Table 1.
Information on 30 mutation features
| Mutationa | avsnp150b | Gene.refGenec | weightsd | Sample Number in LCC(%)e | Sample Number in RCC_(%)f | P valueg |
|---|---|---|---|---|---|---|
| chr7_140753336_140753336_A_T | rs113488022 | BRAF | 0.12 | 2 (1.8) | 35 (20.5) | 4.72E-15 |
| chr12_25245347_25245347_C_T | rs112445441 | KRAS | 0.09 | 5 (4.5) | 20 (11.7) | 4.07E-08 |
| chr5_112839942_112839942_C_T | rs121913332 | APC | 0.09 | 1 (0.9) | 18 (10.5) | 2.93E-07 |
| chr12_25245350_25245350_C_G | rs121913529 | KRAS | 0.09 | 1 (0.9) | 6 (3.5) | 0.02 |
| chr12_25245350_25245350_C_T | rs121913529 | KRAS | 0.07 | 8 (7.1) | 26 (15.2) | 8.74E-11 |
| chr17_7674220_7674220_C_T | rs11540652 | TP53 | 0.06 | 10 (8.9) | 2 (1.2) | 0.56 |
| chr7_135929761_135929762_AT_A | . | LUZP6;MTPN | 0.06 | 4 (3.6) | 2 (1.2) | 0.56 |
| chr3_179234297_179234297_A_G | rs121913279 | PIK3CA | 0.05 | 5 (4.5) | 7 (4.1) | 0.01 |
| chr12_25245350_25245350_C_A | rs121913529 | KRAS | 0.04 | 11 (9.8) | 13 (7.6) | 3.46E-05 |
| chr3_179218294_179218294_G_A | rs121913273 | PIK3CA | 0.04 | 4 (3.6) | 5 (2.9) | 0.04 |
| chr12_25225628_25225628_C_T | rs121913527 | KRAS | 0.03 | 2 (1.8) | 6 (3.5) | 0.02 |
| chr5_112780895_112780895_C_T | rs587781392 | APC | 0.03 | 4 (3.6) | 4 (2.3) | 0.08 |
| chr5_78039082_78039083_GT_G | . | AP3B1 | 0.03 | 2 (1.8) | 10 (5.8) | 5.37E-4 |
| chr15_23567535_23567536_CT_C | . | MKRN3 | 0.02 | 1 (0.9) | 15 (8.8) | 5.29E-06 |
| chr17_7673802_7673802_C_T | rs28934576 | TP53 | 0.02 | 5 (4.5) | 6 (3.5) | 0.02 |
| chr3_46375665_46375666_TG_T | rs939905165 | LOC102724297 | 0.02 | 0 (0) | 15 (8.8) | 5.29E-06 |
| chr1_244056271_244056272_GA_G | rs972665297 | ZBTB18 | 0.02 | 2 (1.8) | 17 (9.9) | 7.77E-07 |
| chr7_1747914_1747915_TA_T | . | ELFN1 | 0.02 | 2 (1.8) | 8 (4.7) | 3.08E-3 |
| chr12_109581434_109581435_GC_G | . | MVK | 0.02 | 0 (0) | 11 (6.4) | 2.16E-4 |
| chr4_105242265_105242266_CT_C | . | TET2-AS1 | 0.02 | 1 (0.9) | 8 (4.7) | 3.08E-3 |
| chr8_13568071_13568072_CT_C | rs1014242184 | C8orf48 | 0.01 | 1 (0.9) | 14 (8.2) | 1.36E-05 |
| chr17_58357799_58357800_AC_A | rs781215815 | RNF43 | 0.01 | 0 (0) | 17 (9.9) | 7.77E-07 |
| chr2_68464196_68464197_AT_A | . | FBXO48 | 0.01 | 0 (0) | 9 (5.3) | 1.29E-3 |
| chr4_154609909_154609910_GT_G | . | FGG | 0.01 | 0 (0) | 10 (5.8) | 5.32E-4 |
| chr17_7675088_7675088_C_T | rs28934578 | TP53 | 0.01 | 10 (8.9) | 13 (7.6) | 3.46E-05 |
| chr2_147926116_147926117_TA_T | rs764719749 | ACVR2A | 0.01 | 1 (0.9) | 11 (6.4) | 2.16E-4 |
| chr5_112838220_112838220_C_T | rs121913333 | APC | 0.01 | 3 (2.7) | 7 (4.1) | 7.22E-3 |
| chr13_108232109_108232110_CA_C | rs977361714 | ABHD13 | 0.003 | 1 (0.9) | 9 (5.3) | 1.29E-3 |
| chr4_44698597_44698598_GA_G | . | GUF1 | 0.003 | 1 (0.9) | 11 (6.4) | 2.16E-4 |
| chr6_98837428_98837429_CT_C | rs898072886 | POU3F2 | 0.003 | 1 (0.9) | 10 (5.8) | 5.32E-4 |
aPosition of variants. For example, chr7_140753336_140753336_A_T represents base A being replaced by T at position 140,753,336 of chromosome 7
bThe annotation of variants with dbSNP identifiers by ANNOVAR
cThe annotated genes of the variants by ANNOVAR
dThe weights (importance) of the mutation features for the classification model
eThe number of samples (percent of samples) with the variants among LCC samples
fThe number of samples (percent of samples) with the variants among RCC samples
gThe P-value from Fisher’s exact test for each variant