Table 2.
Selected mutations analyzed for Group PT after FPT filtering and relative ASO–qPCR and ddPCR results.
| ID | NGS | ddPCR | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Selected SNVs | |||||||||||||||||
| Reads | % of Variant Allele | ||||||||||||||||
| SNV Tot | Somatic ¥ | Coding | MAF < 1% & TD > 20 | AD = 0 in Blood | Gene | Type | ID or Position | MAF a | AD/TD (Blood) | AD/TD (Tumor) | AD (%) (Tumor) | qPCR | Blood | Tumor | PF | Plasma | |
| 01T | 122,995 | 2509 | 158 | 54 | 2 | JADE1 | S | rs775483821 | 3.99 × 10−6 | 0/81 | 13/53 | 24.53 | Yes | 0.00 | 7.48 | 12.75 | 0.20 |
| SS18 | M | NM_001007559.3:c.98A > G | NA | 0/44 | 6/20 | 30.00 | Yes | 0.06 | 0.00 | 0.10 | - | ||||||
| 02T | 102,753 | 1948 | 203 | 97 | 22 | FLT1 | M | NM_002019.4:c.3697C > A | NA | 0/125 | 23/55 | 41.82 | Yes | 0.07 | 32.85 | 24.85 | 2.68 |
| BAP1 | SG | COSM4411449(C > T) | NA b | 0/145 | 21/96 | 21.88 | Yes | 0.00 | 33.50 | 22.90 | 1.39 | ||||||
| 03T | 117,237 | 2525 | 281 | 104 | 39 | DCAF8 | M | COSM319811 | NA | 0/105 | 47/129 | 36.43 | Yes | 0.00 | 33.95 | 36.35 | 0.58 |
| PEG10 | M | rs368939059 COSM1093296 | 8.03 × 10−6 | 0/78 | 42/102 | 41.18 | Yes | 0.00 | 35.90 | 39.70 | 1.65 | ||||||
| 04T | 130,073 | 2755 | 152 | 75 | 27 | FAM71B | M | rs1404037352 | 1.6 × 10−5 | 0/145 | 38/138 | 27.54 | Yes | 0.00 | 30.80 | 9.70 | N.A. |
| CSMD2 | S | rs770364421, COSM5951197 | 6.60 × 10−5 | 0/118 | 32/117 | 27.35 | Yes | 1.45 | 25.00 | 8.95 | N.A. | ||||||
| 05T | 126,782 | 2833 | 227 | 81 | 23 | FAT1 | M | rs776531396 | 4.01 × 10−6 | 0/150 | 61/236 | 25.85 | Yes | 0.07 | 23.25 | 0.00 | 0.00 |
| BAP1 | SG | rs771713346, COSM6945226 | 4.00 × 10−6 | 0/93 | 18/75 | 24.00 | Yes | 0.00 | 31.75 | 36.50 | 0.14 | ||||||
| 02P | 128,899 | 3027 | 266 | 66 | 13 | VIL1 | S | NM_007127.3:c.2070C > T | NA | 0/293 | 29/143 | 20.28 | Yes | 0.04 | 13.20 | N.A. | 0.29 |
| OR10A4 | M | rs547489107 | 4.40 × 10−5 | 0/137 | 14/62 | 22.58 | No | - | - | N.A. | - | ||||||
| 03P | 122,214 | 3120 | 239 | 88 | 42 | NF2 | SG | NM_016418.5:c.985A > T | NA | 0/155 | 10/37 | 27.03 | Yes | 0.00 | 15.85 | N.A. | 0.14 |
| NLRP6 | SG | NM_138329.2:c.403G > T | NA | 0/123 | 30/151 | 19.87 | No | - | - | N.A. | - | ||||||
MAF = minor allele frequency; TD = total depth; AD = alternative depth; PF = pleural fluid; S = synonymous; M = missense; SG = stop gain. ¥ Predicted by VarScan2 tool (DOI:10.1101/gr.129684.111); a according to gnomAD (https://gnomad.broadinstitute.org accessed on 16 March 2019), global frequency. b There is a SNP, rs770127999 (C > A), with a global frequency of 4.00 × 10−6, at the same genomic position.