Table 2.
Mutations Identified in HCC-tissue and in Plasma
| Patient ID | Size (cm) |
Mutation location (hg.38) |
Gene | Tissue mutation validated by Sanger |
Tissue mutation validated by ddPCR |
Druggable | Sub- clonal |
Ref Allele |
Alt Allele |
VAF (%, Tissue) |
bVAF (%, plasma/serum) |
Plasma mutation validated by ddPCR |
Detection in plasma/serum (Hypergeometric test p-value) |
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 9.8 | 5:1295113 | TERT Prom | Not tested | Not tested | No | No | G | A | 23 | 0 | Not tested | Not detected | |
| 2 | 3.5 | 5:1295135 | TERT Prom | Yes | Not tested | No | No | G | A | 29 | 0.21 | Not tested | Detected (low confidence, p>0.05) | |
| 1:64839716 | JAK1 | Yes | Yes | Yes | No | A | G | 58 | 2.47 | Yes | Detected (high confidence, p<0.05) | |||
| 3:41224610 | CTNNB1 | Yes | Not tested | No | No | C | A | 32 | 0.02 | Not tested | Detected (low confidence, p>0.05) | |||
| 3 | 6.5 | 5:1295113 | TERT Prom | Yes | Not tested | No | No | G | A | 26 | 0.9 | Not tested | Detected (low confidence, p>0.05) | |
| 17:7675223 | TP53 | Yes | Yes | No | No | A | C | 74 | 0.4 | Yes | Detected (high confidence, p<0.05) | |||
| 2:21013095 | APOB | Not tested | Not tested | No | Yes | G | C | 25 | 0 | Not tested | Not detected | |||
| 5:150117795 | PDGFRB | Yes | Yes | Yes | No | C | T | 31 | 0.72 | Yes | Detected (high confidence, p<0.05) | |||
| 7:140800180 | BRAF | Not tested | Not tested | No | Yes | C | G | 21 | 0 | Not tested | Not detected | |||
| 4 | 13.5 | 5:1295113 | TERT Prom | Yes | Not tested | No | No | G | A | 36 | 0 | Not tested | Not detected | |
| 2:21029497 | APOB | Not tested | Not tested | No | Yes | A | G | 86 | 0 | Not tested | Not detected | |||
| 5 | 4.7 | 5:1295113 | TERT Prom | Yes | Not tested | No | No | G | A | 41 | 2.65 | Not tested | Detected (high confidence, p<0.05) | |
| 15:88183508 | NTRK3 | Not tested | Yes | No | No | A | T | 45 | 3.25 | Yes | Detected (high confidence, p<0.05) | |||
| 17:7674885 | TP53 | Yes | Yes | No | No | C | A | 80 | 4.12 | Yes | Detected (high confidence, p<0.05) | |||
| 17:7674888 | TP53 | Yes | Yes | No | No | T | G | 80 | 3.92 | Yes | Detected (high confidence, p<0.05) | |||
| 3:41224607 | CTNNB1 | Yes | Yes | No | No | A | C | 45 | 0.04 | Yes | Detected (low confidence, p>0.05 | |||
| 4:73417849 | ALB | Not tested | Not tested | No | Yes | A | G | 23 | 0 | Not tested | Not detected | |||
| 6 | 4.5 | No mutation identified in tissue | ||||||||||||
| 7 | 2.1 | 16:346446 | AXIN* | Not tested | Not tested | No | NA | C | A | 33 | 0.03 | Not tested | Detected (low confidence, p>0.05 | |
| 16:346447 | C | A | 33 | 0.02 | ||||||||||
| 17:7674216 | TP53 | Not tested | Yes | No | NA | C | A | 46 | 0.09 | Yes | Detected (high confidence, | |||
| p<0.05) | ||||||||||||||
| 7:116783444 | MET | Not tested | Not tested | Yes | NA | A | T | 28 | 0.05 | Not tested | Detected (low confidence, p>0.05) | |||
| 7:140777205 | BRAF | Yes | Yes | No | NA | T | A | 30 | 8.93 | Yes | Detected (high confidence, p<0.05) | |||
| 8 | 2.1 | No mutation identified in tissue | ||||||||||||
Ref All: Reference allele; Alt All: Alternative allele; tVAF : Variant allele frequency in tissue; bVAF : Variant allele frequency in blood; HCC: Hepatocellular carcinoma.
*
Dinucleotide mutation; Draggable is defined as per http://dgidb.genome.wustl.edu/