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

Table 1 Comparison of the targeted capture-based to the multiplex PCR-based NGS strategy applied to DNA originating from FFPE tissue samples from 13 ovarian cancers

ID	Material	Sample group	Known pathogenic variant in blood	Multiplex PCR-based NGS		Targeted capture-based NGS
ID	Material	Sample group	Known pathogenic variant in blood	Pathogenic variant detected?^a	False positive path. Variants	Pathogenic variant detected?^a	False positive path. Variants
P01	FFPE tissue	Routine diagnostic	BRCA2:p.Ala1327fs	yes	3	yes	0
P02			BRCA2:p.Asn1747fs	yes	3	yes	0
P03			BRCA1:p.Gln1756fs	yes	3	yes	0
P04			BRCA1:p.Leu786fs	yes	3	yes	0
P05			BRCA1:p.Cys61Gly	(no)	3	yes	0
P06			BRCA2:p.Val1283fs	yes	3	yes	0
P07			BRCA2:p.Asn433fs	yes	3	yes	0
P08			BRCA2:p.Asn1747fs	yes	3	yes	0
P09			–	no^b	3	no^b	0
P10			BRCA1:NM_007294.3:c.4675 + 1G > A	(no)	2	yes	0
P11			BRCA1:p.Glu23fs	yes	3	yes	0
P12			BRCA2:p.Asn2135fs	yes	3	yes	0
P13			BRCA1:NM_007294.3:c.4675 + 1G > A	yes	3	yes	0

^aSee Additional file 3: Table S2 for detailed information on type of pathogenic variant
^bno pathogenic germline BRCA1/2 variant detected in blood from the same patient

ISSN: 1471-2407