Table 1. Enrichment efficiency (OC, FE, FENGS, and FEqPCR) after 1st and 2nd steps of enrichment of the three analyzed samples.
| OC | FE | FENGS | FEqPCR | |||||
|---|---|---|---|---|---|---|---|---|
| 1st enrichment | 2nd enrichment | 1st enrichment | 2nd enrichment | 1st enrichment | 2nd enrichment | 1st enrichment RN/ratio | 2nd enrichment RN/ratio | |
| Normal_1 | 0.91 | 1 | 11.2 | 50 | 10.9 | 23.1 | 8.3/10.5 | 13.0/34.9 |
| Leukemia_1 | 0.92 | 1 | 11.0 | 50 | 9.6 | 23.7 | 9.5/11.6 | 14.0/45.1 |
| Leukemia_2 | 0.92 | 0.98 | 10.5 | 32.2 | 11.3 | 29.5 | 12.1/11.9 | 20.5/32.9 |
Normal_1, Leukemia_1, and Leukemia_2 – three samples used in the experiment; OC – overall clearance; FE – fold enrichment; FENGS – fold enrichment of the fraction of NGS reads mapping to the targeted sequences; FEqPCR – fold enrichment calculated based on qPCR analyses; RN – calculated as proposed by the Roche NimbleGen protocol and [16]; ratio – calculated based on ratio of enrichment of targeted and non-targeted regions weighted by proportion of targeted/non-targeted regions in the genome. Note that some differences between FEqPCR (RN) and FEqPCR (ratio) may result from imprecision of measurement of the DNA concentration. Amount of input DNA is assumed to be a normalization factor in FEqPCR (RN) calculation. According to Roche NimbleGen (SeqCap EZ Library SR User's Guide, v4.2), two-fold differences in the FEqPCR (RN) measures should be considered as the same.