An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform.
An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform.
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DOI：
10.4161/epi.24008
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发表时间：
2013-03
期刊：
影响因子：
3.7
通讯作者：
Gomez-Cabrero D
中科院分区：
文献类型：
--
作者：
Marabita F;Almgren M;Lindholm ME;Ruhrmann S;Fagerström-Billai F;Jagodic M;Sundberg CJ;Ekström TJ;Teschendorff AE;Tegnér J;Gomez-Cabrero D
在大多数表观遗传学研究中，差异甲基化CpG的正确鉴定至关重要。Illumina HumanMethylation450芯片被广泛用于DNA甲基化的定量分析；然而，由于生物和技术变异性的卷积以及Infinium I和II型探针设计之间存在信号偏差，设计合适的分析流程面临着严峻挑战。尽管近期有人尝试研究如何分析具有这种阵列设计的DNA甲基化数据，但由于缺乏既有大样本量又有足够数量技术重复的合适数据集，无法对不同的生物信息学流程进行全面比较。在此，我们利用两个未发表的数据集进行了这样的比较分析，这些数据集包含技术重复，并且对外周血、单核细胞或肌肉活检样本进行了DNA甲基化分析，旨在解决降低技术变异性、消除探针设计偏差和减少批次效应的问题。我们评估了不同分析流程的性能，并证明：(1)校正探针设计类型至关重要，因为所测甲基化变化的幅度取决于基础化学原理；(2)不同的归一化方案效果不一，我们所采用的最有效方法是分位数归一化和β混合分位数扩张（BMIQ）；(3)校正批次效应是有益的。总之，我们使用综合数据集进行的比较分析为使用Illumina 450K芯片正确鉴定差异甲基化CpG提出了一个有效的流程。
The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; (2) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); (3) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive data set suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
4.4
作者：
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通讯作者：
Shen, Richard
影响因子：
3.8
作者：
Dedeurwaerder, Sarah;Defrance, Matthieu;Fuks, Francois
通讯作者：
Fuks, Francois
DOI：
10.1007/978-1-62703-011-3_9
发表时间：
2012-01-01
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Borgel, Julie;Guibert, Sylvain;Weber, Michael
通讯作者：
Weber, Michael
DOI：
10.1056/nejmoa1005143
发表时间：
2010-12-16
期刊：
The New England journal of medicine
影响因子：
--
作者：
Ley TJ;Ding L;Walter MJ;McLellan MD;Lamprecht T;Larson DE;Kandoth C;Payton JE;Baty J;Welch J;Harris CC;Lichti CF;Townsend RR;Fulton RS;Dooling DJ;Koboldt DC;Schmidt H;Zhang Q;Osborne JR;Lin L;O'Laughlin M;McMichael JF;Delehaunty KD;McGrath SD;Fulton LA;Magrini VJ;Vickery TL;Hundal J;Cook LL;Conyers JJ;Swift GW;Reed JP;Alldredge PA;Wylie T;Walker J;Kalicki J;Watson MA;Heath S;Shannon WD;Varghese N;Nagarajan R;Westervelt P;Tomasson MH;Link DC;Graubert TA;DiPersio JF;Mardis ER;Wilson RK
通讯作者：
Wilson RK