SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis
SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis
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DOI：
10.1093/nar/gnf070
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发表时间：
2002-08-01
影响因子：
14.9
通讯作者：
Evans, KL
中科院分区：
文献类型：
--
作者：
Le Hellard, S;Ballereau, SJ;Evans, KL
我们比较了三种方法的准确性，效率和鲁棒性的单核苷酸多态性的基因分型合并DNAs。我们的结论是：（i）池中两个等位基因的频率应该用等位基因扩增不相等的因子进行校正，该因子应该根据一组杂合子的平均比率（k）进行估计;（ii）在估计等位基因频率时，测定的重复性比精确度更重要，因此应该优化测定以增加重复性;以及（iii）库的大小对等位基因频率估计的准确性具有相对小的影响。因此，我们建议对大型样本池进行基因分型，并至少重复4次。此外，我们描述了统计方法，允许严格比较DNA池的结果。最后，我们描述了一个扩展到我们的ACeDB数据库，便于管理和分析关联研究产生的数据。
We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of a set of heterozygotes (k); (ii) the repeatability of an assay is more important than pinpoint accuracy when estimating allele frequencies, and assays should therefore be optimised to increase the repeatability; and (iii) the size of a pool has a relatively small effect on the accuracy of allele frequency estimation. We therefore recommend that large pools are genotyped and replicated a minimum of four times. In addition, we describe statistical approaches to allow rigorous comparison of DNA pool results. Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies.