PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays
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DOI：
10.1093/nar/gni142
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Hannan, GN
中科院分区：
文献类型：
--
作者：
Brohede, J;Dunne, R;Hannan, GN
对DNA池中等位基因频率的可靠估计有可能降低基因分型成本和/或增加参与研究的个体数量，这些研究需要在非常大的种群样本集中对数十万个遗传标记进行基因分型，例如全基因组关联研究。为了从混合样本中得到准确的等位基因频率估计，必须对等位基因不均匀表示进行校正。我们提出了一种基于多项式的探针特定校正（PPC）算法，用于精确估计高密度微阵列数据中的等位基因频率。通过比较来自一组10个单独基因型DNA的等位基因频率和使用GeneChip 10K Mapping Xba 131阵列从这10个DNA池中估计的频率，验证了该算法。我们的研究结果表明，当使用PPC校正等位基因偏差时，等位基因频率估计的准确性显着提高。
Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/ or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high- density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.