nebnext enzymatic methyl seq v2 conversion kit  (New England Biolabs)

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) Samples used in study arms: Arm 1 HCT116 cell line, Arm 2 NA12878 & K562 cell lines, Arm 3 patient-derived material, and Arm 4 CLL samples. B) Data generated on each arm of the study. C) Arm 4 CLL patient clinical characteristics. CLL, chronic lymphocytic leukemia; CRC, colorectal cancer; EPIC, MethylationEPIC array; NSCLC, non-small cell lung cancer; WGMS, whole genome methylation sequencing

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Derivative Assay, Generated, Methylation, Sequencing

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) HCT116 DNMT1 and DNMT3b knockout cell lines diluted with in vivo methylated DNA at the indicated percentages (ns). Each dilution point includes three replicates per preparation methodology. B) K562 and C) NA12878 pairwise Pearson correlations of cytosine methylation in CpG contexts with at least 10 × coverage. D) Normalized genome coverage by %GC content in 100 bp windows*. E) Normalized coverage over CpG islands and CpG island density by GC%*. F) Fraction of Cs called in CpG islands as a fraction of total fragment pairs (p = 1.4e −4 ). *Shaded areas represent 95% CI windows; zoom shown for context. BS-seq, bisulfite cytosine conversion and next-generation sequencing; C, cytosine; EM-seq, enzymatic cytosine conversion and next-generation sequencing; GC, guanine/cytosine

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Knock-Out, In Vivo, Methylation, Next-Generation Sequencing

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) Library yield*. B) Percent duplicates from Bismark deduplication*. C) Average insert size using Bismark with default parameters*. D) Fraction of called cytosines in CpG Islands as a fraction of total fragments*. E) Total number of called extracted cytosines in CpG context across Bismark parameters**. F) Clustered heatmap of sample-to-sample Pearson correlations of average methylation over CpG islands. * P -value < P < 1e −6 . **Shaded regions reflect 95% CI. BS-seq, bisulfite cytosine conversion and next-generation sequencing; CRC, colorectal cancer; EM-seq, enzymatic cytosine conversion and next-generation sequencing; FFPE, formalin-fixed paraffin-embedded; FFZN, fresh frozen; NSCLC, non-small cell lung cancer

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Methylation, Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) Average percent methylation in panel regions in WGMS vs Capture sequencing for Arm1 EM-seq dilution samples. (p < 1e-4, R = 0.99, Pearson Correlation). B) Percent methylation for Arm1 samples at indicated methylation dilutions across CpGs with > = 10 × CpG coverage at a CpG Island within MYC. C) Coverage and On Target Percentage for panel capture sequencing. (*p = 0.03, **p < 1e-4) for all EM v BS except cfDNA. D) Mean insert size for panel capture cfDNA. (p = 3.9e-3, Wilcoxon signed-rank). E) Clustering samples by Pearson correlation across panel region average methylation. F). Percent methylation by CpG across the IGF2 CpG Island for CpGs with 10X coverage or greater

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Methylation, Sequencing

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) Heatmap of differentially methylated regions hypermethylated in tumor vs normal samples. B) Average methylation across two CpG islands in panel capture-sequencing from cfDNA of a NSCLC patient. C) PCA plot of Arm 3 samples from EPIC, panel, and WGMS. D) Density plot of panel regions by average percent methylation (NGS) or normalized beta values (EPIC). BS-seq, bisulfite cytosine conversion and next-generation sequencing; cfDNA, circulating cell-free plasma DNA; CRC, colorectal cancer; EM-seq, enzymatic cytosine conversion and next-generation sequencing; EPIC, MethylationEPIC array; NGS, next-generation sequencing; NSCLC, non-small cell lung cancer; WGMS, whole genome methylation sequencing

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Methylation, Sequencing, Next-Generation Sequencing, Clinical Proteomics

Journal: Clinical Epigenetics

Article Title: Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples

doi: 10.1186/s13148-025-01959-0

Figure Lengend Snippet: A) Volcano plot highlighting significant methylation differences in TSS regions of progressed vs non-progressed patients following treatment. B) Correlation of IL15 methylation with expression from bulk RNA-Seq data from corresponding samples ( R = -0.73, p < 1e-6). C) IL15 expression correlates with the Biocarta G2 pathway, showing a significant relationship between IL15 expression and cell cycle signaling ( R = 0.63, p = 1e-5). D) Methylation signal profile across a CpG island at the IL15 TSS. Line represents the average methylation of each group with shaded regions reflecting 95% CI. TSS, transcriptional start site

Article Snippet: In this study, we directly compared enzymatic methylation conversion (NEBNext EM-seq; New England Biolabs, Ipswich, MA, USA [ ]) with the gold-standard bisulfite conversion, using a post-bisulfite adapter tagging (PBAT) approach (EZ-96 DNA Methylation-Gold, Zymo Research, Irvine, CA, USA and Accel-NGS methyl-seq DNA library kit [hereafter referred to as BS-seq, also used generally to refer to bisulfite conversion followed by NGS, and not to be confused with the original BS-Seq method [ ]], Swift Bioscience, Ann Arbor, MI, USA) for whole genome methylation sequencing (WGMS), targeted methylation panel sequencing and MethylationEPIC [ ] arrays (EPIC; Illumina, San Diego, CA, USA) (Supplemental Fig. ).

Techniques: Methylation, Expressing, RNA Sequencing