Yin Bin-Cheng, Li Honghua, Ye Bang-Ce
Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, PR China.
BMC Genomics. 2008 Dec 16;9:605. doi: 10.1186/1471-2164-9-605.
High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele frequency in pooled DNA samples, based on the physical principles of DNA immobilization and hybridization on solid surface using the Langmuir kinetic model and quantitative analysis of the allelic signals.
This method can successfully distinguish allele frequencies differing by 0.01 in the actual pool of clinical samples, and detect alleles with a frequency as low as 2%. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and actual frequencies having an r2 = 0.9992. These results demonstrated that this method could allow the accurate estimation of absolute allele frequencies in pooled samples of DNA in a feasible and inexpensive way.
We conclude that this novel strategy for quantitative analysis of the ratio of SNP allelic sequences in DNA pools is an inexpensive and feasible alternative for detecting polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans.
全基因组关联研究中，单核苷酸多态性（SNP）的高通量基因分型需要能够相对轻松地生成数百万种基因型的技术，同时成本要合理且准确性要高。在这项工作中，我们基于DNA在固体表面固定和杂交的物理原理，利用朗缪尔动力学模型和等位基因信号的定量分析，开发了一种理论方法来估计混合DNA样本中的等位基因频率。
该方法能够在实际临床样本池中成功区分相差0.01的等位基因频率，并检测到频率低至2%的等位基因。测量已知等位基因频率的准确性非常高，测量频率与实际频率之间的相关强度r2 = 0.9992。这些结果表明，该方法能够以可行且廉价的方式准确估计DNA混合样本中的绝对等位基因频率。
我们得出结论，这种用于定量分析DNA池中SNP等位基因序列比例的新策略，是检测候选基因关联研究和全基因组连锁不平衡扫描中多态性差异的一种廉价且可行的替代方法。
