Table 4.
Assay Performance and Optimization at the Sequencing Sites
| BCM-HGSC |
Broad |
|||||
|---|---|---|---|---|---|---|
| Acceptance Criteria | Original | Low Input | Acceptance Criteria | Measured at ∼250× MTC | Measured at ∼400× MTC | |
| Assay sensitivity (SNV + indel) | 100% | 100% | ≥95% | 100% | 100% | |
| Assay sensitivity (CNV) | 97.7% | 98.3% | n/a | 100%a | n/a | |
| Assay specificity (point variant + indel) | 100% | 100% | ≥95% | 100% | 100% | |
| Assay reproducibility | ≥95% | >98% | >97% | ≥95% | 98.5% | 99.6% |
| % of >20× coverage for targeted regions | ≥99% | >99% | >99% | ≥95% | 99% | 99% |
| Depth of mean coverage | >200× | >200× | >200× | n/a | ≥250× | ≥400× |
a
CNV sensitivity at Broad/LMM is for events ≥3 consecutive exons.