Table 5.
A comparison of Two Enrichment Methodologies, RainDance Technologies and SureSelect, Relative to the Sequencing Gold Standard, the Sanger Method
| Parameters | RainDance Technologies | SureSelect | Sanger |
|---|---|---|---|
| Clinical implementation | Yes | Yes | Yes |
| Cost per PCR amplicon | $1.56 | $2.34 | $5.48 |
| Equipment | Use of specialized equipment, automation | Use of specialized equipment, automation or manual execution | None required |
| Ease of use | Easier, small number of steps | Complicated, many manipulations | Labor intensive |
| DNA requirement | 3 μg for 1 Mb target | 3 μg for up to 30 Mb target | 19 μg for 65 Kb region |
| Length of region for enrichment | Up to 1 Mb | Up to exome | Most limited |
| Scalability (samples/day) | One patient per time (8 samples/day) | Eight patients per time (8 samples/day) | One exon per time (1 sample/day) |
| Variant calls | >20× coverage needed | >20× coverage needed | 2× |
| Limitation | May be used for genes with pseudogenes | Cannot be used for pseudogenes | May be used for genes with pseudogenes |
| Analytical sensitivity | >85% (95% CI: 72–88%) | >85% (95% CI: 77%–91%) | >99.5% (95% CI: 95.6%–100%) |
| Analytical specificity | >99.5% (95% CI: 99.9%–100%) | 85–99.5%⁎ (95% CI: 79.9%–99.9%) | >99.5% (95% CI: 99.9%–100%) |
| Uniformity | >85% uniform amplification | >85% uniformity capture | >95% uniform amplification |
| Reproducibility | >99% reproducibility at 10-fold between two samples | >85% reproducibility at 10-fold between two samples† | 100% reproducibility at 2-fold between two samples |
⁎
The specificity variation depends on which exons are captured in a given experiment. Exon capture variability has been observed in SureSelect. Therefore, RainDance Technologies amplifications are more reproducible than SureSelect captures.
†
The average exon coverage profile of each gene varies between SureSelect capture experiments, whereas the RainDance Technologies average exon coverage profile is much more consistent.