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==Abstract== [Background]Circulating cell-free DNA methylation in plasma have been demonstrated to be powerful potential in non-invasive cancer early diagnosis. However, the genome-wide profile of DNA methylation for the free circulating DNA methylation has not been depicted in a signal base resolution. [Method] In the present study, we carried out a genome-wide survey of single-base resolution methylome across 45 plasma from cancer patients, 30 normal plasma and solid cancer tissues with RRBS, SeqCap and BSPP assays. [Result] In the discovery stage, both RRBS and SeqCap dataset identified large number classification potential biomarkers (N=1592 and 516, respectively) and high level prediction ability with Random Forest model (accuracy=100% and 98.18%, respectively). The above biomarkers were validated in the BSPP dataset and we found the methylation status of 30 derived regions in plasma could explain 93.75% cancers incidence and the specificity is 100%. Whatβs more, the pattern of the DNA methylation fragment transferring were depicted with paired tissue-plasma methylation dataset. We identified 1590 fragments significantly prefer-selected in the releasing process of the DNA methylation fragment from solid tissues to plasma (P<1.98*10-6, binomial test, Bonferroni correction). These fragments were located in the regions of 1190 genes. Function enrichment analysis showed these genes were significantly associated with cancer relevant biological functions, including embryonic morphogenesis, regulation of transcription, neuron differentiation, regionalization, tissue morphogenesis, transcription factor activity, sequence-specific DNA binding, transcription regulator activity. [Conclusion] Methylation haplotype loading based DNA methylation biomarker would be potential cancer diagnosis biomarker and DNA methylation fragment releasing process were regulated rather than a random event.
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