed taking advantage of freely available tools and finally with light green rectangles those performed thanks to ad hoc developed programs.</p

Sample A main clone sequence analysis.

<p>In Subfigure A and B are respectively shown the main clone V(D)J sequence in absence and in presence of enzymatic processes. The blue nucleotides are those introduced by different enzymes, such as the TdT, in the VD and DJ junctions during the rearrangement, whereas the red ones those deleted. Subfigure C shows instead how the initially VDJ unmapped reads are aligned on the main clone sequence provided by VDJSeq-Solver tool.</p

V(D)J sequences retrieving.

<p>In Figure are represented two situations that might occur during the V(D)J main clone sequence creation: i) The two mates are partially overlapped in the D region (A); ii) the two mates are not overlapped in the D region (B). In green letters are represented the extensions in both 5’ and 3’ directions of the V, D and J gene segments previously identified as rearranged, in black characters the portions of the considered mates that have been mapped on the V, D or J gene segments of interest and in red characters the nucleotides, extracted from the considered mates, that have been assigned to the VD and DJ junctions.</p

D alleles individuation.

<p>In Figure are detailed all the activities executed during the D alleles research, as well as inputs and outputs. With yellow ellipses are depicted respectively input and output data, with exception of the final result that is highlighted with a dark blue rectangle. With light blue boxes are represented the operations performed taking advantage of freely available tools and finally with light green rectangles those performed thanks to ad hoc developed programs.</p

PCR and VDJSeq-Solver main clone sequences comparisons. Gene assignments for the PCR and the VDJSeq-Solver provided main clone sequences from five online tools.

<p>PCR and VDJSeq-Solver main clone sequences comparisons. Gene assignments for the PCR and the VDJSeq-Solver provided main clone sequences from five online tools.</p

Supporting reads for the IGHV-IGHJ recombinations detected in the five MCL Samples.

<p>Subfigure A, B, C, D and E report respectively for Samples A, B, C, D, and E on the number of supporting reads for the detected IGHV-IGHJ recombinations. To better highlight the monoclonality feature of the distribution, the results are reported in terms of subgroups instead of gene segments or alleles. The most scored recombinations are identified in each sample with a label.</p

VJ Encompassing Read definition.

<p>In Figure an example of encompassing VJ read is reported. An encompassing VJ read is detected if the two mates of a read are mapped totally or not respectively on a V and on a J gene segment. The number of encompassing reads supporting each recombination allows to sort the different rearrangements detected.</p