Table 2.
Overview over advantages and disadvantages in use of OncoScan for genome-wide analysis of SCNAs in circulating cell-free tumor DNA.
| Characteristics | Comments | Contras | |
|---|---|---|---|
| Input material | 20 ng ccfDNA | 5 ng is possible for recognizable SCNAs profile | Patient with low tumor mass excluded |
| Processing algorithm | TuScan | Freely available via NEXUS (BioDiscovery) | |
| Ploidy assessment | Yes | Manual correction required | |
| Estimation of altered genome | Yes | Only informative, not for diagnostic purposes | |
| Aberrant cell fraction | Yes | Best performance with > 50% of aberrant cell fraction | Composition of ccfDNA might cause false-negative findings |
| Resolution and sensitivity of SCNAs detection | |||
| SCNAs | Precision | ||
| Numerical SCNAs | 20–100% | Visual inspection and correction required | Information about possible biological bias is required; e.g. treatment, heterogeneity, time of sampling |
| Segmental SCNAs | 40–100% | Visual inspection and correction required | |
| High amplitude amplification | 100% | Deviation in assignment of break-points is 7% of segment length | |
| Biallelic losses | Yes | ||
| Clinically relevant aberration | 70(100)% | Precision is 100% after manual correction of LOH | Need for manual interference |