Project description:The Oxford Nanopore technology has a great potential for the analysis of genome methylation, including full-genome methylome profiling. However, there are certain issues while identifying methylation motif sequences caused by low sensitivity of the currently available motif enrichment algorithms. Here, we present Snapper, a new highly-sensitive approach to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper has shown higher enrichment sensitivity compared with the MEME tool coupled with Tombo or Nanodisco instruments, which was demonstrated on H. pylori strain J99 studied earlier using the PacBio technology. In addition, we used Snapper to characterize the total methylome of a new H.pylori strain A45. The analysis revealed the presence of at least 4 methylation sites that have not been described for H. pylori earlier. We experimentally confirmed a new CCAG-specific methyltransferase and indirectly inferred a new CCAAK-specific methyltransferase.
Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).
Project description:This is a comparative study. This study is to compare the diagnostic sensitivity between circulating tumor DNA methylation and carcinoembryonic antigen in detecting colorectal cancer. There are two steps in this study. Firstly, the diagnostic model is established based on tumor-specific plasma circulating tumor DNA methylation markers. Secondly, the sensitivity, specificity and accuracy of plasma circulating tumor DNA methylation are compared with that of carcinoembryonic antigen in detecting colorectal cancer.
Project description:This is a prospective, clinical study. This study is to evaluate the sensitivity of plasma ctDNA methylation haplotypes in detecting local residual or lymph node metastasis.
Project description:This is a multicenter, clinical study. This study is to evaluate the sensitivity of plasma ctDNA methylation haplotypes in detecting colorectal cancer, adenoma and the specificity in healthy individuals.
Project description:This study dynamically monitored the prognosis of stage I-IV colorectal cancer patients who could receive radical surgical resection by detecting the levels of polygene methylation in plasma samples from patients with colorectal cancer. In patients with colorectal cancer feasible radical surgery, plasma ctDNA methylation detection was performed before and after surgical treatment and during regular follow-up to explore the predictive effect of plasma ctDNA methylation status at different time points on postoperative recurrence. To explore whether postoperative dynamic monitoring of plasma ctDNA methylation can be used for adjuvant chemotherapy efficacy evaluation and whether it can indicate tumor recurrence and metastasis earlier than imaging examination.
Project description:Using a public reference data set of 82 unique entities, 382 nanopore-sequenced brain tumor samples were classified based on their methylation status through an ad hoc random forest algorithm. As a measure of confidence, score recalibration was performed and platform-specific thresholds were defined.
