Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2024 Mar 30;15:2790. doi: 10.1038/s41467-024-47196-6

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 3 — a Workflow to benchmark the model performance. Created with BioRender.com. b Pearson and Spearman correlation of DNA methylation at single CpGs with different coverages at CpG island and CpG island shore regions between matched cfDNA WGBS and WGS. Blue bars represent the Pearson correlation coefficient. Orange bars represent the Spearman correlation coefficient. c Scatterplot of DNA methylation level within 1 kb non-overlapped bins (n = 116,133) at CpG island and CpG island shore regions between matched cfDNA WGBS and WGS. The correlation coefficient and p-value is calculated by two sided Pearson correlation test in cor.test function in R. d Heatmap of measured (left panel, cfDNA WGBS, purple) and predicted (right panel, matched cfDNA WGS, black) DNA methylation level at hypermethylated differentially methylated windows (1 kb) characterized in CGI and CGI shore regions (n = 2822). The row orders in both WGBS and WGS datasets were based on the clustering of DNA methylation levels in WGBS only. e Average ground truth (WGBS) and predicted (WGS) DNA methylation level at CpG island promoter regions (n = 17,880) from cancer and healthy individuals. Orange line represents the ground truth from WGBS in the cancer patient. Red line represents the predicted value from WGS in the cancer patient. Green line represents the ground truth from WGBS in the healthy individual. Blue line represents the predicted value from WGS in the healthy individual. f The fraction of cell types that contributed to cfDNA was estimated by matched WGS and WGBS. Red: Neutrophil. Orange: B cell. Yellow: T cell. Blue: Macrophage. Cyan: Erythroblast. Purple: Endothelia vein. Brown: Liver. Gray: Mammary epithelia. Black: Prostate gland. Source data are provided as a Source Data file.