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Table 2 Comparison of CNV detection by array CGH to CNV detection by panelcn. MOPS using blood-derived DNA

From: Targeted capture-based NGS is superior to multiplex PCR-based NGS for hereditary BRCA1 and BRCA2 gene analysis in FFPE tumor samples

     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
  1. a Hackman et al. 2016
  2. bFor BRCA1/2 target specific panelcn.MOPS results inspect Additional file 5: Excel spreadsheet document 1
  3. cCNVs restricted to introns only are not targeted via targeted capture-based NGS and panelcn.MOPS
  4. dDuplication calling is more difficult compared to deletion calling and individual adjustment of log2 values might be necessary
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