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PDA：聚合DNA分析仪。

PDA: Pooled DNA analyzer.

作者信息

Yang Hsin-Chou, Pan Chia-Ching, Lin Chin-Yu, Fann Cathy S J

机构信息

Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 115, Taiwan.

出版信息

BMC Bioinformatics. 2006 Apr 28;7:233. doi: 10.1186/1471-2105-7-233.

DOI:10.1186/1471-2105-7-233
PMID:16643673
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1539032/
Abstract

BACKGROUND

Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data.

RESULTS

We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB language, but it can also be executed on a Windows system without installing the MATLAB. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples.

CONCLUSION

PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

摘要

背景

利用大量单核苷酸多态性进行关联作图是鉴定复杂性状疾病易感性基因和探索可能的遗传多样性的有力工具。常规情况下需对大量单核苷酸多态性进行个体基因分型，但对于大规模遗传研究而言成本过高。DNA池化是一种可靠且节省成本的替代基因分型方法。然而，尚未开发出用于完整的池化DNA分析的软件，包括数据标准化、等位基因频率估计以及单/多点DNA池化关联测试。这促使我们开发了“PDA”（Pooled DNA Analyzer）软件来分析池化DNA数据。

结果

我们开发了用于分析池化DNA数据的PDA软件。PDA最初是用MATLAB语言实现的，但也可以在不安装MATLAB的Windows系统上运行。PDA可提供优先扩增系数和等位基因频率的估计值。PDA考虑了扩展的单点关联测试，该测试可以比较在不同实验条件下构建的两个DNA池之间的等位基因频率。此外，PDA还基于p值组合和滑动窗口概念提供了全新的全染色体多点关联测试。这种新的多点测试程序克服了DNA池化分析中传统的基于单倍型的多点方法的计算瓶颈，并且能够处理具有大池大小和/或大量多态性标记的数据集。所有PDA功能都在四个真实示例中进行了说明。

结论

PDA操作简单，不要求用户具备深厚的统计学背景。该软件可在http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/7de5fafbaaf4/1471-2105-7-233-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/7e9afd29a48c/1471-2105-7-233-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/3b763554526a/1471-2105-7-233-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/d13fe39172f1/1471-2105-7-233-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/7de5fafbaaf4/1471-2105-7-233-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/7e9afd29a48c/1471-2105-7-233-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/3b763554526a/1471-2105-7-233-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/d13fe39172f1/1471-2105-7-233-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5439/1539032/7de5fafbaaf4/1471-2105-7-233-4.jpg

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本文引用的文献

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Genome-wide association studies: theoretical and practical concerns.全基因组关联研究：理论与实际问题
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Genome-wide association studies for common diseases and complex traits.常见疾病和复杂性状的全基因组关联研究。
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Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.通过基于混合样本的全基因组单核苷酸多态性关联研究来鉴定复杂疾病的遗传基础。
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