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Genome-wide DNA methylation analysis in cfDNA from pancreatic cancer patients

ABSTRACT: Genome-wide DNA methylation analysis in cfDNA from pancreatic cancer patients

PROVIDER: PRJNA632511 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11783519_1.fastq.gz	Fastqsanger.gz
	SRR11783519_2.fastq.gz	Fastqsanger.gz
	SRR11783520_1.fastq.gz	Fastqsanger.gz
	SRR11783520_2.fastq.gz	Fastqsanger.gz
	SRR11783521_1.fastq.gz	Fastqsanger.gz

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Genome-wide DNA methylation analysis in cfDNA from pancreatic cancer patients

Project description:Heterogeneity in DNA methylation status may exist between primary tumors and cfDNA. We compared the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients. MBD-sequencing (seq) was performed in paired samples of FNA and cfDNA from two patients. The majority of DNA methylation peaks overlapped in FNA and cfDNA samples (82.6% and 82.9% in patients #1 and #73, respectively). DNA methylation levels of each gene in FNA and cfDNA samples were highly correlated with each other (r=0.98 and 0.97 in samples 1 and 73, respectively)

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Project description:As a non-invasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma is raising increasing interest due to its diagnostic and biology applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. Through enriching methylated cfDNA fragments with MeDIP followed by deep sequencing, we aimed to characterize cfDNA methylome in cancer patients. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. MEDIPS package was used for the identification of differentially methylated regions (DMRs) between patients and normal ones. Overall, we identified 330 differentially methylated regions (DMRs) in gene promoter regions, 33 hypermethylation and 297 hypomethylation respectively, by comparing lung cancer patients and healthy individuals as controls. The 33 hypermethylation regions represent 32 genes. Some of the genes had been previously reported to be associated with lung cancers, such as GAS7, AQP10, HLF, CHRNA9 and HOPX. Taken together, our study provided an alternative method of cfDNA methylation analysis in lung cancer patients with potential clinical applications.

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