Table 1.
Selected mutations analyzed for Group GE after FGE filtering and relative ASO–qPCR and ddPCR results.
| ID | NGS | ddPCR | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Selected SNVs | ||||||||||||||
| Reads | % of Variant Allele | |||||||||||||
| SNV Tot | AD/TD ≤ 0.25 | Coding | MAF < 10−4 & AD > 20 | Gene | Type | ID or Position | MAF a | AD/TD | AD (%) | qPCR | Tumor | PF | Plasma | |
| 696 | 104,367 | 1330 | 797 | 45 | POTEF | S | NM_001099771.2:c.2118T > C | NA | 22/112 | 19.64 | No | - | - | - |
| COL1A2 | S | rs773494330 | 4.00 × 10−6 | 23/110 | 20.91 | Yes | 0.00 | Inhibitor | 0.00 | |||||
| BACE2 | M | rs770736773, COSM5907863 | 4.00 × 10−5 | 20/91 | 21.98 | Yes | 23.05 | Inhibitor | 0.16 | |||||
| 1148 | 106,264 | 1985 | 938 | 122 | BAP1 | FS | NM_004656.1:g.52443623del | NA | 31/219 | 14.16 | No | - | - | - |
| MUC16 | M | rs75266616 | 9.11 × 10−5 | 22/100 | 22.00 | No | - | - | - | |||||
| RAD50 | FS | rs772667708, COSM1433045 | 2.10 × 10−4 | 23/197 | 11.68 | No | - | - | - | |||||
| MYBPC1 | M | rs752347381 | 8.00 × 10−6 | 26/140 | 18.57 | Yes | 20.80 | 23.80 | 26.55 | |||||
| TRPC7 | M | rs566980923 | <10−6 b | 40/256 | 15.63 | Yes | 12.50 | 4.90 | 0.00 | |||||
| 1725 | 98,442 | 1981 | 920 | 88 | ARPP21 | M | rs1481888266 | 8.88 × 10−6 | 22/124 | 17.74 | Yes | 16.65 | 16.00 | 0.26 |
| OR4K2 | M | rs757533510 | 4.00 × 10−6 | 25/98 | 25.51 | Yes | 22.40 | 22.80 | 24.05 | |||||
| 2294 | 101,976 | 1810 | 886 | 96 | FLG | S | rs564106508, COSM5531298 | 3.60 × 10−5 | 24/196 | 12.24 | No | - | - | - |
| FGFR1 | IF | rs138489552 | 7.20 × 10−5 | 22/143 | 15.38 | No | - | - | - | |||||
| UNC79 | M | NM_020818.1:g.94110000C > A | NA | 21/99 | 21.21 | No | - | - | - | |||||
| HIST1H2AD | M | NM_021065.1:g.26199201G > A | NA | 24/217 | 11.06 | Yes | 12.05 | 16.45 | 0.79 | |||||
| OR5AC2 | S | rs1021819573 | 2.72 × 10−5 | 25/163 | 15.34 | Yes | 11.10 | 12.10 | 5.57 | |||||
| 2324 | 123,405 | 2852 | 1178 | 184 | ERBB4 | M | NC_000002.12:g.211561993C > T | NA | 21/173 | 12.14 | No | |||
| SZT2 | M | rs760370909 | 4.00 × 10−6 | 27/143 | 18.88 | Yes | 0.00 | 0.00 | 0.00 | |||||
| AMPH | M | COSM1673120 (C > A) | NA c | 25/171 | 14.62 | Yes | 15.10 | 4.01 | 0.17 | |||||
| 2438 | 97,826 | 1065 | 593 | 42 | SPTAN1 | M | NM_001130438.3:c.252G > C | NA | 28/141 | 19.86 | Yes | 21.85 | 20.20 | 0.52 |
| NLGN1 | M | COSM479730 (G > T) | NA d | 23/104 | 22.12 | Yes | 21.95 | 1.59 | 0.00 | |||||
| 2829 | 105,292 | 3053 | 1342 | 116 | LATS2 | S | NM_014572.3:c.1698C > A | NA | 22/173 | 12.72 | No | - | - | - |
| CSMD3 | M | COSM6112252 (G > T) | NA e | 47/222 | 21.17 | No | - | - | - | |||||
| CCNL2 | M | NM_030937.3:c.1322747G > T | NA | 23/145 | 15.86 | No | - | - | - | |||||
| DICER1 | M | rs775912475 | 8.00 × 10−6 | 22/234 | 9.40 | Yes | 0.00 | 0.00 | 0.00 | |||||
| FLI1 | M | rs1288594591 | 4.00 × 10−6 | 25/156 | 16.03 | Yes | 11.88 | 10.24 | 0.55 | |||||
MAF = minor allele frequency; TD = total depth; AD = alternative depth, MA = mutated allele; PF = pleural fluid; S = synonymous; M = missense; FS = frame shift; IF = in frame; SG = stop gain. a According to gnomAD (https://gnomad.broadinstitute.org, accessed on 16 March 2019), global frequency. b This SNV does not have a frequency in gnomAD (https://gnomad.broadinstitute.org accessed on 16 March 2019). c There is a nearby SNP, rs140004238 (G > A), with a global frequency of 3.98 × 10−6, at 7:38516516 (+1bp). d There is a SNP, rs1349519137 (G > C), with a global frequency of 3.19 × 10−5, at the same genomic position. e There is a nearby SNP, rs1377012777 (A > G), with a global frequency of 3.98 × 10−6, at 8:113988191 (+2 bp).