Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
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DOI：
10.1101/gr.7080508
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发表时间：
2008-03-01
期刊：
影响因子：
7
通讯作者：
Liu, X. Shirley
中科院分区：
文献类型：
--
作者：
Johnson, David S.;Li, Wei;Liu, X. Shirley
检测全基因组蛋白-DNA相互作用的最广泛使用的方法是在平铺微阵列上的染色质免疫沉淀，通常称为芯片芯片。在这里，我们在模拟芯片芯片实验中对平铺阵列平台，放大程序和信号检测算法进行了第一个客观分析。人类基因组DNA和“尖峰INS”的混合物由近100个浓度的近100个人类序列组成，由八个独立组杂交与四个平铺阵列平台杂交。对尖峰的数量，它们的位置和浓度范围视而不见，每组都对尖峰的位置进行了预测。我们发现，微阵列平台选择不是整体性能的主要决定因素。实际上，同一数组平台内实验室，协议和算法之间的性能变化大于数组平台之间性能的变化。但是，每个数组平台都有独特的性能特征，随着平铺分辨率和重复的数量而异，这对成本与检测功率具有影响。长寡核苷酸阵列在检测非常低的富集时稍微敏感。在所有平台上，简单的序列重复序列和基因组冗余往往会导致误报。 LM-PCR和WGA是最受欢迎的样品扩增技术，它以高富度性再现了相对富集水平。信号检测算法之间的性能很大程度上取决于数组平台。此处提供的SPIKE-IN DNA样品和数据提供了稳定的基准，可以评估未来的芯片平台，协议改进和分析方法。
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols, and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.