Details of confirmed novel gene mutations occurring in ≥2 cases in the 11 FL and 1 t-FL discovery-set NHL cases
| FL case no. . | Gene . | Nucleotide (genomic) NCBI 36 Hg 18 . | Amino acid change (protein) . | Sanger sequencing result (T/N) . | SNP array-based aCNA/LOH/aUPD . | PolyPhen-2 prediction results . | SIFT prediction results . | Next-gen sequencing % mutant tags . |
|---|---|---|---|---|---|---|---|---|
| ML2 | ARID1A | chr1_26970196-26970196_G_T | Splice site acceptor | Mut-Heter/WT | None | 44 | ||
| ML30 | ARID1A | chr1_26972534-26972534_C_T | 1276R/X | Mut-Heter/WT | None | 27 | ||
| ML47 | CHRM3 | chr1_238138618-238138618_A_G | 415D/G | Mut-Heter/WT | Gain | Benign (0) | Tolerated (0.38) | 39 |
| ML66 | CHRM3 | chr1_238138543-238138543_A_T | 390Q/L | Mut-Heter/WT | Gain | Benign (0.087) | Tolerated (0.31) | 26 |
| ML51 | DMRT3 | chr9_980911-980911_G_A | 442C/Y | Mut-Heter/WT | None | Probably damaging (0.999) | Damaging (0.02) | 31 |
| ML90 | DMRT3 | chr9_980691-980691_C_A | 369P/T | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 43 |
| ML30 | GRM7 | chr3_6878496-6878496_C_T | 141P/S | Mut-Heter/WT | None | Benign (0.245) | Tolerated (1.0) | 23 |
| ML42 | GRM7 | chr3_6878401-6878401_G_T | 109C/F | Mut-Heter/WT | None | Probable damaging (0.977) | Damaging (0.00) | 40 |
| ML47 | GRM7 | chr3_6878556-6878556_G_A | 161V/I | Mut-Heter/WT | None | Probable damaging (0.992) | Damaging (0.02) | 42 |
| ML47 | HIST1H1E | chr6_26264736-26264736_G_A | 47A/T | Mut-Heter/WT | Gain | Possibly damaging (0.597) | Tolerated (0.08) | 21 |
| ML90 | HIST1H1E | chr6_26264905-26264905_G_A | 103A/T | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 55 |
| ML90 | HIST1H1E | chr6_26264991-26264991_G_A | 132G/D | Mut-Heter/WT | None | Benign (0) | Tolerated (0.56) | 41 |
| ML55 | IRF8 | chr16_85954737_85954737_G_ | Frameshift deletion | Mut-Heter/WT | None | 56 | ||
| ML51 | IRF8 | chr16_85954790_85954790_G_T | 395E>X | Mut-Homo/WT | aUPD | 82 | ||
| ML51 | KLHDC7B | chr22_49334644-49334644_C_T | 296R/X | Mut-Heter/WT | None | 32 | ||
| ML55 | KLHDC7B | chr22_49333831-49333831_T_A | 25S/T | Mut-Heter/WT | None | Benign (0.004) | Tolerated (0.78) | 33 |
| ML55 | LYST | chr1_234017235-234017235_C_A | 1584E/X | Mut-Heter/WT | None | 57 | ||
| ML66 | LYST | chr1_234005012-234005012_A_ | Splice site acceptor | Mut-Heter/WT | Loss | 42 | ||
| ML47 | MCL1 | chr1_150551543_150551543_C_G | 155S/T | Mut-Heter/WT | None | Benign (0.001) | Tolerated (0.19) | 46 |
| ML90 | MCL1 | chr1_150551543_150551543_C_T | 155S/N | Mut-Heter/WT | Gain | Benign (0.0) | Tolerated (0.21) | 19 |
| ML55 | PCLO | chr7_82422909-82422909_G_T | 1766L/I | Mut-Heter/WT | None | Possibly damaging (0.617) | NA | 50 |
| ML66 | PCLO | chr7_82421122-82421122_A_T | 2361F/L | Mut-Heter/WT | None | Benign (0.0) | NA | 16 |
| ML47 | OCT2 | chr19_47291387-47291387_A_ | Frameshift deletion | Mut-Heter/WT | None | 45 | ||
| ML90 | OCT2 | chr19_47291598-47291598_C_T | 282R/H | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 51 |
| ML47 | TNFRSF14 | chr1_2484552-2484552_T_A | 88N>I | Mut-Homo/WT | aUPD | Probably damaging (1.000) | Damaging (0) | 100 |
| ML55 | TNFRSF14 | chr1_2483126-2483126_C_T | 112S>F | Mut-Homo/WT | aUPD | Probably damaging (1.000) | Damaging (0) | 92 |
| ML93 | TP53 | chr17_7518947-7518948_TC_ | Frameshift deletion | Mut-Homo/WT | Loss | 80 | ||
| ML79 | TP53 | chr17_7517845-7517845_C_T | 273R>H | Mut-Homo/WT | Loss | Possibly damaging (0.831) | Damaging (0.01) | 100 |
| ML66 | VPS39 | chr15_40287584-40287584_A_C | 20 C/W | Mut-Heter/WT | None | Probable damaging (0.977) | Damaging (0.01) | 52 |
| ML87 | VPS39 | chr15_40270618-40270618_A_T | 82 L>I | Mut-Homo/WT | aUPD | Possibly damaging (0.929) | Tolerated (0.38) | 87 |
| ML66 | WDR64 | chr1_240031064-240031066_GAA_ | In-frame deletion | Mut-Heter/WT | Gain | 19 | ||
| ML93 | WDR64 | chr1_239913455-239913455_G_A | 213C/Y | Mut-Heter/WT | None | Probably damaging (1.0) | Tolerated (0.07) | 42 |
| ML55 | ZNF541 | chr19_52736020-52736020_C_T | 802G/S | Mut-Heter/WT | None | Probable damaging (1.0) | Damaging (0.00) | 13 |
| ML66 | ZNF541 | chr19_52739383-52739383_G_ | Frameshift deletion | Mut-Heter/WT | None | 47 |
| FL case no. . | Gene . | Nucleotide (genomic) NCBI 36 Hg 18 . | Amino acid change (protein) . | Sanger sequencing result (T/N) . | SNP array-based aCNA/LOH/aUPD . | PolyPhen-2 prediction results . | SIFT prediction results . | Next-gen sequencing % mutant tags . |
|---|---|---|---|---|---|---|---|---|
| ML2 | ARID1A | chr1_26970196-26970196_G_T | Splice site acceptor | Mut-Heter/WT | None | 44 | ||
| ML30 | ARID1A | chr1_26972534-26972534_C_T | 1276R/X | Mut-Heter/WT | None | 27 | ||
| ML47 | CHRM3 | chr1_238138618-238138618_A_G | 415D/G | Mut-Heter/WT | Gain | Benign (0) | Tolerated (0.38) | 39 |
| ML66 | CHRM3 | chr1_238138543-238138543_A_T | 390Q/L | Mut-Heter/WT | Gain | Benign (0.087) | Tolerated (0.31) | 26 |
| ML51 | DMRT3 | chr9_980911-980911_G_A | 442C/Y | Mut-Heter/WT | None | Probably damaging (0.999) | Damaging (0.02) | 31 |
| ML90 | DMRT3 | chr9_980691-980691_C_A | 369P/T | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 43 |
| ML30 | GRM7 | chr3_6878496-6878496_C_T | 141P/S | Mut-Heter/WT | None | Benign (0.245) | Tolerated (1.0) | 23 |
| ML42 | GRM7 | chr3_6878401-6878401_G_T | 109C/F | Mut-Heter/WT | None | Probable damaging (0.977) | Damaging (0.00) | 40 |
| ML47 | GRM7 | chr3_6878556-6878556_G_A | 161V/I | Mut-Heter/WT | None | Probable damaging (0.992) | Damaging (0.02) | 42 |
| ML47 | HIST1H1E | chr6_26264736-26264736_G_A | 47A/T | Mut-Heter/WT | Gain | Possibly damaging (0.597) | Tolerated (0.08) | 21 |
| ML90 | HIST1H1E | chr6_26264905-26264905_G_A | 103A/T | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 55 |
| ML90 | HIST1H1E | chr6_26264991-26264991_G_A | 132G/D | Mut-Heter/WT | None | Benign (0) | Tolerated (0.56) | 41 |
| ML55 | IRF8 | chr16_85954737_85954737_G_ | Frameshift deletion | Mut-Heter/WT | None | 56 | ||
| ML51 | IRF8 | chr16_85954790_85954790_G_T | 395E>X | Mut-Homo/WT | aUPD | 82 | ||
| ML51 | KLHDC7B | chr22_49334644-49334644_C_T | 296R/X | Mut-Heter/WT | None | 32 | ||
| ML55 | KLHDC7B | chr22_49333831-49333831_T_A | 25S/T | Mut-Heter/WT | None | Benign (0.004) | Tolerated (0.78) | 33 |
| ML55 | LYST | chr1_234017235-234017235_C_A | 1584E/X | Mut-Heter/WT | None | 57 | ||
| ML66 | LYST | chr1_234005012-234005012_A_ | Splice site acceptor | Mut-Heter/WT | Loss | 42 | ||
| ML47 | MCL1 | chr1_150551543_150551543_C_G | 155S/T | Mut-Heter/WT | None | Benign (0.001) | Tolerated (0.19) | 46 |
| ML90 | MCL1 | chr1_150551543_150551543_C_T | 155S/N | Mut-Heter/WT | Gain | Benign (0.0) | Tolerated (0.21) | 19 |
| ML55 | PCLO | chr7_82422909-82422909_G_T | 1766L/I | Mut-Heter/WT | None | Possibly damaging (0.617) | NA | 50 |
| ML66 | PCLO | chr7_82421122-82421122_A_T | 2361F/L | Mut-Heter/WT | None | Benign (0.0) | NA | 16 |
| ML47 | OCT2 | chr19_47291387-47291387_A_ | Frameshift deletion | Mut-Heter/WT | None | 45 | ||
| ML90 | OCT2 | chr19_47291598-47291598_C_T | 282R/H | Mut-Heter/WT | None | Probably damaging (1.0) | Damaging (0) | 51 |
| ML47 | TNFRSF14 | chr1_2484552-2484552_T_A | 88N>I | Mut-Homo/WT | aUPD | Probably damaging (1.000) | Damaging (0) | 100 |
| ML55 | TNFRSF14 | chr1_2483126-2483126_C_T | 112S>F | Mut-Homo/WT | aUPD | Probably damaging (1.000) | Damaging (0) | 92 |
| ML93 | TP53 | chr17_7518947-7518948_TC_ | Frameshift deletion | Mut-Homo/WT | Loss | 80 | ||
| ML79 | TP53 | chr17_7517845-7517845_C_T | 273R>H | Mut-Homo/WT | Loss | Possibly damaging (0.831) | Damaging (0.01) | 100 |
| ML66 | VPS39 | chr15_40287584-40287584_A_C | 20 C/W | Mut-Heter/WT | None | Probable damaging (0.977) | Damaging (0.01) | 52 |
| ML87 | VPS39 | chr15_40270618-40270618_A_T | 82 L>I | Mut-Homo/WT | aUPD | Possibly damaging (0.929) | Tolerated (0.38) | 87 |
| ML66 | WDR64 | chr1_240031064-240031066_GAA_ | In-frame deletion | Mut-Heter/WT | Gain | 19 | ||
| ML93 | WDR64 | chr1_239913455-239913455_G_A | 213C/Y | Mut-Heter/WT | None | Probably damaging (1.0) | Tolerated (0.07) | 42 |
| ML55 | ZNF541 | chr19_52736020-52736020_C_T | 802G/S | Mut-Heter/WT | None | Probable damaging (1.0) | Damaging (0.00) | 13 |
| ML66 | ZNF541 | chr19_52739383-52739383_G_ | Frameshift deletion | Mut-Heter/WT | None | 47 |
T/N, tumor/normal; WT, wild-type.