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Figure 7 | Genome Medicine

Figure 7

From: Ultradeep analysis of tumor heterogeneity in regions of somatic hypermutation

Figure 7

DDiMAP shows high sensitivity, estimated with logistic model of mixed BCL2 reads from SOLiD data. Ten million reads were randomly selected from two specimens in proportions ranging from 1:31 to 31:1, mapped using BFAST and analyzed using the ROA threshold and verify procedure with a conservative threshold setting of 750 ppm applied in each direction (see Additional file 1 for experimental details). A set of 71 indicator mutations from the single specimens that had pure specimen frequencies ranging from 5% to 40% in BCL2 were selected. The presence (1) or absence (0) of each of the indicator mutations in the various blends is plotted against their diluted frequencies on a log scale (non-informative data above 2% and below 0.05% are not shown). Also plotted is the logistic model (solid line) and 95% confidence limits (dashed lines). This model indicates that the method has 80% ±10% sensitivity for mutations occurring at a frequency of 0.4% indicated by the circle on the model plot. The data also indicate the method is unlikely to observe SNVs below the lowest observed indicator mutation frequency recovered from the blend (0.25%), where a modeled sensitivity of 30% ± 14% is marked by a square.

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