Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data
Figure 1
Read error of Ion Torrent PGM in the EGFR target region.
a, Relationship between the read error rate, read depth, and detection limit for mutations when the significance level is p=2x10-5. Horizontal axis, read depth; vertical axis, detection limit (%). From top to bottom, each line indicates a read error rate (RER) of 1%, 0.2%, 0.05%, or 0.01%. b, Three-dimensional representation of substitution RER. x-axis, base positions of EGFR exons 19–21. From left to right, the arrowheads indicate the positions of T790M, L858R, and L861Q. y-axis, 48 DNA samples from normal individuals. From front to back, conversions to A (green), C (yellow), G (magenta), or T (blue) are aligned for each sample. z-axis, RER (%). c, Three-dimensional representation of the insertion/deletion error. x-axis, base positions of EGFR exons 19–21. The bar indicates the position of the exon 19 deletion. y-axis, 48 DNA samples from normal individuals. Blue, plasma DNA; light blue, WBC DNA (large amount); dark blue, WBC DNA (small amount). z-axis, RER (%). d, Distribution of the RER. White column, substitution error; gray column, insertion/deletion error. Horizontal axis, range of RER (%); vertical axis, incidence (%).