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Fig. 2 | Genome Medicine

Fig. 2

From: Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

Fig. 2

Benchmarking Exo-C against conventional and molecular methods of karyotype and genome analysis (namely karyotyping, aCGH or WGS). A Graphical summary of the 66 samples analyzed in this study. Each sample was examined using the Exo-C protocol, with most undergoing additional orthogonal profiling methods. B Representative example of translocation detected using Exo-C: contacts map of P136 sample P136, which exhibits a chr4-chr9 translocation (above diagonal), and P114, with a normal karyotype (below diagonal). A schematic representation of the translocation and its breakpoint coordinates ([hg19] chr4:174,328,001–174,336,000; chr9:108,424,001–108,432,000) is also included. C Performance of the translocation caller. This graph displays the F1 score, a measure of the translocation caller's performance. Each data point corresponds to a subset of samples, filtered according to their deviation from the cohort average cis-score. The X-axis specifies the maximum allowable deviation for each data point, while the Y-axis represents the observed F1 score for the corresponding filtered sample set. D The distribution of cis-scores across samples is shown, with vertical lines indicating the average for XX and XY genotypes. The shaded area highlights the optimal cis-score range (± 8% from average). E Percentage of True Positive (TP) and False Negatives (FN) calls for modeled translocations of varying lengths. Red bars denote TP calls, while blue bars represent FN. The Y-axis shows the percentage of TP and FN calls for modeled translocations of varying lengths. F Representative example of inversion detected by Exo-C: contacts map of P137 sample (with an inversion on chromosome 7; above diagonal) and P114 sample (with normal karyotype; below diagonal). G F1-score of the inversion-calling algorithm, based on a dataset of simulated inversions of different lengths. H The number of TP calls for simulated inversions, grouped by length intervals, each containing 20 simulations. J Distributions of CNV types and length classes in the low-confidence list of CNVs present in analyzed samples. Bars represent the count of amplifications (blue) or deletions (green) in each length class. K Precision and recall of CNV predictions by GATK, CoNIFER, and CNVkit tools. Color of markers represent evaluation of tools based on low- or high-confidence lists of CNVs with or without CNV size filtration; shape of markers represents evaluation of tools with or without predictions, intersected with known CNVs for less than 50% (in terms of Jaccard Index) and with or without common CNVs (DGV Gold database). Note that precision and recall outcomes in analyzes excluding or including DGV Gold CNVs are almost similar, therefore corresponding markers may not be fully visible due to overlap

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Genome Medicine

ISSN: 1756-994X

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