Table 1 Number of plasma ASVs that met each decontamination criterion separately and in combination
From: Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
All ASVs (%) | Low abundance ASVs (%) | Med. abundance ASVs (%) | High abundance ASVs (%) | |
|---|---|---|---|---|
Total | 1506 (100) | 1384 (100) | 110 (100) | 12 (100) |
Criterion (i) | ||||
No batch effect by sequencing run | 612 (40.64) | 582 (42.05) | 25 (22.73) | 5 (41.67) |
No batch effect by DEB | 277 (18.39) | 260 (18.79) | 12 (10.91) | 5 (41.67) |
No batch effect by DNA ext. day | 1113 (73.9) | 1069 (77.24) | 38 (34.55) | 6 (50) |
No batch effect by any tech. var. | 239 (15.87) | 227 (16.4) | 8 (7.27) | 4 (33.33) |
Criterion (ii) | ||||
Decontam in DEB A | 183 (12.15) | 144 (10.4) | 36 (32.73) | 3 (25) |
Decontam in DEB B | 364 (24.17) | 307 (22.18) | 51 (46.36) | 6 (50) |
Decontam in DEB C | 573 (38.05) | 504 (36.42) | 68 (61.82) | 1 (8.33) |
Decontam in DEB D | 431 (28.62) | 385 (27.82) | 45 (40.91) | 1 (8.33) |
Decontam in DEB E | 452 (30.01) | 395 (28.54) | 55 (50) | 2 (16.67) |
Decontam across DEBs | 329 (21.85) | 313 (22.62) | 16 (14.55) | 0 (0) |
Criterion (iii) | ||||
Sample association | 20 (1.33) | 14 (1.01) | 6 (5.45) | 0 (0) |
Complete bioinformatics decontamination strategy | 38 (2.52) | 38 (2.75) | 0 (0) | 0 (0) |
Final list after literature-based filter | 31 (2.06) | 31 (2.24) | 0 (0) | 0 (0) |