Pooled DNA genotyping on Affymetrix SNP genotyping arrays
Pooled DNA genotyping on Affymetrix SNP genotyping arrays
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DOI：
10.1186/1471-2164-7-27
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发表时间：
2006-02-15
期刊：
影响因子：
4.4
通讯作者：
O'Donovan, MC
中科院分区：
文献类型：
--
作者：
Kirov, G;Nikolov, I;O'Donovan, MC
背景：基因分型技术已经取得进展，基于密集标记图谱对复杂疾病进行全基因组关联研究在技术上现已可行。然而，此类项目的成本仍然很高。混合DNA基因分型提供了以较低成本应用相同技术的可能性，并且有一些证据表明某些超高通量平台也能以可接受的准确度运行。然而，到目前为止，这一结论仅基于涉及少量单核苷酸多态性（SNP）的已发表数据。
结果：在当前研究中，我们从30个亲子三联体的父母和后代制备了DNA池，这些三联体已由国际人类基因组单体型图计划（HapMap）进行了广泛的基因分型。我们使用Affymetrix 10K Xba 142 2.0芯片分析了这两个DNA池。HapMap数据的可用性使我们能够验证6843个SNP的性能，对于这些SNP我们同时拥有完整的个体和混合基因分型数据。对5 - 6个微阵列进行平均的混合分析产生了高度可重复的结果。此外，使用这种超高通量系统估计DNA池之间等位基因频率差异的准确性与先前基于较低通量平台的混合研究报告相当，两个DNA池之间预测的等位基因频率差异的平均误差为1.37%，并且95%的SNP显示误差<3.2%。
结论：使用Affymetrix微阵列通过DNA混合对数千个SNP进行基因分型可产生高度准确的结果，并可用于全基因组关联研究。
Background: Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs.Results: In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5 - 6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of < 3.2%.Conclusion: Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.