Table 1.
Sequencing assays.
| Characteristic | DNA sequencing | RNA-seq | |||
|---|---|---|---|---|---|
| Targeted genomic regions | Whole exome | Whole genome | Targeted | Transcriptome profiling | |
| Capture method∗ | Amplicon-based targeting; hybrid capture; in-solution capture | Hybrid capture; in-solution capture | None | Hybridization only; hybridization and extension; multiplexed PCR | None |
| Amount of genome/transcriptome sequenced | ~150 bp–62 Mb (≤2% of genome) | ~30–60 Mb (1-2% of genome) | ~3 Gb (≥95% of genome) | Variable: transcripts of ~10–1000 genes | Entire transcriptome |
| Amplification | Yes | Yes | Not required | Yes | Required for low-quantity RNA samples |
| Sequencing depth | 100–1000xÜ | 80–100xÜ | 30–50xÜ | 0.3–25 million reads‡ | 15–200 million reads‡ |
| Amount of sequence data generated per sample | ~0.3–5 Gb | ~4-5 Gb | ~90 Gb | ~0.5–3 Gb | ~5-6 Gb |
bp, base pairs; Mb, megabases; Gb, gigabases; PCR, polymerase chain reaction.
∗Method used to select genomic regions for sequencing.
ÜNumber of times a single base is read during a sequencing run.
‡A greater number of reads are needed to detect rare transcripts.