Supplementary Tables – Methylated circulating cell-free DNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing

<strong>Supplementary table 1:</strong> Plasma samples from 22 Caucasian individuals. <strong>Supplementary table 2</strong> : Custom gene panel of our targeted bisulfite sequencing protocol. DMCs and/or DMRs were identified in the literature from brain, blood or plasma samples of AD compared to control and were identified in brain-specific. <strong>Supplementary table 3</strong> : Tissue specificity of genes (RNA and protein expression) in the targeted-bisulfite capture gene panel according to the Protein Atlas Database. Genes with an "enriched" expression in a tissue show at least four-fold higher mRNA level compared to any other tissue. Genes with an "enhanced" expression mean that there is at least four-fold higher mRNA level in a tissue compared to the average level in all other tissues. <strong>Supplementary table 4</strong> : 632 DMCs in ccfDNA from plasma (q-value ≤0.05, Methylation change &gt;5%) <strong>Supplementary table 5</strong>: 22 CpG segments and 2 DMRs identified in our plasma study of Alzheimer’s disease. The longest transcript is bold, a slash indicates that two genes overlap the segment and an asterisk indicates that this segment overlapped partially region identified. The two segments of DUP22 gene overlap two DMRs: chr6:291686-293332 identified in the superior temporal gyrus [13] and chr6:291687-292823 identified in the hippocampus, entorhinal cortex, dorsolateral prefrontal cortex and cerebellum [33]. The CpG segment and the DMR of the MBP gene overlap two DMRs identified on cortical pyramidal layers (chr18:74799500-74799572) [11] and on the pre-frontal cortex (chr18:74799495-74799572)[34].