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

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 CGH^a	CNVs^b	no CNVs^b
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)	0.39^d	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

ISSN: 1471-2407