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Genetic, epigenetic and fragmentomic profiling of plasma cell-free DNA in cancer patients

The primary goal of the study is to explore the temporal changes in cfDNA profiles in liver cancer patients undergoing therapeutic treatment. Serial blood collection and plasma cfDNA analysis were performed in patients with liver cancer, including patients with primary hepatocellular carcinoma, or those with secondary liver metastasis. Various molecular features of cfDNA were studied, including tumor fraction, epigenetic and fragmentomic analysis.

Type: Whole Genome Sequencing
Archive: European Genome-phenome Archive (EGA)

1 Dataset

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Dataset ID	Description	Technology	Samples
EGAD50000002912	The uploaded data includes sequencing of plasma cfDNA from a total of 33 cancer patients. Plasma cfDNA samples were sequenced for whole-genome sequencing analysis using double-stranded DNA libraries, and paired bisulfite sequencing using single-stranded DNA libraries. All sequencing data are of extracted plasma cfDNA from human patients, and sequenced using the Illumina NovaSeq6000 platform. Alignment was performed to the human genome (hg19). Lambda DNA was added to samples subjected to bisulfite sequencing for quality control.	Illumina NovaSeq 6000	467