A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays.
A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays.
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DOI：
10.1186/1471-2164-13-737
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发表时间：
2012-12-27
期刊：
影响因子：
4.4
通讯作者：
Cutler DJ
中科院分区：
文献类型：
--
作者：
Jakubek YA;Cutler DJ
DNA微阵列既可用于研究，也可用于诊断。在研究中，Affymetrix阵列通常用于全基因组关联研究、重测序和基因表达分析。这些数组提供了大量的数据。这些数据是用统计方法分析的，而统计方法往往会丢弃大部分信息。大部分丢失的信息来自系统地跨芯片失败的探针和批处理效应。本研究的目的是建立一个综合的杂交模型，预测Affymetrix阵列的探针强度，并为改进微阵列分析和探针开发提供基础。模型的第一部分使用Langmuir等温线计算探针与杂交溶液中所有可能目标的结合亲和力。在模型的第二部分，我们整合了特定于每个实验的细节，并有助于在溶液中杂交和微阵列上杂交之间的差异。这些细节包括破碎度、洗涤强度、温度、盐浓度和扫描仪设置。此外，该模型将探针合成效率和目标浓度参数直接拟合到数据中。模型中使用的所有参数都有一个确定的物理来源。对于分析的302个芯片，预期和观察到的探针强度之间的平均相关性为0.701，范围为0.88至0.55。无论数据质量如何，所有可用的芯片都被纳入分析。我们的研究结果表明，批次效应是由探针合成、扫描仪设置、洗涤强度和目标破碎程度的差异引起的。我们还表明，不同核苷酸的探针合成效率并不均匀。迄今为止，这是微阵列上最完整的结合模型。这是第一个同时包含探针合成效率和杂交动力学/交叉杂交的模型。这两个因素是序列相关的，对探针强度有很大影响。本文提出的结果为探针合成误差对Affymetrix微阵列的影响提供了新的见解；此外，本工作中开发的算法为分析交叉杂交、探针合成效率、碎片化、洗涤强度、温度和盐浓度对微阵列强度的影响提供了有用的工具。
DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These two factors are sequence dependent and have a large impact on probe intensity. The results presented here provide novel insight into the effect of probe synthesis errors on Affymetrix microarrays; furthermore, the algorithms developed in this work provide useful tools for the analysis of cross-hybridization, probe synthesis efficiency, fragmentation, wash stringency, temperature, and salt concentration on microarray intensities.
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