Table 2.
Experimental setup for comparison of sequencing platforms.
| Provider | A | B | ||
|---|---|---|---|---|
| Samples | Samples 1–4 | Samples 5–8 | ||
| Sample Type | Whole Blood | Isolated cell subtypes | ||
| Library Preparation Method | Swift | |||
| DNA input (ng) | 200 | 50 | ||
| DNA fragmentation before bisulfite treatment | Yes | |||
| Bisulfite conversion kit | EZ DNA Methylation-Gold Kit | |||
| Sequencing Platform | HiSeq X | NovaSeq | HiSeq X | NovaSeq |
| Spike-in (%) | PhiX (5%) | WGS sequences (12~89.6%) | WGS sequences (86~96%) | |
| PCR enzyme | Enzyme R3 | |||
| PCR cycles | 7 | 9 | ||
| Effective number of lanes per sample | 1 | 0.25 | 1.17 | 0.56 |
| Average data output per sample1,2 | 150.88 Gb, 499.61 Mrp | 226.95 Gb, 751.50 Mrp | 157.49 Gb, 524.95 Mrp | 250.91 Gb, 836.38 Mrp |
1Gb: giga base. Mrp: million read pair.
2In these experiments, one lane of HiSeq X flow cell generates 150.88 ± 0.82 (mean ± SD) Gb from provider A, and 134.75 ± 17.31 Gb from provider B. One lane of NovaSeq S4 flow cell generates 907.81 ± 103.92 Gb from provider A, and one lane of S2 flow cell generates 448.06 ± 60.07 Gb from provider B.