Supplemental Table S2. Comprehensive List of Mutations Identified by Targeted Next-Generation
Supplemental Table S2. Comprehensive list of mutations identified by targeted next-generation sequencingwith detailed information.
Gene ID / Sample / Chrom / Genome Coordinates (GRCh38) / Mutation / Ref / Var / Freq / Quality / Allele Source / Cove-rage / Strand Bias / Common Signal Shift / Relative Read Quality / HP Length / Provean / SIFTAKT1 / 65 / chr14 / 104780189 / p.R25H / C / T / 13 / 91 / Novel / 183 / 0,6 / 0,1 / 298 / 1 / deleterious / damaging
BRAF / 37 / chr7 / 140781611 / p.G466E / C / T / 9 / 21 / Hotspot / 53 / 0,8 / 0,0 / 76 / 2 / deleterious / damaging
BRAF / 15 / chr7 / 140781624 / p.R462-70G / T / C / 5 / 17 / Novel / 225 / 0,6 / 0,1 / 69 / 3 / deleterious / damaging
BRAF / 56 / chr7 / 140781677 / p.R444-52Q / C / T / 5 / 20 / Novel / 642 / 0,5 / 0,0 / 243 / 3 / deleterious / damaging
CTNNB1 / 22 / chr3 / 41224587 / p.W25-18* / G / A / 8 / 21 / Novel / 92 / 0,6 / 0,1 / 96 / 2 / NA
CTNNB1 / 7 / chr3 / 41224589 / p.Q26-19R / A / G / 8 / 21 / Novel / 92 / 0,6 / 0,1 / 205 / 1 / deleterious / damaging
DDR2 / 59 / chr1 / 162759830 / p.V236M / G / A / 23 / 83 / Novel / 62 / 0,5 / 0,1 / 118 / 1 / neutral / damaging
DDR2 / 60 / chr1 / 162778641 / p.T782I / C / T / 8 / 18 / Novel / 64 / 0,8 / 0,0 / 371 / 2 / deleterious / tolerated
EGFR / 32 / chr7 / 55174029 / p.G724S / G / A / 9 / 67 / Hotspot / 321 / 0,5 / 0,0 / 157 / 2 / deleterious / damaging
EGFR / 65 / chr7 / 55181396 / p.G796D / G / A / 8 / 37 / Hotspot / 225 / 0,5 / 0,1 / 95 / 2 / deleterious / damaging
EGFR / 19 / chr7 / 55160296 / p.Q486-356-433-441-280* / C / T / 7 / 16 / Novel / 92 / 0,6 / 0,0 / 263 / 1 / NA
EGFR / 11 / chr7 / 55173976 / p.I706-576-653-661T / T / C / 7 / 23 / Novel / 168 / 0,6 / 0,0 / 266 / 1 / deleterious / damaging
EGFR / 59 / chr7 / 55173976 / p.I706-576-653-661T / T / C / 8 / 20 / Novel / 76 / 0,9 / 0,0 / 282 / 1 / deleterious / damaging
EGFR / 34 / chr7 / 55174806 / p.K757-627-704-712E / A / G / 11 / 49 / Novel / 126 / 0,5 / 0,0 / 328 / 2 / neutral / damaging
EGFR / 55 / chr7 / 55181372 / p.L788-658-735-743R / T / G / 6 / 29 / Novel / 266 / 0,5 / 0,1 / 255 / 1 / deleterious / damaging
EGFR / 58 / chr7 / 55181402 / p.L798-668-745-753P / T / C / 8 / 21 / Novel / 73 / 0,8 / 0,0 / 408 / 1 / deleterious / damaging
ERBB2 / 28 / chr17 / 39724772 / p.L785-755-509-770P / T / C / 8 / 16 / Novel / 53 / 0,7 / 0,1 / 66 / 2 / deleterious / damaging
ERBB2 / 28 / chr17 / 39725077 / p.L841-811-565-826P / T / C / 10 / 28 / Novel / 69 / 0,8 / 0,0 / 311 / 1 / deleterious / damaging
ERBB2 / 10 / chr17 / 39725124 / p.N857-827-581-842Y / A / T / 7 / 18 / Novel / 84 / 0,6 / 0,0 / 163 / 2 / deleterious / tolerated
ERBB2 / 57 / chr17 / 39725193 / p.D880-850-604-865N / G / A / 5 / 23 / Novel / 354 / 0,7 / 0,0 / 352 / 1 / deleterious / tolerated
ERBB4 / 18 / chr2 / 211665425 / p.V590A / A / G / 9 / 22 / Novel / 70 / 0,7 / 0,0 / 158 / 1 / deleterious / damaging
FBXW7 / 21 / chr4 / 152328233 / p.R385-465C / G / A / 9 / 89 / Hotspot / 444 / 0,5 / 0,0 / 287 / 1 / deleterious / damaging
FBXW7 / 50 / chr4 / 152326137 / p.R266-505-425C / G / A / 14 / 1274 / Hotspot / 2650 / 0,5 / 0,1 / 211 / 2 / deleterious / deleterious
FBXW7 / 52 / chr4 / 152326136 / p.R505H / C / T / 5 / 34 / Hotspot / 1333 / 0,5 / 0,0 / 112 / 1 / deleterious / damaging
FBXW7 / 39 / chr4 / 152324309 / p.L497-577-459-401S / A / G / 8 / 19 / Novel / 60 / 0,6 / 0,0 / 133 / 2 / deleterious / damaging
FBXW7 / 1 / chr4 / 152324312 / p.T496-576-458-400M / G / A / 7 / 15 / Novel / 55 / 0,6 / 0,0 / 166 / 1 / deleterious / damaging
FBXW7 / 22 / chr4 / 152324331 / p.T490-570-452-394A / T / C / 7 / 18 / Novel / 104 / 0,5 / 0,0 / 213 / 1 / deleterious / damaging
FBXW7 / 46 / chr4 / 152326130 / p.V427-507-389-331A / A / G / 10 / 22 / Novel / 50 / 0,7 / 0,0 / 274 / 2 / deleterious / damaging
FBXW7 / 57 / chr4 / 152328218 / p.H390-470-352-294Y / G / A / 7 / 30 / Novel / 177 / 0,6 / 0,0 / 98 / 1 / deleterious / tolerated /damaging
FBXW7 / 28 / chr4 / 152328226 / p.M387-467-349-291T / A / G / 9 / 23 / Novel / 67 / 0,8 / 0,0 / 229 / 1 / deleterious / damaging
FGFR2 / 19 / chr10 / 121520167 / p.R251-162-136* / G / A / 9 / 26 / Novel / 90 / 0,5 / 0,0 / 198 / 1 / NA
FGFR3 / 58 / chr4 / 1801837 / p.R248C / C / T / 27 / 136 / Hotspot / 77 / 0,5 / 0,0 / 260 / 1 / deleterious / deleterious
FGFR3 / 59 / chr4 / 1801849 / p.R252W / C / T / 8 / 21 / Novel / 91 / 0,8 / 0,0 / 111 / 2 / deleterious / damaging
FGFR3 / 59 / chr4 / 1806163 / p.K538-650-651-652R / A / G / 7 / 15 / Novel / 76 / 0,6 / 0,1 / 80 / 2 / deleterious / damaging
KRAS / 9 / chr12 / 25245347 / p.G13D / C / T / 11 / 267 / Hotspot / 934 / 0,5 / 0,0 / 229 / 2 / deleterious / deleterious
KRAS / 32 / chr12 / 25245350 / p.G12D / C / T / 9 / 69 / Hotspot / 295 / 0,5 / 0,0 / 435 / 2 / deleterious / deleterious
KRAS / 35 / chr12 / 25225713 / p.K117N / T / G / 11 / 27 / Hotspot / 55 / 0,8 / 0,1 / 88 / 3 / deleterious / damaging
KRAS / 44 / chr12 / 25245350 / p.G12A / C / G / 24 / 97 / Hotspot / 66 / 0,5 / 0,0 / 292 / 2 / deleterious / deleterious
KRAS / 49 / chr12 / 25225628 / p.A146T / C / T / 44 / 28200 / Hotspot / 7324 / 0,5 / 0,0 / 385 / 1 / deleterious / deleterious
KRAS / 50 / chr12 / 25245350 / p.G12D / C / T / 26 / 1602 / Hotspot / 1009 / 0,5 / 0,0 / 407 / 2 / deleterious / deleterious
KRAS / 52 / chr12 / 25245351 / p.G12S / C / T / 5 / 20 / Hotspot / 690 / 0,5 / 0,1 / 105 / 2 / deleterious / deleterious
KRAS / 56 / chr12 / 25245351 / p.G12S / C / T / 7 / 52 / Hotspot / 383 / 0,7 / 0,0 / 108 / 2 / deleterious / deleterious
KRAS / 65 / chr12 / 25245347 / p.G13D / C / T / 7 / 40 / Hotspot / 273 / 0,7 / 0,0 / 295 / 2 / deleterious / deleterious
KRAS / 34 / chr12 / 25227336 / p.E63G / T / C / 6 / 25 / Novel / 245 / 0,6 / 0,0 / 409 / 1 / deleterious / damaging
KRAS / 22 / chr12 / 25227397 / p.Q43* / G / A / 6 / 17 / Novel / 155 / 0,7 / 0,0 / 512 / 1 / NA
KRAS / 56 / chr12 / 25245294 / p.E31K / C / T / 7 / 45 / Novel / 394 / 0,7 / 0,0 / 271 / 1 / del/neutral / tolerated
KRAS / 65 / chr12 / 25245312 / p.Q25* / G / A / 8 / 54 / Novel / 274 / 0,6 / 0,1 / 235 / 1 / NA
KRAS / 27 / chr12 / 25245326 / p.T20M / G / A / 8 / 23 / Novel / 103 / 0,6 / 0,1 / 74 / 1 / deleterious / damaging
MAP2K1 / 65 / chr15 / 66435136 / p.K64* / A / T / 9 / 24 / Novel / 79 / 0,7 / 0,0 / 377 / 2 / NA
MAP2K1 / 65 / chr15 / 66435152 / p.E69G / A / G / 8 / 19 / Novel / 78 / 0,5 / 0,0 / 399 / 1 / deleterious / damaging
MET / 54 / chr7 / 116699605 / p.D174-193G / A / G / 32 / 221 / Novel / 95 / 0,6 / 0,0 / 115 / 1 / deleterious / damaging
MET / 47 / chr7 / 116771869 / p.R988-970C / C / T / 11 / 32 / Novel / 72 / 0,6 / 0,1 / 218 / 1 / neutral / damaging
MET / 54 / chr7 / 116777469 / p.R1132-1114G / A / G / 10 / 25 / Novel / 61 / 0,5 / 0,0 / 157 / 1 / deleterious / damaging
NRAS / 28 / chr1 / 114716145 / p.L6M / G / T / 13 / 41 / Novel / 69 / 0,5 / 0,1 / 143 / 1 / neutral / damaging
PTEN / 39 / chr10 / 87957973 / p.D252G / A / G / 14 / 36 / Hotspot / 50 / 0,5 / 0,0 / 266 / 1 / deleterious / deleterious
PTEN / 65 / chr10 / 87864515 / p.Y16H / T / C / 8 / 24 / Novel / 119 / 0,7 / 0,0 / 205 / 1 / deleterious / tolerated
PTEN / 6 / chr10 / 87864524 / p.D19N / G / A / 6 / 16 / Novel / 163 / 0,8 / 0,1 / 77 / 2 / deleterious / tolerated
PTEN / 59 / chr10 / 87961092 / p.N334D / A / G / 8 / 23 / Novel / 104 / 0,6 / 0,0 / 99 / 2 / deleterious / tolerated
SMAD4 / 28 / chr18 / 51048821 / p.N129Y / A / T / 8 / 16 / Novel / 50 / 0,6 / 0,0 / 271 / 2 / deleterious / damaging
SMAD4 / 55 / chr18 / 51058205 / p.Q250* / C / T / 11 / 94 / Novel / 270 / 0,6 / 0,0 / 330 / 1 / NA
SMAD4 / 33 / chr18 / 51065492 / p.P342L / C / T / 7 / 30 / Novel / 240 / 0,6 / 0,0 / 68 / 2 / deleterious / tolerated
SMAD4 / 19 / chr18 / 51067101 / p.F408L / T / C / 10 / 26 / Novel / 74 / 0,8 / 0,1 / 67 / 3 / deleterious / damaging
SMAD4 / 59 / chr18 / 51067113 / p.Y412H / T / C / 8 / 16 / Novel / 50 / 0,7 / 0,0 / 419 / 2 / deleterious / damaging
SMAD4 / 30 / chr18 / 51067117 / p.Y413C / A / G / 13 / 36 / Novel / 63 / 0,6 / 0,0 / 219 / 1 / deleterious / damaging
SMAD4 / 33 / chr18 / 51076720 / p.A464V / C / T / 9 / 45 / Novel / 159 / 0,6 / 0,1 / 95 / 2 / deleterious / damaging
SMAD4 / 41 / chr18 / 51076722 / p.V465M / G / A / 15 / 293 / Novel / 482 / 0,5 / 0,0 / 211 / 1 / neutral / damaging
STK11 / 54 / chr19 / 1221242 / p.F255S / T / C / 14 / 54 / Novel / 84 / 0,6 / 0,0 / 82 / 2 / deleterious / damaging
TP53 / 7 / chr17 / 7670685 / p.R342* / G / A / 21 / 237 / Hotspot / 217 / 0,5 / 0,0 / 351 / 2 / NA
TP53 / 9 / chr17 / 7675085 / p.C176Y / C / T / 15 / 732 / Hotspot / 1315 / 0,5 / 0,1 / 130 / 1 / deleterious / deleterious
TP53 / 10 / chr17 / 7673778 / p.D281G / T / C / 9 / 25 / Hotspot / 78 / 0,7 / 0,0 / 132 / 1 / deleterious / deleterious
TP53 / 11 / chr17 / 7674233 / p.G244S / C / T / 7 / 29 / Hotspot / 245 / 0,6 / 0,0 / 506 / 3 / deleterious / deleterious
TP53 / 11 / chr17 / 7674241 / p.S241F / G / A / 8 / 46 / Hotspot / 246 / 0,7 / 0,1 / 81 / 2 / deleterious / deleterious
TP53 / 11 / chr17 / 7675076 / p.H179R / T / C / 8 / 31 / Hotspot / 131 / 0,7 / 0,1 / 113 / 1 / deleterious / deleterious
TP53 / 22 / chr17 / 7674230 / p.G245S / C / T / 23 / 231 / Hotspot / 171 / 0,5 / 0,0 / 343 / 2 / deleterious / deleterious
TP53 / 24 / chr17 / 7675097 / p.V172D / A / T / 14 / 71 / Hotspot / 122 / 0,6 / 0,0 / 101 / 2 / deleterious / deleterious
TP53 / 44 / chr17 / 7674232 / p.G244A / C / G / 31 / 202 / Hotspot / 90 / 0,6 / 0,1 / 58 / 3 / deleterious / deleterious
TP53 / 53 / chr17 / 7674221 / p.R248W / G / A / 8 / 195 / Hotspot / 1290 / 0,5 / 0,1 / 203 / 2 / deleterious / deleterious
TP53 / 55 / chr17 / 7674945 / p.R196-103-64* / G / A / 11 / 71 / Hotspot / 217 / 0,6 / 0,0 / 311 / 2 / NA
TP53 / 63 / chr17 / 7674221 / p.R248W / G / A / 5 / 133 / Hotspot / 3169 / 0,5 / 0,1 / 215 / 2 / deleterious / deleterious
TP53 / 52 / chr17 / 7670706 / p.R335-324C / G / A / 5 / 34 / Novel / 1389 / 0,6 / 0,0 / 198 / 1 / deleterious / damaging
TP53 / 55 / chr17 / 7674209 / p.L252-241I / G / T / 9 / 82 / Novel / 377 / 0,6 / 0,1 / 272 / 2 / neutral / damaging
TP53 / 41 / chr17 / 7675110 / p.H168-36-157D / G / C / 5 / 15 / Novel / 404 / 0,6 / 0,0 / 278 / 1 / deleterious / damaging
TP53 / 51 / chr17 / 7676554 / p.L14P / A / G / 9 / 23 / Novel / 65 / 0,6 / 0,1 / 241 / 1 / neutral / damaging
In some cases codon number can be variable depending on the transcript for that particular gene.
Ref, reference sequence; Var, variant sequence; Freq, variant frequency in percentage; HP, homopolymer; and NA, not applicable.