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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
  1. Correct positive calls are in bold italic. Theoretical percentages are indicated in brackets