Journal: Cancers

Article Title: Advances in Prognostic Methylation Biomarkers for Prostate Cancer

doi: 10.3390/cancers12102993

Figure Lengend Snippet: Methylation profiling approaches for biomarker discovery and validation. ( A ) Candidate gene approaches: Targeted candidate gene approaches used in a priori studies and for the validation of novel candidate markers. ( B ) Genome wide approaches: Microarray and sequencing-based genome-wide approaches used for the discovery of novel biomarkers—comparison of the methodology, number of CpGs (cytosine-guanine dinucleotides) and/or genes targeted and coverage of the methylome across the different platforms. RefSeq: Reference Sequences; PCR: polymerase chain reaction; MSP: methylation-specific PCR; ddPCR: droplet digital PCR; COBRA: combined bisulphite restriction analysis; qMSP: quantitative methylation-specific PCR; HM: human methylation; RRBS: reduced representation bisulphite sequencing; MBDCap-Seq: methyl-CpG binding domain capture sequencing; WGBS: whole genome bisulphite sequencing.

Article Snippet: These studies used targeted methylation profiling techniques including methylation-specific PCR (MSP) [ ], quantitative methylation-specific PCR (qMSP) [ ], pyrosequencing [ , ] and mass spectrometry (MassARRAY EpiTYPER, Agena Bioscience, San Diego, California, USA) [ ] to assess the methylation profile of a specific gene of interest ( ). lists other targeted approaches that have also been used to assess methylation in cancer, including ddPCR [ ], COBRA [ ], high resolution melt curve [ ] and headloop MSP [ , , ].

Techniques: Methylation, Biomarker Discovery, Genome Wide, Microarray, Sequencing, Comparison, Polymerase Chain Reaction, Digital PCR, Combined Bisulfite Restriction Analysis Assay, Bisulfite Sequencing, Binding Assay

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Overview of different methods for DNA methylation detection and analysis. This figure presents PCR-based techniques for targeted analysis of specific CpG sites, as well as microarray, next-generation sequencing (NGS), and third-generation sequencing methods that provide a comprehensive view of the methylome, enabling large-scale DNA methylation profiling across the genome. Figure was created with BioRender.com. ctDNA circulating-tumor DNA, ddPCR droplet digital PCR, dPCR digital PCR, EM-seq enzymatic methyl-seq, gDNA genomic DNA, MeDIP-seq methylated DNA immunoprecipitation sequencing, MethylCap-seq methylated DNA capture sequencing, MSP methylation-specific PCR, NGS next generation sequencing, PCR polymerase chain reaction, qMSP quantitative methylation-specific PCR, RRBS reduced representation bisulfite sequencing, TAPS TET-assisted pyridine borane sequencing, WGBS whole-genome bisulfite sequencing

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: DNA Methylation Assay, Microarray, Next-Generation Sequencing, Sequencing, Digital PCR, Methylated DNA Immunoprecipitation, Methylation, DNA Immunoprecipitation Sequencing, Polymerase Chain Reaction, Methylation Sequencing

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Comparison of DNA methylation detection methods

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: Comparison, DNA Methylation Assay, Methylation Sequencing, Sequencing, Methylation, Size Selection, Biomarker Discovery, DNA Immunoprecipitation Sequencing, Methylated DNA Immunoprecipitation Sequencing, Microarray, Hybridization, Amplification, Digital PCR, Nanopore Sequencing

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Summary of recent liquid biopsy-based DNA methylation studies in breast cancer

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: DNA Methylation Assay, Clinical Proteomics, Methylation

Journal: Developmental cell

Article Title: A Yap-Myc-Sox2-p53 Regulatory Network Dictates Metabolic Homeostasis and Differentiation in Kras-driven Pancreatic Ductal Adenocarcinomas

doi: 10.1016/j.devcel.2019.07.022

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Bisulfate Conversion and quantitative Methylation-Specific PCR (qMSP) Genomic DNA was purified from the pancreatic tissues of WT, KF, and KYYF using PrepEase Genomic DNA isolation kit (Affymetrix, Cleveland, Ohio) according to the manufacture’s instruction.

Techniques: Recombinant, Viability Assay, Imaging, TUNEL Assay, Methylation, Plasmid Preparation, Polymer, cDNA Synthesis, SYBR Green Assay, Bicinchoninic Acid Protein Assay, DNA Extraction, Amplification, Knock-Out, CRISPR, Software