Table 2.
Number of unique cfDNA molecules mapping to five independent genomic positions (Loc1 to 5; based on unique mapping coordinates of library fragments) in the three library replicates (R1, R2, R3) that were built with either semi-degenerate barcoded adapters (BarAd) or standard sequencing adapters (StdAd) from the same amount of input cfDNA (2.3 ng) in patient NB-pt01.
| Loc1 | Loc2 | Loc3 | Loc4 | Loc5 | |
|---|---|---|---|---|---|
| BarAd - R1 | 280 (0.379) | 394 (0.076) | 457 (0.543) | 418 (0.029) | 396 (0.215) |
| BarAd - R2 | 228 (0.338) | 411 (0.078) | 469 (0.559) | 450 (0.062) | 460 (0.171) |
| BarAd - R3 | 294 (0.259) | 439 (0.032) | 492 (0.583) | 438 (0.046) | 437 (0.158) |
| BarAd - Avg | 267.33 (0.325) | 414.66 (0.062) | 472.66 (0.562) | 435.33 (0.046) | 431 (0.181) |
| StdAd - R1 | 266 (0.349) | 358 (0.047) | 470 (0.521) | 413 (0.041) | 396 (0.186) |
| StdAd - R2 | 293 (0.307) | 386 (0.054) | 520 (0.544) | 405 (0.039) | 408 (0.200) |
| StdAd - R1 | 305 (0308) | 381 (0.063) | 447 (0.544) | 412 (0.034) | 411 (0.200) |
| StdAd - Avg | 288 (0.321) | 375 (0.055) | 479 (0.536) | 410 (0.038) | 405 (0.195) |
| Two-tailed p-value | 0.47 | 0.054 | 0.84 | 0.079 | 0.22 |
Estimated allele frequencies for mutant DNA circulating in the plasma are indicated in parentheses. For each triplicate series, one of the rows (in bold) shows average values. We did not find statistically significant differences concerning recovery efficiencies of cfDNA when comparing the number of unique molecules retrieved by either barcoded or standard sequencing adapters (bottom row). Genomic coordinates for the five single-nucleotide variants targeted in this patient are provided in Table S1.