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. 2017 Apr 8;18:66. doi: 10.1186/s13059-017-1193-3

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© The Author(s). 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 7 — Jaccard Index, sensitivity, and specificity of SynthEx. Statistics of CNA tools from whole exome sequencing (WES) methods SynthEx KNN (black), SynthEx Synthetic (SN, red), VarScan2 (blue), ADTEx (green), and ControlFREEC (purple) compared to SNP arrays (a–c) and whole genome sequencing (WGS) (d–f) in TCGA breast cancer dataset. Compared to SNP arrays, one-sided t-tests tested SynthEx SN to the next highest mean to determine significance for a Jaccard Index (SynthEx SN versus ADTEx p = 4.9e-5), b sensitivity (SynthEx SN versus ADTEx p = 0.40), and c specificity (SynthEx SN versus VarScan2 p = 5.6e-10). Overall mean differences were significant in all plots as measured by ANOVA (Jaccard Index p = 1.7e-8, sensitivity p = 0.00029, specificity p = 0.0055). Compared to WGS, SNP (gold) and SynthEx KNN and SynthEx SN outperformed the other WES callers: d Jaccard Index (ANOVA p < 2e-16), e sensitivity (ANOVA p = 5.4e-9), and f specificity (ANOVA p = 1.5e-8). No statistical differences between SNP and SynthEx SN were measured in d–f (one-sided t-test p > 0.94)