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Figure 4 | BMC Genomics

Figure 4

From: Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment

Figure 4

Correlation between expected and observed allele fractions in pools and comparison of replicated pools. The top panel shows the correlation between expected and observed allele fractions in the three pools, where the expected value is calculated by dividing the allele fraction observed in the ALL1 or ALL2 genomic DNA (gDNA) sample with the number of samples in the pool. Only single nucleotide variants (SNVs) classified as somatic in the ALL1 (n = 227) or ALL2 (n = 305) gDNA samples are shown. The bottom panel shows the correlation between allele fractions in the replicated pools. The x- and y-axes are cut at 0.5, 0.2 and 0.1 for the pools with two, five and ten samples, respectively. SNVs with an observed allele fraction greater than this are shown in black at the cutoff value. The MR value is the median ratio between all x- and y-values in each plot. It represents how close the two distributions are to each other, with a value of 1 indicating similar distributions.

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