Table 1. List of candidate genes for adenocarcinoma, squamous cell carcinoma and small cell carcinoma identified by excess of missense or nonsense mutations.
| Histology | Gene | OBS missense | EXP missense | LOG(OBS/EXP)* | OBS nonsense | EXP nonsense | LOG(OBS/EXP)* |
|---|---|---|---|---|---|---|---|
| Adeno | TP53 | 145 | 1.88 | 5.62 | 24 | 0.16 | 5.14 |
| Adeno | KRAS | 165 | 1.34 | 5.14 | 0 | 0.14 | |
| Adeno | ARID1A | 14 | 19.2 | 2.46 | 13 | 1.43 | 4.56 |
| Adeno | RBM10 | 12 | 7.89 | 1.35 | 17 | 0.71 | 3.71 |
| Adeno | RB1 | 12 | 6.61 | 2.15 | 12 | 0.74 | 3.61 |
| Adeno | STK11 | 28 | 4.12 | 1.43 | 26 | 0.30 | 3.60 |
| Adeno | ENHO | 1 | 0.7 | 0.27 | 1 | 0.03 | 3.42 |
| Adeno | KRTAP19-2 | 1 | 0.43 | 0.68 | 2 | 0.06 | 3.36 |
| Adeno | KRTAP19-4 | 2 | 0.67 | 0.96 | 3 | 0.09 | 3.32 |
| Adeno | KRTAP6-2 | 10 | 0.57 | 3.25 | 0 | 0.07 | |
| Adeno | BRAF | 24 | 6.03 | 3.23 | 2 | 0.62 | 1.40 |
| Adeno | CD109 | 25 | 10.2 | 3.22 | 2 | 1.02 | 1.39 |
| Adeno | DEFB119 | 7 | 0.67 | 3.20 | 0 | 0.06 | |
| Adeno | BICRA | 8 | 15.6 | 0.77 | 4 | 0.70 | 3.18 |
| Adeno | FXYD7 | 1 | 0.68 | 0.43 | 1 | 0.03 | 3.16 |
| Adeno | ARID1B | 23 | 21.41 | 3.16 | 3 | 1.63 | 2.55 |
| Adeno | GNG13 | 6 | 0.55 | 3.14 | 0 | 0.06 | |
| Adeno | RPS29 | 1 | 0.58 | 0.64 | 1 | 0.03 | 3.14 |
| Adeno | HSPA12A | 16 | 5.91 | 3.12 | 1 | 0.47 | 1.21 |
| Adeno | URGCP-MRPS24 | 2 | 1.08 | 0.67 | 3 | 0.11 | 3.10 |
| Adeno | DMXL1 | 27 | 21.7 | 3.09 | 4 | 2.19 | 2.08 |
| Adeno | DACT1 | 19 | 7.71 | 3.08 | 0 | 0.60 | |
| Adeno | ATP5F1E | 0 | 0.35 | 1 | 0.04 | 3.04 | |
| Adeno | ADGRB1 | 18 | 15.8 | 3.04 | 1 | 1.05 | 1.52 |
| Adeno | CHST9 | 5 | 0.52 | 3.03 | 0 | 0.06 | |
| Adeno | SATB2 | 19 | 6.25 | 3.01 | 3 | 0.55 | 2.35 |
| Squamous | CDKN2A | 34 | 2.05 | 3.13 | 27 | 0.09 | 5.79 |
| Squamous | TP53 | 233 | 1.97 | 5.13 | 33 | 0.16 | 4.59 |
| Squamous | RASA1 | 12 | 10.05 | 2.20 | 9 | 0.87 | 3.67 |
| Squamous | SPANXN1 | 9 | 0.65 | 3.60 | 1 | 0.08 | 2.07 |
| Squamous | HLA-A | 7 | 4.26 | 1.86 | 5 | 0.30 | 3.55 |
| Squamous | DEFB110 | 4 | 0.56 | 2.72 | 2 | 0.06 | 3.46 |
| Squamous | DEFB106A | 1 | 0.55 | 0.90 | 1 | 0.03 | 3.43 |
| Squamous | KCNN2 | 24 | 5.85 | 3.39 | 1 | 0.41 | 1.26 |
| Squamous | SLC35G3 | 4 | 3.41 | 1.21 | 3 | 0.18 | 3.37 |
| Squamous | NEFM | 24 | 9.55 | 3.37 | 2 | 1.12 | 1.46 |
| Squamous | LCE3D | 4 | 1.05 | 1.89 | 2 | 0.06 | 3.35 |
| Squamous | BICRA | 3 | 18.11 | 1.11 | 2 | 0.77 | 3.31 |
| Squamous | PASK | 20 | 13.91 | 3.25 | 0 | 1.08 | |
| Squamous | SEC61G | 2 | 0.61 | 1.69 | 1 | 0.03 | 3.23 |
| Squamous | KRTAP21-1 | 8 | 0.78 | 3.20 | 1 | 0.05 | 2.68 |
| Squamous | TSHZ2 | 21 | 10.31 | 3.17 | 3 | 0.86 | 2.45 |
| Squamous | CPAMD8 | 17 | 21.31 | 3.16 | 2 | 1.40 | 2.46 |
| Squamous | ARID1A | 14 | 22.9 | 1.72 | 8 | 1.60 | 3.09 |
| Squamous | KLB | 19 | 10.41 | 3.06 | 0 | 0.86 | |
| Squamous | FOXI2 | 2 | 3.93 | 0.41 | 2 | 0.19 | 3.06 |
| Squamous | CFH | 29 | 11.51 | 3.06 | 6 | 1.33 | 2.41 |
| Squamous | H3F3A | 1 | 1.51 | -0.40 | 2 | 0.08 | 3.05 |
| Squamous | TMPRSS9 | 15 | 11.91 | 3.04 | 2 | 0.76 | 2.56 |
| Squamous | ITGB4 | 16 | 20.62 | 3.02 | 0 | 1.31 | |
| Squamous | SAGE1 | 24 | 8.72 | 3.02 | 2 | 0.62 | 1.81 |
| Squamous | RPL39L | 0 | 0.48 | 1 | 0.04 | 3.02 | |
| Small cell | TP53 | 106 | 0.51 | 6.36 | 19 | 0.04 | 4.74 |
| Small cell | KIAA1211 | 31 | 3.14 | 3.92 | 1 | 0.29 | 0.39 |
| Small cell | SPHKAP | 34 | 3.69 | 3.88 | 1 | 0.31 | 0.37 |
| Small cell | MUC12 | 26 | 12.05 | 3.77 | 1 | 0.82 | 1.05 |
| Small cell | POLR2K | 3 | 0.11 | 3.60 | 0 | 0.01 | |
| Small cell | BLCAP | 0 | 0.19 | 2 | 0.01 | 3.43 | |
| Small cell | KLK8 | 2 | 0.08 | 3.41 | 0 | 0.01 | |
| Small cell | KRTAP23-1 | 3 | 0.13 | 3.33 | 0 | 0.01 | |
| Small cell | FAM47C | 22 | 2.62 | 3.33 | 1 | 0.19 | 0.52 |
| Small cell | OTOF | 19 | 5.07 | 3.30 | 1 | 0.35 | 0.84 |
| Small cell | ZNF208 | 28 | 2.43 | 3.27 | 4 | 0.33 | 1.02 |
| Small cell | NPAS3 | 17 | 2.47 | 3.19 | 0 | 0.16 | |
| Small cell | MYO16 | 17 | 4.28 | 3.15 | 1 | 0.33 | 0.70 |
| Small cell | CACNA1I | 15 | 5.79 | 3.14 | 0 | 0.32 | |
| Small cell | ALG10B | 5 | 0.27 | 3.12 | 0 | 0.02 | |
| Small cell | CD1E | 5 | 0.28 | 3.05 | 1 | 0.02 | 1.71 |
| Small cell | PCDHA3 | 14 | 2.38 | 3.03 | 1 | 0.16 | 0.88 |
| Small cell | HMCN1 | 18 | 11.98 | 3.02 | 3 | 0.97 | 1.89 |
*The LOG ratios of the observed to the expected numbers of mutations are adjusted for the excess of silent mutations.