pISSN 2234-3806eISSN 2234-3814
Table. 2.
Samples used for data analysis, cfDNA pathogenic variants identified by NGS, and allele frequencies
| Case number | cfDNA (ng/mL plasma) | Library concentration (pM) | Median read coverage | Allele frequency (%) | Read coverage | Molecular coverage | Allele frequency (%) | Read coverage | Molecular coverage | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 8.2 | 4,230 | 81,672 | c.80C > T, p.P27L | 0.11 | 15,872 | 2,711 | ND | - | - | - |
| c.182delA, p.D61fs | 0.09 | 24,988 | 2,317 | - | - | - | |||||
| 2 | 1.22 | 4,170 | 55,449 | c.556G > A, p.D186N | 0.12 | 25,544 | 2,476 | c.36G > T, p.M12I | 0.07 | 45,960 | 4,456 |
| 3 | 1.89 | 4,880 | 69,885 | c.733G > A, p.G245S | 0.12 | 75,430 | 8,805 | ND | - | - | - |
| 4 | 5.38 | 12,900 | 44,765 | ND | - | - | - | ND | - | - | - |
| 5 | 0.8 | 3,290 | 53,783 | ND | - | - | - | ND | - | - | - |
| 6 | 3.76 | 10,000 | 57,133 | c.755G > A, p.D259N | 0.06 | 26,406 | 4,634 | ND | - | - | - |
| 7 | 2.34 | 6,150 | 61,343 | c.481G > A, p.A161T | 0.14 | 47,065 | 6,345 | ND | - | - | - |
| 8 | 4.42 | 5,000 | 78,998 | ND | - | - | - | ND | - | - | - |
| 9 | 7.98 | 5,860 | 64,088 | ND | - | - | - | ND | - | - | - |
| 10 | 8.08 | 6,300 | 73,923 | c.592G > T, p.E198* | 1.86 | 69,716 | 9,088 | c.98C > A, p.S33Y | 0.77 | 49,020 | 7,568 |
| - | - | - | - | c.101G > T, p.G34Y | 0.96 | 49,026 | 7,577 | ||||
| - | - | - | - | c.1161T > A, p.N387K | 0.45 | 73,925 | 9,633 | ||||
| 11 | 7.14 | 4,070 | 65,632 | c.673-2A > G, p.? | 6.99 | 33,589 | 5,136 | ND | - | - | - |
| c.695A > G, p.Y220C | 0.24 | 60,416 | 8,251 | - | - | - | |||||
| c.920-1G > A, p.? | 0.19 | 31,154 | 4,692 | - | - | - | |||||
| 12 | 1.46 | 2,050 | 61,806 | ND | - | - | - | ND | - | - | - |
| 13 | 15.3 | 5,250 | 62,876 | ND | - | - | - | c.1286G > A, p.C429Y | 0.05 | 48,146 | 7,369 |
| 14 | 2.26 | 4,830 | 64,926 | ND | - | - | - | ND | - | - | - |
| 15 | 7.98 | 5,400 | 57,979 | ND | - | - | - | c.1624C > T, p.R542C | 0.06 | 58,712 | 8,223 |
| 16 | 9.58 | 2,730 | 74,144 | c.808T > A, p.F270I | 4.15 | 23,459 | 2,433 | c.523G > A, p.V 175I | 0.06 | 67,177 | 6,604 |
| c.821T > G, p.V274G | 0.08 | 63,198 | 7,502 | - | - | - | - | ||||
| 17 | 3.18 | 5,650 | 63,538 | c.200C > T, p.P67L | 0.07 | 55,587 | 5,770 | c.134C > T, p.S45F | 0.07 | 55,644 | 7,624 |
| c.733G > T, p.G245C | 4.20 | 58,779 | 8,350 | - | - | - | - | ||||
| 18 | 5.7 | 14,500 | 53,299 | c.833C > G, p.P278R | 0.84 | 36,285 | 6,086 | ND | - | - | - |
| 19 | 1.28 | 2,170 | 49,597 | c.711G > A, p.M237I | 6.61 | 55,812 | 3,102 | c.1105C > T, p.H369Y | 0.13 | 45,971 | 2,400 |
| 20 | 2.06 | 2,220 | 59 | ND - | - | - | ND | - | - | - |
The TERT promoter variant was not detected in any of the 20 patients, despite a median coverage of 14,519 (range: 8,675–28,661).
Abbreviations: cfDNA, cell-free DNA; ND, not detected; NGS, next-generation sequencing.
Ann Lab Med 2021;41:198~206 https://doi.org/10.3343/alm.2021.41.2.198
© Ann Lab Med