Journal: Nature Communications

Article Title: A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex

doi: 10.1038/s41467-021-23243-4

Figure Lengend Snippet: a A Manhattan plot for the prefrontal cortex (red, N = 961), temporal gyrus (green, N = 608) and entorhinal cortex (blue, N = 189) meta-analyses, with the ten most significant DMPs circled on the plot and Illumina UCSC gene name shown if annotated, or CpG ID if unannotated. The X -axis shows chromosomes 1–22 and the Y -axis shows −log10( p ), with the horizontal red line denoting Bonferroni significance ( P < 1.238 × 10 −7 ). b A Venn diagram highlighting overlapping DMPs at Bonferroni significance across the cortical tissues. c In each cortical brain region the Bonferroni significant DMPs identified in that region usually had a greater effect size (ES) there, than in any of the other cortical regions. The X -axis represents the methylation (beta) ES between individuals that are Braak stage 0 and VI. Data are separated on the Y -axis by tissue analysis (large text) with the corresponding data at these probes in other tissues (small text). The white dot in the centre represents the median, the dark box represents the interquartile range (IQR), whilst the whisker lines represent the “minimum” (quartile 1–1.5 × IQR) and the ‘maximum’ (quartile 3 + 1.5 × IQR). The coloured violin represents all samples including outliers, meaning that the ‘minimum’ and ‘maximum’ may not extend to the end of the violin.

Article Snippet: The 20 most significant DMPs are circled on the plot and Illumina UCSC gene name is shown if annotated, or CpG ID if unannotated.

Techniques: Methylation, Whisker Assay

Journal: Nature Communications

Article Title: A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex

doi: 10.1038/s41467-021-23243-4

Figure Lengend Snippet: a A Miami plot of the cross-cortex meta-analyses ( N = 1408). Probes shown above the X -axis indicate hypermethylation with higher Braak stage, whilst probes shown below the X -axis indicate hypomethylation with higher Braak stage. The chromosome and genomic position are shown on the X -axis. The Y -axis shows –log10( p ). The red horizontal lines indicate the Bonferroni significance level of P < 1.238 × 10 −7 . Probes with a methylation (beta) effect size (ES: difference between Braak 0- Braak VI) ≥ 0.01 and P < 1.238 × 10 −7 are shown in blue. The 20 most significant DMPs are circled on the plot and Illumina UCSC gene name is shown if annotated, or CpG ID if unannotated. Exact P values can be found in Table and Supplementary Data . b A volcano plot showing the ES ( X -axis) and –log10( p ) ( Y -axis) for the cross-cortical meta-analysis results. Grey probes indicate an ES between ≥0.01, whilst blue probes indicate an ES ≥ 0.01 and P < 1.238 × 10 −7 . c The most significant cross-cortex differentially methylated region (DMR) (chr7:27153212–27154305) contained 11 probes and resided in the HOXA region. The horizontal red line denotes the Bonferroni significance level of P < 1.238 × 10 −7 . Red probes represent a positive ES ≥ 0.01, blue probes represent a negative ES ≥ 0.01. Underneath the gene tracks are shown in black with CpG islands in green.

Article Snippet: The 20 most significant DMPs are circled on the plot and Illumina UCSC gene name is shown if annotated, or CpG ID if unannotated.

Techniques: Methylation