Table 3.
Summary of 25 single nucleotide variants subjected to validation experiments.
| Gene | Sample | Chr | Genomic position | Reference | Variant | AA change | Total number of consensus reads | Number of variant reads | VAF (%) | Validation with tumor DNA by amplicon sequencing | Validation with cfDNA by digital PCR |
|---|---|---|---|---|---|---|---|---|---|---|---|
| TERT promoter | RK436 | 5 | 1295228 | G | A | — | 395 | 6 | 1.52 | y | — |
| TP53 | RK432 | 17 | 7577120 | C | T | R273H | 884 | 7 | 0.79 | n | N/A |
| TP53 | RK451 | 17 | 7577133 | T | C | S269G | 1,179 | 3 | 0.25 | n | y |
| TP53 | RK258 | 17 | 7578503 | C | T | V143M | 1,216 | 106 | 8.72 | y | — |
| TP53 | RK436 | 17 | 7578535 | T | G | K132T | 620 | 61 | 9.84 | y | — |
| CTNNB1 | RK451 | 3 | 41274886 | A | G | Q379R | 1,376 | 22 | 1.60 | y | — |
| ARID1A | RK445 | 1 | 27106316 | C | T | S1976F | 1,035 | 3 | 0.29 | n | y |
| ARID2 | RK439 | 12 | 46231342 | T | G | Y394X | 816 | 17 | 2.08 | y | — |
| ACVR2A | RK441 | 2 | 148657079 | G | T | E106X | 696 | 8 | 1.15 | y | — |
| NFE2L2 | RK444 | 2 | 178098809 | T | C | E79G | 622 | 5 | 0.80 | n | y |
| NFE2L2 | RK441 | 2 | 178098956 | A | C | L30R | 751 | 5 | 0.67 | y | — |
| RPS6KA3 | RK439 | X | 20193353 | T | A | S386C | 397 | 10 | 2.52 | y | — |
| COL11A1 | RK456 | 1 | 103405977 | G | A | P1097L | 1,264 | 4 | 0.32 | n | N/A |
| COL11A1 | RK451 | 1 | 103488365 | G | T | P393Q | 1,384 | 10 | 0.72 | n | N/A |
| CTNNA2 | RK445 | 2 | 80097000 | G | A | R175H | 1,079 | 4 | 0.37 | y | — |
| ROBO2 | RK432 | 3 | 77571995 | G | T | M292I | 685 | 3 | 0.44 | y | — |
| CDH9 | RK438 | 5 | 26902700 | G | T | P380T | 1,453 | 3 | 0.21 | y | — |
| APC | RK456 | 5 | 112175232 | G | A | R1314K | 1,174 | 5 | 0.43 | n | y |
| EPHA7 | RK433 | 6 | 93956601 | C | T | E879K | 615 | 4 | 0.65 | n | N/A |
| GLI3 | RK456 | 7 | 42004860 | C | A | A1271S | 1,263 | 7 | 0.55 | n | N/A |
| PREX2 | RK442 | 8 | 69104007 | C | T | A1466V | 857 | 27 | 3.15 | y | — |
| ATM | RK442 | 11 | 108121480 | T | G | C430G | 677 | 5 | 0.74 | n | y |
| LRFN5 | RK445 | 14 | 42356455 | G | C | K209N | 996 | 4 | 0.40 | n | y |
| IGF1R | RK451 | 15 | 99251289 | A | G | N198S | 1,275 | 8 | 0.63 | n | y |
| PAK7 | RK439 | 20 | 9561315 | A | C | L156R | 788 | 6 | 0.76 | n | y |
Note: AA, amino acid; VAF, variant allele frequency; cfDNA, cell-free DNA; y, successfully validated; n, NOT validated; N/A: not assessed due to a lack of sample volume for the experiment.