Table 3 Contamination rate of PCR-introduced adapter library preparation method using MGI lung cancer kit
From: Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform
a. Contamination rate before removing duplication | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Index | Repeats | EGFR (L858R) | KRAS (G12D) | EGFR (19del) | NRAS (p.Q61H) | ||||||||
Reference reads | Mut reads | Mut allele rate | Reference reads | Mut reads | Mut allele rate | Reference reads | Mut reads | Mut allele rate | Reference reads | Mut reads | Mut allele rate | ||
1 | Repeat 1 | 1,423,408 | 4 | negative | 52,589 | 34 | negative | 31,150 | 0 | negative | 188,086 | 0 | negative |
Repeat 2 | 1,158,060 | 4 | negative | 54,331 | 33 | negative | 31,047 | 0 | negative | 201,147 | 0 | negative | |
2 | Repeat 1 | 1,346,831 | 17,200 | 1.2610% | 59,590 | 39 | negative | 40,077 | 0 | negative | 205,321 | 0 | negative |
Repeat 2 | 1,148,168 | 11,231 | 0.9687% | 57,175 | 27 | negative | 36,381 | 0 | negative | 192,472 | 0 | negative | |
3 | Repeat 1 | 1,604,176 | 6 | negative | 53,555 | 7713 | 12.5890% | 32,294 | 0 | negative | 199,296 | 2 | negative |
Repeat 2 | 1,430,975 | 5 | negative | 54,029 | 7296 | 11.8973% | 36,961 | 0 | negative | 200,989 | 4 | negative | |
4 | Repeat 1 | 1,321,771 | 3 | negative | 56,766 | 20 | negative | 22,370 | 9038 | 28.7761% | 150,478 | 0 | negative |
Repeat 2 | 1,275,573 | 7 | negative | 59,610 | 31 | negative | 22,914 | 9660 | 29.6556% | 204,544 | 0 | negative | |
b. Contamination rate after removing duplication | |||||||||||||
Index | Repeats | EGFR (L858R) | KRAS (G12D) | EGFR (19del) | NRAS (p.Q61H) | ||||||||
Reference templates | Mut templates | Mut allele rate | Reference templates | Mut templates | Mut allele rate | Reference templates | Mut templates | Mut allele rate | Reference templates | Mut templates | Mut allele rate | ||
1 | Repeat 1 | 26,824 | 0 | negative | 6889 | 2 | negative | 5295 | 0 | negative | 10,798 | 0 | negative |
Repeat 2 | 21,904 | 0 | negative | 6209 | 1 | negative | 5088 | 0 | negative | 9617 | 0 | negative | |
2 | Repeat 1 | 24,550 | 324 | 1.3026% (1%) | 6903 | 3 | negative | 5509 | 0 | negative | 10,770 | 0 | negative |
Repeat 2 | 21,673 | 241 | 1.0998% (1%) | 6757 | 2 | negative | 5565 | 0 | negative | 9911 | 0 | negative | |
3 | Repeat 1 | 23,017 | 0 | negative | 4651 | 656 | 12.3610% (10%) | 4622 | 0 | negative | 8788 | 0 | negative |
Repeat 2 | 23,485 | 0 | negative | 5066 | 692 | 12.0181% (10%) | 5274 | 0 | negative | 9391 | 0 | negative | |
4 | Repeat 1 | 31,688 | 0 | negative | 7203 | 0 | negative | 1032 | 996 | 49.1124% (50%) | 13,032 | 0 | negative |
Repeat 2 | 30,261 | 0 | negative | 8300 | 1 | negative | 1047 | 991 | 48.6261% (50%) | 13,937 | 0 | negative | |