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SynthEx: a synthetic normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling

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Academic year: 2020

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Figure

Fig. 1 Sample-specific bias of read ratios due to sequencing quality metrics of the tumor–normal pair
Fig. 2 Hierarchical clustering of the top 2500 most variable exons in TCGA breast normal
Fig. 3 Generation of synthetic normal and improvement of technical noise with synthetic normal.normals
Fig. 4 Varying bin sizes for the synthetic normal and K nearest neighbor. Copy number ratios were calculated from the K nearest neighbordifference at 100-kb non-overlapping bin sizes;20 (strategy for K = 5 at varying bins and compared to SynthEx Synthetic (composite synthetic normal) using: a the mean square successive b the Jaccard Index; c sensitivity; and d specificity using SNP array as the ground truth at 10 (red),blue), 50 (green), and 100 kb (purple)
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