Performance of the B and T panels in DNA from matched blood and tumor FFPE samples.

<p><b>A:</b> B panel; <b>B:</b> T panel. Read ratios for all amplicons for matched samples sorted per gene are shown, corresponding to 70192 observations with the B and 26128 observations with the T panel. Lanes and dots therein represent mean read ratios per amplicon for all samples tested in the respective group. Amplicon order is the same in all graphs. Solid and dotted horizontal lines within graphs: mean values + 3xSD per panel per sample type, respectively. Amplicon reading efficiency was overall constant between blood—FFPE samples with the same panel. For some genes with frequent gains in breast cancer, e.g., <i>CCND1</i>, <i>EGFR</i>, <i>ERBB2</i>, <i>PIK3CA</i> (B panel) and <i>AKT1</i>, <i>EGFR</i> (T panel) outliers with maximal amplicon read ratios outside the Y-axis were observed (A & B, red stars in tumor graphs). By contrast, for genes frequently lost in breast cancer, e.g., TP53 with both panels, mean read ratios in tumor DNA were lower than in blood (A & B, turquoise stars). FFPE-specific over-representation of individual amplicons was occasionally observed (A & B, diagonal arrows). Importantly, patterns of read ratios occasionally differed for genes targeted with the same amplicons in panels B and T, e.g., for <i>ARID1B</i>, <i>MAP3K1</i>, <i>TP53</i> (A & B, black stars with coloured outlines in blood graphs).