Table 2.
Comparison of quality metrics for ICCv2 (marketed as the TruSight Cardio Sequencing Kit) panel (M3, MiSeq; M4, NextSeq 500), WES, Deep WES and WGS
| Sequencing summary | Method 3 (M3) | Method 4 (M4) | WES | Deep WES | WGS |
|---|---|---|---|---|---|
| Nextera Rapid Capture kit | ICCv2 | ICCv2 | WES | WES | TruSeq Nano DNA |
| Sequencer | MiSeq | NextSeq 500 | HiSeq 2500 | HiSeq 2500 | HiSeq X |
| Sequencing reagent kit | MiSeq v2, 300 cycles | Mid Output v2, 300 cycles | SBS v4, 250 cycles | SBS v4, 250 cycles | V2.5, 300 cycles |
| Samples per lane | 12 | 48 | 12 | 2 | 0.5 |
| Average output per sample (GB) | 0.5 | 1.2 | 5.4 | 43.7 | 200 |
| Mean read depth of ICC target (95 % CI) | 329× (317×–342×) | 578× (568×–587×) | 74× (71×–78×) | 522× | 69.4× (65.4×–73.5×) |
| Mean ICC bases ≥20× (%) (95 % CI) | 99.8 (99.8–99.9) | 99.9 (99.9–99.9) | 88.1 (87.3–88.9) | 99.2 | 99.3 (99.2–99.5) |
| Targeted enrichment and sequencing cost per sample (USD) | 200 | 200 | 900 | 5400 | 2800 |
| Library preparation and sequencing time per run (days) | 4 | 4 | 9 | 9 | 4 |
A full comparison of methods 1–4 using ICCv1 and ICCv2 panels is shown in Table S4