Whole-Genome Amplification Enables Accurate Genotyping for Microarray-Based High-Density Single Nucleotide Polymorphism Array
Whole-Genome Amplification Enables Accurate Genotyping for Microarray-Based High-Density Single Nucleotide Polymorphism Array
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DOI：
10.1158/1055-9965.epi-08-0482
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发表时间：
2008-12-01
影响因子：
3.8
通讯作者：
Kibriya, Muhammad G.
中科院分区：
文献类型：
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作者：
Jasmine, Farzana;Ahsan, Habibul;Kibriya, Muhammad G.
在基于高密度单核苷酸多态性（SNP）基因分型阵列的大规模全基因组关联研究中，可用基因组DNA （gDNA）的数量和质量是一个实际问题。我们研究了在这种平台上使用全基因组扩增（WGA）的多重位移扩增（MDA）方法的可行性。使用Affymetrix Early Access Mendel Nsp 250K基因芯片对28份DNA样本进行基因分型，每个样本224,940个snp。我们比较了14份gDNA样本及其对应的14份WGA样本的通话一致性。gDNA和相应WGA样本的总体平均基因型召唤率可比较，分别为97.07%[95%置信区间（CI）， 96.17-97.97]和97.77% （95% CI, 97.26-98.28; P = 0.154）。该平台的重现性，以重复样品的一致性计算，为99.45%。97.74% （95% CI, 97.03-98.44）的基因型在gDNA和WGA样本中一致。当分析局限于表现良好的SNP （gDNA和WGA基因分型成功的样本占90%）时，平均99.11% （95% CI, 98.80-99.42）的SNP是一致的，而总体而言，0.92% （95% CI, 0.90-0.94）的配对样本显示一个SNP是不一致的。在一对gDNA和WGA DNA中，在Illumina的Infinium 610 Quad平台上也可以重现类似的一致性。虽然拷贝数分析显示6条染色体中有7个小的端粒区拷贝数缺失，但估计基因组代表率为99.29%。总之，我们的研究证实基于高密度寡核苷酸阵列的基因分型可以产生可重复的数据，MDA-WGA DNA产物可以有效地用于全基因组SNP基因分型分析。（癌症流行病学杂志，2008;17(12):3499-508）
In large-scale genome-wide association studies based on high-density single nucleotide polymorphism (SNP) genotyping array, the quantity and quality of available genomic DNA (gDNA) is a practical problem. We examined the feasibility of using the Multiple Displacement Amplification (MDA) method of whole-genome amplification (WGA) for such a platform. The Affymetrix Early Access Mendel Nsp 250K GeneChip was used for genotyping 224,940 SNPs per sample for 28 DNA samples. We compared the call concordance using 14 gDNA samples and their corresponding 14 WGA samples. The overall mean genotype call rates in gDNA and the corresponding WGA samples were comparable at 97.07% [95% confidence interval (CI), 96.17-97.97] versus 97.77% (95% CI, 97.26-98.28; P = 0.154), respectively. Reproducibility of the platform, calculated as concordance in duplicate samples, was 99.45%. Overall genotypes for 97.74% (95% CI, 97.03-98.44) of SNPs were concordant between gDNA and WGA samples. When the analysis was restricted to well-performing SNPs (successful genotyping in gDNA and WGA in > 90% of samples), 99.11% (95% CI, 98.80-99.42) of the SNPs, on average, were concordant, and overall a SNP showed a discordant call in 0.92% (95% CI, 0.90-0.94) of paired samples. In a pair of gDNA and WGA DNA, similar concordance was reproducible on Illumina's Infinium 610 Quad platform as well. Although copy number analysis revealed a total of seven small telomeric regions in six chromosomes with loss of copy number, the estimated genome representation was 99.29%. In conclusion, our study confirms that high-density oligonucleotide array-based genotyping can yield reproducible data and MDA-WGA DNA products can be effectively used for genome-wide SNP genotyping analysis. (Cancer Epidemiol Biomarkers Prev 2008;17(12):3499-508)