Table 2.
Comparison of commonly used sequencing applications
| Category | Sanger | Gene panel | WES | WGS |
|---|---|---|---|---|
| Number of genes | 1–10 | 10–300 | ∼20 000 | Whole genome |
| Covered regions | Single region per run; up to 500 bp | Targeted regions in genome, i.e. coding regions of set of genes | Most coding regions, flanking non-coding sequences | Whole genome but some regions are missing, i.e. repetitive sequences |
| Detectable variants | SNVs and small deletions and insertions | SNVs and deletions and insertions (exonic/whole gene) | SNVs and deletions and insertions (exonic/whole gene) | All variants including large deletions and insertions and CNVs |
| Typical coverage | NA | 200–1000× | 30–100× | 30–60× |
| Data size (GB) | 0.01 | <1 | 5–10 | 50–200 |
| Estimated raw sequencing costs per sample (US$)a | 10–20 | 200–500 | 800–1000 | 1500–2500 |
a
Analysis costs not included. bp: base pair; CNV: copy number variant; GB: gigabyte; NA: not applicable; Sanger: Sanger sequencing; SNV: single nucleotide variant; WES: whole exome sequencing; WGS: whole genome sequencing.