A stepwise framework for the normalization of array CGH data
A stepwise framework for the normalization of array CGH data
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DOI：
10.1186/1471-2105-6-274
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发表时间：
2005-11-18
影响因子：
3
通讯作者：
MacAulay, C
中科院分区：
文献类型：
--
作者：
Khojasteh, M;Lam, WL;MacAulay, C
背景资料：在双通道竞争性基因组杂交微阵列实验中，微阵列上每个点处的两种荧光信号强度的比率通常用于推断测试和参考样品DNA水平的相对量。这一比率可能受到非生物来源的系统测量效应的影响，这可能会在估计比率中引入偏倚。在得出关于DNA相对水平的结论之前，应该消除这些偏见。现有的基因表达微阵列标准化策略的性能尚未进行评估，以消除基于阵列的比较基因组杂交（CGH）中遇到的系统性偏差，其目的是检测单拷贝的增益和损失，通常在样品中的异质细胞群，导致信号比只有轻微的变化。本工作的目的是建立一个框架，以纠正高密度CGH阵列图像中的系统性变异来源，同时保持真实的生物学variation.Results的系统性变异的调查后，从两个阵列CGH平台，SMRT（亚兆基分辨率Tiling）BAC阵列和cDNA阵列的Pollack等，我们已经开发了一种逐步的归一化框架，该框架集成了新颖的和现有的归一化方法，以便减少强度、空间、板和背景偏差。我们使用严格的措施来量化这种逐步标准化的性能，使用来自5组实验的数据，这些实验代表自体-自体杂交、重复实验、单拷贝变化检测、模拟细胞群体异质性的阵列CGH实验以及模拟不同水平的基因扩增和缺失的阵列CGH实验。我们的研究结果表明，三步标准化程序提供了显着的改善，在检测单拷贝变化的灵敏度相比，传统的单步标准化方法在SMRT BAC阵列和cDNA阵列platforms.Conclusion：建议逐步规范化框架保留分钟拷贝数的变化，同时消除所观察到的系统偏差。
Background: In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effects from non-biological sources that can introduce biases in the estimated ratios. These biases should be removed before drawing conclusions about the relative levels of DNA. The performance of existing gene expression microarray normalization strategies has not been evaluated for removing systematic biases encountered in array-based comparative genomic hybridization (CGH), which aims to detect single copy gains and losses typically in samples with heterogeneous cell populations resulting in only slight shifts in signal ratios. The purpose of this work is to establish a framework for correcting the systematic sources of variation in high density CGH array images, while maintaining the true biological variations.Results: After an investigation of the systematic variations in the data from two array CGH platforms, SMRT (Sub Mega base Resolution Tiling) BAC arrays and cDNA arrays of Pollack et al., we have developed a stepwise normalization framework integrating novel and existing normalization methods in order to reduce intensity, spatial, plate and background biases. We used stringent measures to quantify the performance of this stepwise normalization using data derived from 5 sets of experiments representing self-self hybridizations, replicated experiments, detection of single copy changes, array CGH experiments which mimic cell population heterogeneity, and array CGH experiments simulating different levels of gene amplifications and deletions. Our results demonstrate that the three-step normalization procedure provides significant improvement in the sensitivity of detection of single copy changes compared to conventional single step normalization approaches in both SMRT BAC array and cDNA array platforms.Conclusion: The proposed stepwise normalization framework preserves the minute copy number changes while removing the observed systematic biases.