(a)

1. (a) Figure A: Sanger Sequencing Validation of CRIPAK mutation and the relationship between CRIPAK and other known genes mutated in lymphoma. cDNA sequencing of additional 20 FL and 31 DLBCL tumor samples from Mayo were performed using Sanger sequencing techonology. (b) MetaCore regulatory network of CRIPAK and other FL/DLBCL genes. CRIPAK is located in the same regulatory network with 25 other FL/DLBCL genes where the distances between the genes are no more than one steps (nodes) away from each other. Only three previously implicated genes were not placed in the network: CD58, PCLO, and GNA13 (Supplement File S4). The legend of the node symbols was obtained from the MetaCore. (c) the proximity of CRIPAK to the other known genes mutated in FL/DLBCL is significantly non-random. The average pair-wise distance of the shortest paths between these genes (indicated by the vertical red line) was shorter than any of the 10,000 random samplings from the protein-protein interaction network database. 11/20 12/31 % of Tumor with CRIPAK Mutations (b) (c)

2. Patient 7 Patient 6 Patient 6 Patient 8 Patient 6 Patient 7 CBLAK7 MAP4->GNL3 TFG->GPR128 100 bp Ladder C17orf68NXN VCPIP1->MYBL1 LOC100132273->CCDC117 Figure B: RT-PCR validation of the detected fusion transcripts. The right most lane is the 100 bp ladder, and lanes 1-6 show the PCR product of the 6 validated fusions. The name of the fusion genes, and the corresponding case numbers are also displayed. For more details of the fusion, please refer to Supplement File S5 and the appendix