MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples.
MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples.
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DOI：
10.2217/epi.12.59
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发表时间：
2012-12
期刊：
影响因子：
3.8
通讯作者：
van den Oord EJ
中科院分区：
文献类型：
--
作者：
Aberg KA;McClay JL;Nerella S;Xie LY;Clark SL;Hudson AD;Bukszár J;Adkins D;Swedish Schizophrenia Consortium;Hultman CM;Sullivan PF;Magnusson PK;van den Oord EJ
我们研究了甲基-CpG结合域(MBD)蛋白丰富的基因组测序(MBD-SEQ)作为一种经济有效的甲基组广泛关联研究(MWAS)筛查工具的使用。由于MBD-SEQ尚未大规模应用，我们首先开发并测试了一条用于数据处理的管道，使用了1500例精神分裂症病例和对照，外加75个技术重复，平均每个样本阅读6800万次。这包括使用技术复制来优化多次和重复读取的质量控制，在有比对问题的基因座中识别CPG的电子实验，基于片段大小分布的多参数估计的CpG覆盖率计算，合并来自相关的相邻CpG站点的数据的两阶段自适应算法，控制混杂因素的主成分分析，以及为处理大数据集而量身定做的新软件。我们使用一种提供单一碱基分辨率的不同技术，在独立样本中复制了MWAS的发现。在一项与年龄相关的甲基化变化的最新研究中，我们最重要的发现之一是之前报道的与GRIA2有关的强有力的关联。我们的结果还表明，由于许多混杂的影响，MWAs的一个相当大的挑战是识别那些对疾病过程有信息的影响。这项研究显示了MBD-SEQ在大规模疾病研究中作为一种经济有效的工具的潜力。
We studied the use of methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) as a cost-effective screening tool for methylome-wide association studies (MWAS). Because MBD-seq has not yet been applied on a large scale, we first developed and tested a pipeline for data processing using 1500 schizophrenia cases and controls plus 75 technical replicates with an average of 68 million reads per sample. This involved the use of technical replicates to optimize quality control for multi- and duplicate-reads, an in silico experiment to identify CpGs in loci with alignment problems, CpG coverage calculations based on multiparametric estimates of the fragment size distribution, a two-stage adaptive algorithm to combine data from correlated adjacent CpG sites, principal component analyses to control for confounders and new software tailored to handle the large data set. We replicated MWAS findings in independent samples using a different technology that provided single base resolution. In an MWAS of age-related methylation changes, one of our top findings was a previously reported robust association involving GRIA2. Our results also suggested that owing to the many confounding effects, a considerable challenge in MWAS is to identify those effects that are informative about disease processes. This study showed the potential of MBD-seq as a cost-effective tool in large-scale disease studies.