Adjacent CpG sites in mammalian genomes can be co-methylated owing to the processivity of methyltransferases or demethylases, yet discordant methylation patterns have also been observed, which are related to stochastic or uncoordinated molecular processes. We focused on a systematic search and investigation of regions in the full human genome that show highly coordinated methylation. We defined 147,888 blocks of tightly coupled CpG sites, called methylation haplotype blocks, after analysis of 61 whole-genome bisulfite sequencing data sets and validation with 101 reduced-representation bisulfite sequencing data sets and 637 methylation array data sets. Using a metric called methylation haplotype load, we performed tissue-specific methylation analysis at the block level. Subsets of informative blocks were further identified for deconvolution of heterogeneous samples. Finally, using methylation haplotypes we demonstrated quantitative estimation of tumor load and tissue-of-origin mapping in the circulating cell-free DNA of 59 patients with lung or colorectal cancer.
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data
Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming
Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia
Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments
An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer
Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC)
Enrichment of methylated molecules using enhanced-ice-co-amplification at lower denaturation temperature-PCR (E-ice-COLD-PCR) for the sensitive detection of disease-related hypermethylation
Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci
Tumor-specific methylations in circulating cell-free DNA as clinically applicable markers with potential to substitute mutational analyses
Towards precision medicine: advances in 5-hydroxymethylcytosine cancer biomarker discovery in liquid biopsy
5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers
Genome-wide methylation and expression profiling identify methylation-associated genes in colorectal cancer
Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing
Liver- and Colon-Specific DNA Methylation Markers in Plasma for Investigation of Colorectal Cancers with or without Liver Metastases
Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics
Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches
5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
Opioid Exposure is Associated with Aberrant DNA Methylation of OPRM1 Promoter Region in a Chinese Han Population
Molecular characterisation and liquid biomarkers in Carcinoma of Unknown Primary (CUP): taking the 'U' out of 'CUP'
The 150 most important questions in cancer research and clinical oncology series: questions 94-101 : Edited by Cancer Communications
Digital Droplet PCR for Monitoring Tissue-Specific Cell Death Using DNA Methylation Patterns of Circulating Cell-Free DNA
HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations
Noninvasive chimeric DNA profiling identifies tumor-originated HBV integrants contributing to viral antigen expression in liver cancer
Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data
Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease
Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker
Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans
Comprehensive DNA methylation analysis of tissue of origin of plasma cell-free DNA by methylated CpG tandem amplification and sequencing (MCTA-Seq)
Future of Liquid Biopsies With Growing Technological and Bioinformatics Studies: Opportunities and Challenges in Discovering Tumor Heterogeneity With Single-Cell Level Analysis
BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues
Distal regulatory elements identified by methylation and hydroxymethylation haplotype blocks from mouse brain
The interplay of circulating tumor DNA and chromatin modification, therapeutic resistance, and metastasis
Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis
An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray
Preliminary Analysis of Within-Sample Co-methylation Patterns in Normal and Cancerous Breast Samples
A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral epithelial dysplasia: observation from a prospective study
Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers
Colon and liver tissue damage detection using methylated SESN3 and PTK2B genes in circulating cell-free DNA in patients with acute graft-versus-host disease
Epigenetically Silenced Candidate Tumor Suppressor Genes in Prostate Cancer: Identified by Modeling Methylation Stratification and Applied to Progression Prediction
Histone-related genes are hypermethylated in lung cancer and hypermethylated HIST1H4F could serve as a pan-cancer biomarker
The methylomic landscape of fallopian tube lesions associated with ovarian high-grade serous carcinoma
DNA methylation haplotype block markers efficiently discriminate follicular thyroid carcinoma from follicular adenoma
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Synthetic Genetic Array Analysis
Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.
Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.
Neural Activity: Imaging
Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.
Cell Atlas of the Human Eye
Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.
Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.
STING Receptor Agonists
Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.