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Fig. 1 | BMC Cancer

Fig. 1

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

Fig. 1

Comparison of normalized coverage of targeted capture-based NGS and multiplex PCR-based NGS in control blood and diagnostic FFPE tumor samples. a Normalized coverage (y-axis) of targeted capture-based and multiplex PCR-based NGS at single-base resolution along all concatenated BRCA1/2 targets (x-axis) of five blood control samples (Additional file 3: Table S2, K1 to K5). The five blood samples are color-coded. The vertical green line indicates the end of BRCA1 targets and the start of the BRCA2 targets (target number is increasing from left to right which corresponds to five to three prime orientation of the gene). The horizontal green line displays normalized coverage of 1.0. All target exons are separated via gray dotted vertical lines. Selected target exons are marked. Exemplary, two randomly chosen amplicon dropouts are marked by a red arrow. b Normalized coverage (y-axis) of targeted capture-based and multiplex PCR-based NGS of FFPE samples from patient 1 to 15 (Additional file 3: Table S2, P01 to P15) at single-base resolution along all concatenated BRCA1/2 targets (x-axis) Samples P1 to P13 are color encoded in blue. Exemplary, randomly chosen capture target dropouts and amplicon dropouts are marked by a red arrow. The vertical green line indicates the end of the BRCA2 targets (target number is increasing from left to right which corresponds to five to three prime orientation of the gene) and the start of the BRCA1 targets (decreasing from left to right). The horizontal green line displays normalized coverage of 1.0. All target exons are separated by gray dotted vertical lines. Selected target exons are marked. Exemplary, two randomly chosen amplicon dropouts are marked with a red arrow. c To illustrate the advantages of the targeted capture-based protocol over the multiplex PCR-based approach for analysis of low-quality DNA the normalized coverages (y-axis) of targets of capture-based and multiplex PCR-based NGS of two FFPE samples (P 5 and P10) are displayed at single-base resolution along all concatenated BRCA1/2 targets (x-axis). Exemplary, two randomly chosen amplicon dropouts are marked with a red arrow

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