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The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

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Wenlei Peng
wenleipeng@cuhk.edu.hk

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This DAC controls 6 datasets

Dataset ID	Description	Technology	Samples
EGAD00001008809	5 human plasma cell-free DNA cases (BS-seq)	NextSeq 500	5
EGAD50000000458	Universal targeted haplotyping by droplet digital PCR sequencing (amplicon sequencing)	NextSeq 500	22
EGAD50000000459	Universal targeted haplotyping by droplet digital PCR sequencing (Target Capture sequencing)	NextSeq 500	25
EGAD50000000541	This dataset was generated using single-molecule real-time sequencing for both training and testing purposes. The DNA samples isolated from human buffy coats or placenta of healthy individuals (n=4,) were prepared in a way that four types of base modifications were incorporated, including unmodified controls, 5mC, 5hmC, and 6mA. The sequence data for each sample consists of subreads produced by single-molecule real-time sequencing and stored in a bam format. Details of the specific experiments conducted in this study are outlined in our manuscript.	Sequel II	7
EGAD50000000580	This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format.	NextSeq 500	360
EGAD50000000970	The uploaded data includes sequencing data of 862 individuals from the nasopharyngeal carcinoma (NPC) screening study. Samples from this cohort were sequenced using targeted sequencing methods for the Epstein Barr Virus (EBV) and selected autosomal DNA, but only ‘off-target’ reads were used for fragmentomic analyses. We have also performed genome-wide (non-targeted sequencing) for 1) Individuals with the highest and lowest cell-free DNA concentration (40 individuals); 2) A subsequent collection of the subjects with the highest and lowest DNA concentrations after six years (26 individuals); 3) 30 cases of pregnancy and 4) 20 patients with hepatocellular carcinoma. All sequencing data are of extracted plasma cfDNA from human subjects. The targeted sequencing samples from 862 individuals were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19). The alignments were provided in bam format. The original fastq files of the remaining non-target sequencing samples were provided.	NextSeq 2000 NextSeq 500	977