Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns
Fig 5
Nucleosome footprints interfered with cfDNA WGS sequencing uniformity.
(A-C) Coverage depth at each nucleotide normalized to regional mean depth within ±1000bp of the TSS (A) and ±500bp of the ESS (B) and EES (C) in blood samples. Each grey line represents a sample. Red line represented the mean value of all samples. (D-F) Coverage depth at each nucleotide normalized to regional mean depth within ±1000bp of the TSS (D) and ±500bp of the ESS (E) and EES (F) in cfDNA samples. Each grey line represents a plasma cfDNA sample. Black lines represents the body fluid cfDNA sample. Orange line represents the mean value of all plasma cfDNA samples. Vertical dashed lines mark local coverage depth maxima. (G-I) Coverage depth at each nucleotide normalized to regional mean depth within ±1000bp of the TSS (G) and ±500bp of the ESS (H) and EES (I) in tumor samples. Each grey line represents a sample. Blue lines represent the mean value of all samples. (J-L) Per base GC content within ±1000bp of the TSS (J) and ±500bp of the ESS (K) and the EES (L).