Table 3 Frequency of putative genetic variants identified in plasma ctDNA from patients with HCC (n = 23)
Gene | Position | DNA change | Variant Classification | Protein change | Number (%) of HCC patients with mutation (n = 22) | Number (%) HCC patients with gene affected (n = 22) |
|---|---|---|---|---|---|---|
APC | chr5:112775613 | A > T | Intron | - | 2 (9%) | 3 (14%) |
chr5:112828978 | T > A | Intron | - | 1 (5%) | ||
chr5:112841202 | G > A | Missense | p.D1870N | 1 (5%) | ||
chr5:112843530 | C > T | Nonsense | p.Q2646* | 1 (5%) | ||
ARID1A | chr1:26696303 | T > G | 5’UTR | - | 2 (9%) | 8 (36%) |
chr1:26696243 | delG | 5’UTR | - | 1 (5%) | ||
chr1:26696939 | C > T | Missense | p.P179L | 1 (5%) | ||
chr1:26781181 | delA | 3’UTR | - | 1 (5%) | ||
chr1:26781181 | insA | 3’UTR | - | 1 (5%) | ||
chr1:26781180 | CA > AA | 3’UTR | - | 1 (5%) | ||
chr1:26775548 | T > A | Intron | - | 1 (5%) | ||
chr1:26765502 | T > A | Intron | - | 1 (5%) | ||
chr1:26780431 | A > G | Missense | p.D1961G | 1 (5%) | ||
chr1:26764279 | delTTA | Intron | - | 1 (5%) | ||
chr1:26775642 | G > T | Missense | p.A1470S | 1 (5%) | ||
chr1:26766179 | A > T | Intron | - | 1 (5%) | ||
chr1:26771867 | insGA | Intron | - | 1 (5%) | ||
chr1:26781594 | G > A | 3’UTR | - | 1 (5%) | ||
ARID2 | chr12:45907298 | G > A | 3’UTR | - | 1 (5%) | 5 (23%) |
chr12:45776208 | G > C | Intron | - | 1 (5%) | ||
chr12:45850291 | T > C | Missense | p.I723T | 1 (5%) | ||
chr12:45851855 | C > T | Silent | p.C1244C | 1 (5%) | ||
chr12:45893906 | delAA | Intron | - | 1 (5%) | ||
ATM | chr11:108368056 | T > C | 3’UTR | - | 1 (5%) | 11 (50%) |
chr11:108366325 | T > A | 3’UTR | - | 1 (5%) | ||
chr11:108226129 | delCT | Intron | - | 1 (5%) | ||
chr11:108368079 | G > A | 3’UTR | - | 1 (5%) | ||
chr11:108317331 | T > C | Intron | - | 2 (9%) | ||
chr11:108229848 | delTTT | Intron | - | 2 (9%) | ||
chr11:108353824 | C > G | Silent | p.L2910L | 1 (5%) | ||
chr11:108226465 | A > G | Intron | - | 1 (5%) | ||
chr11:108236535 | delAA | Intron | - | 1 (5%) | ||
chr11:108253979 | A > G | Silent | p.E688E | 1 (5%) | ||
chr11:108336314 | G > A | Intron | - | 1 (5%) | ||
AXIN1 | chr16:292909 | delTC | Intron | - | 1 (5%) | 5 (23%) |
chr16:287828 | delG | 3’UTR | - | 1 (5%) | ||
chr16:287827 | TG > GG | 3’UTR | - | 1 (5%) | ||
chr16:291664 | G > A | Intron | - | 1 (5%) | ||
chr16:291690 | G > A | Intron | - | 1 (5%) | ||
chr16:292771 | C > T | Intron | - | 1 (5%) | ||
chr16:346333 | C > T | Silent | p.G231G | 1 (5%) | ||
chr16:290341 | delC | Intron | - | 1 (5%) | ||
chr16:289748 | CA > AG | Intron | - | 1 (5%) | ||
CDKN2A | chr9:21971112 | G > A | Missense | p.H32Y | 1 (5%) | 4 (18%) |
chr9:21995246 | C > G | 5’UTR | - | 2 (9%) | ||
chr9:21969809 | delG | Intron | - | 1 (5%) | ||
chr9:21994124 | G > A | Intron | - | 1 (5%) | ||
chr9:21994137 | A > G | Splice Site | - | 1 (5%) | ||
CTNNB1 | chr3:41222081 | delA | 5’UTR | - | 1 (5%) | 5 (23%) |
chr3:41222080 | TA > AA | 5’UTR | - | 1 (5%) | ||
chr3:41222080 | insA | 5’UTR | - | 1 (5%) | ||
chr3:41233410 | C > A | Missense | p.T384N | 1 (5%) | ||
chr3:41237312 | T > C | Intron | - | 1 (5%) | ||
chr3:41195090 | G > C | 5’UTR | - | 1 (5%) | ||
chr3:41221852 | T > A | 5’UTR | - | 1 (5%) | ||
HNF1A | chr12:120994312 | delG | Frame Shift | p.P291fs | 1 (5%) | 2 (9%) |
chr12:120993492 | delC | Intron | - | 1 (5%) | ||
chr12:120997748 | insCC | Intron | - | 1 (5%) | ||
JAK1 | chr1:64869304 | G > A | Intron | - | 1 (5%) | 3 (14%) |
chr1:64834085 | G > A | 3’UTR | - | 1 (5%) | ||
chr1:64875319 | G > A | Intron | - | 1 (5%) | ||
chr1:64860150 | delG | Frame Shift | p.P430fs | 1 (5%) | ||
KEAP1 | chr19:10500119 | G > A | Intron | - | 1 (5%) | 4 (18%) |
chr19:10503405 | C > T | 5’Flank | - | 1 (5%) | ||
chr19:10503181 | C > T | Intron | - | 1 (5%) | ||
chr19:10489604 | A > G | Intron | - | 1 (5%) | ||
LZTR1 | chr22:20982316 | C > A | 5’UTR | - | 1 (5%) | 3 (14%) |
chr22:20992853 | C > T | Silent | p.F403F | 1 (5%) | ||
chr22:20997565 | C > G | 3’UTR | - | 1 (5%) | ||
chr22:20997892 | T > C | 3’UTR | - | 1 (5%) | ||
PDGFRA | chr4:54278426 | T > G | Missense | p.N689K | 1 (5%) | 1 (5%) |
PIK3CA | chr3:179204485 | CC > AA | Intron | - | 1 (5%) | 6 (27%) |
chr3:179237557 | C > T | 3’UTR | - | 1 (5%) | ||
chr3:179236267 | T > C | 3’UTR | - | 1 (5%) | ||
chr3:179195993 | A > G | Intron | - | 1 (5%) | ||
chr3:179197765 | A > G | Intron | - | 1 (5%) | ||
chr3:179235739 | C > T | 3’UTR | - | 1 (5%) | ||
PTEN | chr10:87967851 | G > T | 3’UTR | - | 1 (5%) | 3 (14%) |
chr10:87966104 | C > T | 3’UTR | - | 1 (5%) | ||
chr10:87966298 | delG | 3’UTR | - | 1 (5%) | ||
SF3B1 | chr2:197400448 | insA | Intron | - | 1 (5%) | 9 (41%) |
chr2:197402110 | T > C | Missense | p.K700E | 2 (9%) | ||
chr2:197400447 | delT | Intron | - | 1 (5%) | ||
chr2:197405293 | T > C | Silent | p.Q473Q | 1 (5%) | ||
chr2:197390330 | T > G | 3’UTR | - | 1 (5%) | ||
chr2:197419393 | delCA | Intron | - | 1 (5%) | ||
chr2:197398107 | T > C | Silent | p.E1048E | 1 (5%) | ||
chr2:197402637 | T > C | Missense | p.K666E | 2 (9%) | ||
chr2:197390456 | G > A | 3’UTR | - | 1 (5%) | ||
SMARCA4 | chr19:11019395 | T > C | Intron | - | 1 (5%) | 5 (23%) |
chr19:11025373 | A > C | Intron | - | 1 (5%) | ||
chr19:10996186 | A > G | Intron | - | 1 (5%) | ||
chr19:10961396 | T > G | Intron | - | 1 (5%) | ||
chr19:11007936 | C > A | Missense | p.P679H | 1 (5%) | ||
TERT | chr5:1282922 | A > G | Intron | - | 1 (5%) | 7 (32%) |
chr5:1295113 | G > A | 5’Flank | - | 1 (5%) | ||
chr5:1294720 | delC | Intron | - | 1 (5%) | ||
chr5:1255402 | T > C | Silent | p.A1014A | 1 (5%) | ||
chr5:1295234 | A > G | 5’Flank | - | 1 (5%) | ||
chr5:1296371 | A > G | 5’Flank | - | 1 (5%) | ||
chr5:1294550 | delG | Frame Shift | p.E113fs | 1 (5%) | ||
chr5:1253800 | delC | Frame Shift | p.T1110fs | 1 (5%) | ||
TP53 | chr17:7675124 | T > C | Missense | p.Y163C | 1 (5%) | 1 (5%) |
