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. 2021 May 28;12:3230. doi: 10.1038/s41467-021-23445-w

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Conceptual outline of the LIQUORICE method and software for fragment analysis of cfDNA based on tumor-specific epigenetic alterations. b Aggregated, bias-corrected, and normalized coverage signals at selected genomic region sets shown for healthy controls, for non-EwS sarcomas, and for EwS cfDNA samples. EwS samples are grouped by genetically inferred tumor-derived DNA content and clinical tumor evidence. cfDNA samples with coverage signals significantly different (three standard deviations) from healthy controls are displayed in red; the total number of those samples and the direction of the deviation (arrow) are indicated. Total dip depth was used as the metric of choice for the sharp dips at hematopoietic-specific and universal DHSs; area over the curve (AOC) was used for the other region sets. c cfDNA-based coverage signal at EwS-specific DHSs (bottom, n_EwS = 38) reflects the aggregate DNA methylation profiles at these regions in matched tumor biopsies (top, n_EwS = 38). d Scatterplots showing the correlation of the coverage signal at EwS-specific DHSs with the genetically inferred tumor-derived DNA content of the cfDNA samples. Pearson correlation coefficients (r) and linear trend lines are shown. The x-axes are shown in a log scale from 1% onwards. e Same as d but showing the coverage signal at hematopoietic-specific DHSs. Blue arrows indicate samples with significant liver signature. f Aggregated, bias-corrected, and normalized coverage signal (AOC) at alveolar rhabdomyosarcoma (ARMS)-specific DHSs for cfDNA samples from healthy controls and patients with EwS, RMS, and other pediatric sarcomas (left; p-values were calculated using two-sided Mann–Whitney U tests without correction for multiple testing). For ARMS patients with at least 9% ctDNA (genetic-based evidence), a striking reduction of fragment coverage was observed (right). A cfDNA sample from a patient with embryonal rhabdomyosarcoma (ERMS) did not show any reduction of fragment coverage at ARMS-specific DHSs (bottom right).