copy number, and fragmentomic patterns in a single assay. Using a total of 950 plasma samples (361 healthy controls and 107 colon, 113 liver, 238 lung, and 131 prostate cancer patients) and 240 tissue samples, we generated whole-genome methylation sequencing (WGMS) data,...
confirming their ESCC-specificity (Supplementary Fig.6). To evaluate the value of these DMRs in ESCC molecular subtyping, we classified the 155 ESCC patients into three groups based on the average methylation levels of these 50 DMRs using hierarchical clustering in the ECG...
2021年7月,清华大学自动化系的汪小我教授团队在Briefings in Bioinformatics上发表了题为“DISMIR: deep learning-based non-invasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA re...
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9(1). Grabuschnig S, Bronkhorst AJ, Holdenrieder S, Rodriguez IR, Schliep KP, Schwendenwein D, et al. Putative origins of cell-free DNA in humans: a ...
Sequence alignment and CpG site methylation calling were done by the Bismark suite (version 0.23.1, [28]). We used picard MarkDuplicate (version 2.18.7 [29]) to mark and remove duplicated reads. Reads were then filtered by samtools (version 1.18, [30]) to keep only reads whose quality ...
2021年7月9日,清华大学自动化系的汪小我教授团队在Briefings in Bioinformatics上发表了题为“DISMIR: deep learning-based non-invasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads”的文章。基于深度学习方法,该研究实现了通过血浆cfDNA的WGBS数据进行高...
methylation enrichment, which removed the need for filler DNA (as used by Huang et al.32) and enabled efficient analysis of samples at low cfDNA inputs (down to 1 ng). Ligated DNA was pooled (to a minimum of 75 ng in total) and combined with 0.3 ng of control methylated ...
These strategies are either very targeted, as methylation events of interest occur at known, stereotyped positions [117], or larger to identify methylation patterns, which have been shown to enable accurate determination of cell-of-origin from cfDNA and non-invasive cancer classification. For example...
Additionally, the analysis of specific DNA methylation present in the cancer’s cells shows the presence of recurrence after the conclusion of the treatment or which type of therapy is better [25,51]. To maintain homeostasis, the cfDNA produced is typically removed by the endonucleases, such as...
The mean methylation at CpG sites for the fully methylated pUC19 control DNA was high for both methods (ssLP: 96.6%; dsLP: 91.1%). The methylation proportion across each position in the read was analyzed separately for the forward and reverse read to assess within-read methylation bias. ...