Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA -: art. no. e129
Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA -: art. no. e129
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DOI：
10.1093/nar/gng129
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发表时间：
2003-11-01
影响因子：
14.9
通讯作者：
Syvänen, AC
中科院分区：
文献类型：
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作者：
Lovmar, L;Fredriksson, M;Syvänen, AC
全基因组扩增（WGA）程序，如引物延伸预扩增（PEP）或多重置换扩增（MDA）有可能为大规模遗传研究提供无限的DNA来源。我们已经进行了定量评估PEP和MDA的基因分型单核苷酸多态性（SNP），使用多重，四色荧光微测序的微阵列格式。对45个SNP进行基因分型，并对WGA方法的基因分型成功率、信噪比、基因型区分能力、MDA产物中等位基因的产量和不平衡扩增进行评价。PEP和MDA产品均提供了与基因组DNA高度一致的基因分型结果。对于PEP产品，由于信噪比低2倍，基因型区分的能力低于MDA。MDA产物在所研究的各个方面与基因组DNA难以区分。为了获得SNP等位基因的忠实代表，每个MDA反应应使用至少0.3ng DNA。我们的结论是，使用WGA，特别是MDA，是一个非常有前途的程序，生产足够数量的DNA，甚至全基因组SNP作图研究。
Whole genome amplification (WGA) procedures such as primer extension preamplification (PEP) or multiple displacement amplification (MDA) have the potential to provide an unlimited source of DNA for large-scale genetic studies. We have performed a quantitative evaluation of PEP and MDA for genotyping single nucleotide polymorphisms (SNPs) using multiplex, four-color fluorescent minisequencing in a microarray format. Forty-five SNPs were genotyped and the WGA methods were evaluated with respect to genotyping success, signal-to-noise ratios, power of genotype discrimination, yield and imbalanced amplification of alleles in the MDA product. Both PEP and MDA products provided genotyping results with a high concordance to genomic DNA. For PEP products the power of genotype discrimination was lower than for MDA due to a 2-fold lower signal-to-noise ratio. MDA products were indistinguishable from genomic DNA in all aspects studied. To obtain faithful representation of the SNP alleles at least 0.3 ng DNA should be used per MDA reaction. We conclude that the use of WGA, and MDA in particular, is a highly promising procedure for producing DNA in sufficient amounts even for genome wide SNP mapping studies.