Table 2.
Performance Comparison of Four Whole‐Exome Capture Methods
| SureSelect (Agilent) | SeqCap (Nimblegen) | HaloPlex (Agilent) | AmpliSeq (Life Technologies) | |
|---|---|---|---|---|
| Sample preparation time | 2.5 days | 4.5 days | 1.5 days | 6 hr |
| Recommended DNA input (μg) | 2 | 1 | 0.2 | 0.05 |
| Alignment (manufacturer specified) | 30%–70%a | 70%–80%a | 30%–70%a | >90%b |
| Alignment (this study) | 84.97%a | 79.71%a | 97.09%a | 93.68%a |
| Library complexity | 60.10% | 67.21% | 3.24% | 20.92% |
| Base calls on positive strand | 49.90% | 50.11% | 50.05% | 45.52% |
| Uniformity | High | High | Low | Low |
| SNV | √ | √ | √ | √ |
| CNV | √ | √ | √ | √ |
a
Alignment denotes the percentage of mapped reads that aligned or should align to targeted regions.
b
Alignment denotes the percentage of bases that cover the target region.