Table 2.
Comparison of CNV detection by array CGH to CNV detection by panelcn. MOPS using blood-derived DNA
| Acurracy for calling of | |||||
|---|---|---|---|---|---|
| ID | Sample group | Material | array CGHa | CNVsb | no CNVsb |
| K01 | Control | Blood | without pathological findings | – | 0.96 |
| K02 | – | 0.97 | |||
| K03 | – | 0.97 | |||
| K04 | – | 0.90 | |||
| K05 | – | 0.97 | |||
| P01 | Control routine diagnostic | Blood | without pathological findings | – | 1.00 |
| P02 | – | 1.00 | |||
| P03 | – | 1.00 | |||
| P04 | – | 0.98 | |||
| P05 | – | 1.00 | |||
| P06 | – | 1.00 | |||
| P07 | – | 1.00 | |||
| P08 | – | 1.00 | |||
| P09 | – | 1.00 | |||
| P16 | Known CNVs | Blood | BRCA1: 41.200.842–41.201.265 × 1 (loss E22) | 1.00 | 1.00 |
| P17 | BRCA1: 41.167.511–41.338.305 × 1 (BRCA1 loss) | 0.86 | 0.89 | ||
| P18 | BRCA1: 41.215.214–41.242.384 × 1 (loss E12-E18) | 1.00 | 0.99 | ||
| P19 | BRCA1: 41.215.214–41.242.384 × 1 (loss E12-E18) | 0.75 | 0.75 | ||
| P20 | BRCA1: 41.261.356–41.261.915 × 1 (loss Intron3) | not possible c | 1.00 | ||
| P21 | BRCA2: 32.891.687–32.916.514 × 3 (dup. E4–13, E27) | 0.39d | 0.97 | ||
| P22 | BRCA1: 41.227.803–41.258.803 × 1 (loss E4–13) | 0.95 | 1.00 | ||
a Hackman et al. 2016
bFor BRCA1/2 target specific panelcn.MOPS results inspect Additional file 5: Excel spreadsheet document 1
cCNVs restricted to introns only are not targeted via targeted capture-based NGS and panelcn.MOPS
dDuplication calling is more difficult compared to deletion calling and individual adjustment of log2 values might be necessary