Journal: Scientific Reports

Article Title: Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

doi: 10.1038/s41598-019-44765-4

Figure Lengend Snippet: Neither SOD1 nor C9orf72 CpG islands are differentially methylated between mutation-positive ALS-discordant twins/triplets. The relative location of targeted CpG islands (CGI) and exon 1 are indicated for SOD1 ( A , top) and C9orf72 ( B , top). ( A ) Methylation of the CpG island spanning the promoter region and exon 1 of SOD1 does not show differential methylation between an ALS-affected triplet and unaffected co-triplets, concordant for SOD1 p.I114T. Methylation status was determined using both EpiTYPER (bottom) and 450K (middle) assays. ( B ) Transcript variants (T1, T2, and T3) and the position of the repeat expansion (black diamond) relative to exon 1 are shown for C9orf72 (top). Methylation of the C9orf72 promoter region/expansion flanking CpG islands are not differentially methylated between ALS-discordant co-twins that carry the C9orf72 hexanucleotide repeat expansion in either EpiTYPER (bottom) or 450K data sets (middle).

Article Snippet: To perform a high-density, targeted analysis, we used EpiTYPER, with additional support from a number of Infinium HumanMethylation450K CpG sites present in the same region.

Techniques: Methylation, Mutagenesis

Journal: Scientific Reports

Article Title: Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

doi: 10.1038/s41598-019-44765-4

Figure Lengend Snippet: Twin cohort details.

Article Snippet: To perform a high-density, targeted analysis, we used EpiTYPER, with additional support from a number of Infinium HumanMethylation450K CpG sites present in the same region.

Techniques: Mutagenesis, Sampling, Control

Journal: Nature immunology

Article Title: A comprehensive analysis of AID's effects on the transcriptome and methylome of activated B cells

doi: 10.1038/ni.2616

Figure Lengend Snippet: ( a,b ) Pairwise comparisons of methylation frequency in AID-overexpressing and Aicda −/− B cells for ( a ) 1 kb windows and ( b ) all CpGs, as determined by RRBS. ( c,d ) Comparison of DNA methylation frequencies as determined by RRBS and Epityper for a random subset of CpGs with ( c ) > 20% greater methylation in Aicda −/− than in WT and ( b ) CpGs with < 10% difference between Aicda −/− and WT. Lines are linear fit for Aicda −/− or pooled WT and AID–miR-155T data. ( e ) Comparison of differences in gene expression and methylation in the associated promoters for AID–miR-155T and Aicda −/− B cells. (n = 1 mouse per genotype; r = Pearson's correlation coefficient)

Article Snippet: Epityper assays were performed by the Weill Cornell Medical College Epigenomics Core.

Techniques: Methylation, Comparison, DNA Methylation Assay, Gene Expression

Journal: Clinical Epigenetics

Article Title: Quantitative survey of multiple CpGs from 5 genes identifies CpG methylation panel discriminating between high- and low-grade cervical intraepithelial neoplasia

doi: 10.1186/s13148-014-0037-1

Figure Lengend Snippet: Sample characteristics and number of samples whose CpG islands for each gene were successfully amplified for EpiTYPER analysis

Article Snippet: We cloned the EpiTYPER PCR products into pGEM-T Easy vectors (Promega, WI).

Techniques: Amplification

Journal: Clinical Epigenetics

Article Title: Quantitative survey of multiple CpGs from 5 genes identifies CpG methylation panel discriminating between high- and low-grade cervical intraepithelial neoplasia

doi: 10.1186/s13148-014-0037-1

Figure Lengend Snippet: Bisulfite sequencing (BS) of CpGs assayed by EpiTYPER. Three genes were bisulfite-sequenced in eight cervical samples of various stages. In each panel, sample ID is shown at the top , and EpiTYPER results are shown below the gene name as the average level for all measured CpGs. BS results are summarized as filled circles representing methylated CpGs and open circles representing unmethylated CpGs. Each line is an independently sequenced clone. Each column is a CpG of the gene.

Article Snippet: We cloned the EpiTYPER PCR products into pGEM-T Easy vectors (Promega, WI).

Techniques: Methylation Sequencing, Methylation

Journal: Clinical Epigenetics

Article Title: Quantitative survey of multiple CpGs from 5 genes identifies CpG methylation panel discriminating between high- and low-grade cervical intraepithelial neoplasia

doi: 10.1186/s13148-014-0037-1

Figure Lengend Snippet: The positions of CpGs analyzed by EpiTYPER. Drawings are schematic and not to scale. The orientation of each gene is indicated by the arrow at the end. Boxes indicate exons or UTRs; vertical lines indicate individual CpGs in the CGI regions, and the horizontal bars indicate the regions analyzed by EpiTYPER.

Article Snippet: We cloned the EpiTYPER PCR products into pGEM-T Easy vectors (Promega, WI).

Techniques:

Journal: Human Molecular Genetics

Article Title: Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits

doi: 10.1093/hmg/ddt430

Figure Lengend Snippet: CpG–metabotype associations limited to loci that also show a strong association with a genetic variant

Article Snippet: Association between genotype, CpG–methylation and metabolic phenotype at the ACADM locus. ( A ) Scatterplot of b-values at cg10523679 and hexanoylcarnitine, colored by the genotype of SNP rs12134854; ( B ) correlation between methylation of cg10523679 determined by EpiTYPER and by the Infinium HumanMethylation450 BeadChip for selected samples ( r 2 = 0.954); ( C ) as in (A), but for cg10523679 methylation determined on a subset of samples using the EpiTYPER system (fragment 4, which contains cg10523679); ( D ) boxplots of hexanoylcarnitine concentrations as a function of rs12134854 genotype; ( E ) methylation of cg10523679 determined using the Infinium HumanMethylation450 BeadChip as a function of the rs12134854 genotype.

Techniques:

Journal: Human Molecular Genetics

Article Title: Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits

doi: 10.1093/hmg/ddt430

Figure Lengend Snippet: Association between genotype, CpG–methylation and metabolic phenotype at the ACADM locus. ( A ) Scatterplot of b-values at cg10523679 and hexanoylcarnitine, colored by the genotype of SNP rs12134854; ( B ) correlation between methylation of cg10523679 determined by EpiTYPER and by the Infinium HumanMethylation450 BeadChip for selected samples ( r 2 = 0.954); ( C ) as in (A), but for cg10523679 methylation determined on a subset of samples using the EpiTYPER system (fragment 4, which contains cg10523679); ( D ) boxplots of hexanoylcarnitine concentrations as a function of rs12134854 genotype; ( E ) methylation of cg10523679 determined using the Infinium HumanMethylation450 BeadChip as a function of the rs12134854 genotype. This figure shows that there is a strong three-way association between genotype, CpG methylation, and hexanoylcarnitine concentrations at the ACADM locus. Note that hexanoylcarnitine is essentially a substrate of the ACADM enzyme, rs12134854 is in linkage equilibrium of the ACADM gene, and cg10523679 is located in the promoter region of the ACADM gene.

Article Snippet: Association between genotype, CpG–methylation and metabolic phenotype at the ACADM locus. ( A ) Scatterplot of b-values at cg10523679 and hexanoylcarnitine, colored by the genotype of SNP rs12134854; ( B ) correlation between methylation of cg10523679 determined by EpiTYPER and by the Infinium HumanMethylation450 BeadChip for selected samples ( r 2 = 0.954); ( C ) as in (A), but for cg10523679 methylation determined on a subset of samples using the EpiTYPER system (fragment 4, which contains cg10523679); ( D ) boxplots of hexanoylcarnitine concentrations as a function of rs12134854 genotype; ( E ) methylation of cg10523679 determined using the Infinium HumanMethylation450 BeadChip as a function of the rs12134854 genotype.

Techniques: CpG Methylation Assay, Methylation