1. 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

2. 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.

3. 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

4. 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

5. 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
neg
neg/weak
weak/positive
pos
n/a
FL_7
1-2
II A
FL_10
FL_2 3a
FL_3
FL_9
I A
FL_11
FL_8 3A
II-III A, staging not complete
FL_4
FL_5
negative
Relapse
Initial III A, Relapse: IIIa
FL_1
weak/neg
Initial III B, Relapse: II A