MSA: Scalable DNA methylation BeadChip for human trait screening. MSA: Scalable DNA methylation BeadChip for human trait screening

We designed and introduced a new methylation array concentrating on human trait screening and discovery. The new MSA (Methylation Screening Array) leveraged the massive Infinium platform-based data from epigenome-wide association studies, combined with updated knowledge from the latest single cell and cell type-resolution whole genome methylome profiles, to achieve scalable screening of epigenetics-trait association in an ultra-high sample-throughput. Our design encompassed diverse human trait associations, including those with genetic, biological, and demographical variables, environmental exposures, and common human diseases such as neurodegenerative, genetic, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity in supporting 5-hydroxymethylation profiling and comprehensive cell-type deconvolution in diverse human tissues. Our first data using this platform uncovered dynamic chromatin and tissue contexts of DNA modification variations and genetic variants with human trait associations. Overall design: Cell line (GM12878, K562, LNCaP, HeLa, Raji, MCF7, Jurkat, HCT116 and other Coriell cell lines), and 25 human tissue (Adrenal, Bladder, Cerebellum, Colon, Esophagus, Eye, Heart, Kidney, Larynx, Liver, Lung, Lymph Node, Motor cortex, Ovary, PBMC, Pancreas, Placenta, Prostate, Skin, Spinal Cord, Spleen, Stomach, Testis, Thymus, Thyroid, Trachea) and purified cell DNA (CD4+ T cells, CD8+ T cells, total T cell, NK cells, monocytes) and methylation titration control DNA is run on the MSA BeadChip to evaluate MSA reproducibility, accuracy, performance at low input ranges, and capability at capturing biological methylation variation. Tissues including cerebellum, motor cortex, colon, pancreas, skin, heart are additionally processed with bACE conversion to obtain 5hmC profiles.

本研究设计并推出了一款聚焦人类性状筛选与发现的新型甲基化阵列，即甲基化筛查阵列（Methylation Screening Array，MSA）。该阵列依托表观基因组全关联研究（epigenome-wide association studies）中基于Infinium平台的海量数据，并结合最新的单细胞（single cell）及细胞类型分辨率全基因组甲基化组图谱（cell type-resolution whole genome methylome profiles）的更新认知，可实现超高样本通量下表观遗传-性状关联的规模化筛选。
本芯片的设计覆盖了多样化的人类性状关联类型，涵盖遗传、生物学及人口统计学变量、环境暴露，以及神经退行性疾病、遗传性疾病、心血管疾病、感染性疾病与免疫性疾病等常见人类疾病。
我们对该阵列的重复性、准确性，以及在多样化人类组织中支持5-羟甲基化（5-hydroxymethylation）谱分析与全面细胞类型反卷积（cell-type deconvolution）的能力进行了全方位评估。
本研究使用该平台生成的首批数据，揭示了与人类性状相关的DNA修饰变异及遗传变异的动态染色质与组织背景特征。

整体实验设计：将细胞系（GM12878、K562、LNCaP、HeLa、Raji、MCF7、Jurkat、HCT116等Coriell细胞系）、25种人类组织（肾上腺、膀胱、小脑、结肠、食管、眼、心脏、肾脏、喉、肝、肺、淋巴结、运动皮层、卵巢、外周血单个核细胞（Peripheral Blood Mononuclear Cell，PBMC）、胰腺、胎盘、前列腺、皮肤、脊髓、脾脏、胃、睾丸、胸腺、甲状腺、气管）、纯化细胞DNA（CD4+ T细胞、CD8+ T细胞、总T细胞、NK细胞、单核细胞）以及甲基化梯度对照DNA置于MSA微珠芯片上进行检测，以评估MSA的重复性、准确性、低起始量下的性能，以及捕获生物学甲基化变异的能力。此外，针对小脑、运动皮层、结肠、胰腺、皮肤、心脏这几种组织，额外采用bACE转化法进行处理，以获取5-羟甲基胞嘧啶（5-hydroxymethylcytosine，5hmC）谱图。