A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data.
A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data.
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DOI：
10.18632/aging.100718
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发表时间：
2015-02
期刊：
影响因子：
--
通讯作者：
Garagnani P
中科院分区：
文献类型：
--
作者：
Bacalini MG;Boattini A;Gentilini D;Giampieri E;Pirazzini C;Giuliani C;Fontanesi E;Remondini D;Capri M;Del Rio A;Luiselli D;Vitale G;Mari D;Castellani G;Di Blasio AM;Salvioli S;Franceschi C;Garagnani P
衰老的特征在于DNA甲基化模式的表观遗传结构的深刻重塑。迄今为止，研究全基因组DNA甲基化变化的最有效工具是Infinium HumanMethylation 450 BeadChip（Infinium 450k）。尽管Infinium 450k分析工具丰富，但识别最具生物学相关性的DNA甲基化变化仍然具有挑战性。在这里，我们提出了一个分析管道来选择差异甲基化区域（DMR），定制的微阵列架构，这是非常有效的突出生物学相关的结果。流水线基于微阵列探针相对于CpG岛和基因序列的定位对微阵列探针进行分组，并且根据探针密度，通过考虑多个相邻CpG探针的伴随变化的单探针或区域中心方法来识别DMR。我们成功地将这种分析管道应用于3个独立的Infinium 450k数据集，这些数据集研究了与年龄相关的血液DNA甲基化变化。我们提供了一个基因的共识列表，这些基因在0到100年的DNA甲基化水平上系统地变化，并且在衰老过程中具有潜在的相关作用。
Aging is characterized by a profound remodeling of the epigenetic architecture in terms of DNA methylation patterns. To date the most effective tool to study genome wide DNA methylation changes is Infinium HumanMethylation450 BeadChip (Infinium 450k). Despite the wealth of tools for Infinium 450k analysis, the identification of the most biologically relevant DNA methylation changes is still challenging. Here we propose an analytical pipeline to select differentially methylated regions (DMRs), tailored on microarray architecture, which is highly effective in highlighting biologically relevant results. The pipeline groups microarray probes on the basis of their localization respect to CpG islands and genic sequences and, depending on probes density, identifies DMRs through a single-probe or a region-centric approach that considers the concomitant variation of multiple adjacent CpG probes. We successfully applied this analytical pipeline on 3 independent Infinium 450k datasets that investigated age-associated changes in blood DNA methylation. We provide a consensus list of genes that systematically vary in DNA methylation levels from 0 to 100 years and that have a potentially relevant role in the aging process.
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影响因子：
4.4
作者：
Bibikova, Marina;Barnes, Bret;Shen, Richard
通讯作者：
Shen, Richard
影响因子：
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作者：
Bocklandt S;Lin W;Sehl ME;Sánchez FJ;Sinsheimer JS;Horvath S;Vilain E
通讯作者：
Vilain E
全基因组甲基化谱揭示了人类衰老速度的定量观点。
影响因子：
16
作者：
Hannum, Gregory;Guinney, Justin;Zhao, Ling;Zhang, Li;Hughes, Guy;Sadda, SriniVas;Klotzle, Brandy;Bibikova, Marina;Fan, Jian-Bing;Gao, Yuan;Deconde, Rob;Chen, Menzies;Rajapakse, Indika;Friend, Stephen;Ideker, Trey;Zhang, Kang
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Zhang, Kang
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作者：
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通讯作者：
Goell, Ajay
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作者：
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