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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

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

ID Material Sample group Known pathogenic variant in blood Multiplex PCR-based NGS Targeted capture-based NGS
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 nob 3 nob 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
  1. aSee Additional file 3: Table S2 for detailed information on type of pathogenic variant
  2. bno pathogenic germline BRCA1/2 variant detected in blood from the same patient