Filtering for Biological Relevance S_Figure 1 String-Analysis depicting BCL2-association of genes mutated in t(14;18)-negative FL at low confidence. See also gene lists in S_Table 6b, S_Table 8 and Table 2 as well as BCL2-association results given in Table 3a-c, S_Table 11a-d and S_Table 12a+b. Selectively mutated in t(14;18)-negative FL recurrently and more frequently mutated in t(14;18)-negative FL n= 1.435 n= 88, without pipeline bias n= 23 BCL2 BCL2 BCL2 Filtering for Biological Relevance (e.g. bioinformatics predictors, literature) Validation by Sanger Sequencing

S_Figure 2 Heatmap with t(14;18)-negative and t(14;18)-positive FL depicting mutations in IGV-genes within the WES dataset. None of the mutations affecting a t(14;18)-negative FL led to an amino acid (AA)-exchange that resulted in an asparagin while ~21% of the mutations in t(14;18)-positive FL revealed an asparagin (see also Table 4). ?>?: exchange to any AA; ?>N: exchange to an asparagin. The occurence of mutations is highlighted in yellow. Exchanges to asparagin are highlighted in green. 1x: the exchange to asparagin was detected only for one of the detected mutations in the respective gene.

included in the KEGG-NFkB-pathway. SNVs were significantly enriched S_Figure 3 Comparison of the SNV-profile of FL with and without t(14;18) with regard to genes included in the KEGG-NFkB-pathway. SNVs were significantly enriched in t(14;18)-negative FL by a p-value of 0.01 or lower according to Fisher‘s exact test. p<0.01

S_Table 15 Comparison of the SNV-profiles of FL with and without t(14;18) with regard to genes differentially mutated between ABC and GCB DLBCL according to a previous publication. 56 Values are given in percent and are rounded up and down according to mathematical guidelines. Gene Signature ABC GCB PMBL T_NEG T_POS MYD88 28 10 23 4 cd79b 25 2 PIM1 33 8 11 CREBBP 6 31 38 61 EZH2 18 15 14 TNFRSF14 17 BCL2 1 24 46

S_Table 1 Clincal information as well as BCL2-breakpoint and BCL2-protein status of11 FL cases (10 t(14;18)-negative and 1 t(14;18)-positive) that were retrieved from the files of the Institute of Pathology in Würzburg. These cases were applied to whole exome sequencing.   Grade DOB BCL2_BAP BCL2_IHC_DAKO BCL2_IHC_E17 BCL2_IHC_final Note Clinical Stage FL_6 2 03.12.1955 neg neg/weak weak/positive pos n/a FL_7 1-2 10.05.1942 II A FL_10 26.03.1934 FL_2 3a 23.11.1922 FL_3 07.04.1928 FL_9 12.11.1960 I A FL_11 17.01.1958 FL_8 3A 28.03.1924 II-III A, staging not complete FL_4 09.10.1938 FL_5 26.01.1938 negative Relapse Initial III A, Relapse: IIIa FL_1 19.06.1928 weak/neg Initial III B, Relapse: II A