Jasmine Farzana, Ahsan Habibul, Andrulis Irene L, John Esther M, Chang-Claude Jenny, Kibriya Muhammad G
Department of Health Studies, The University of Chicago, 5841 South Maryland Avenue, MC 2007, Chicago, IL 60637, USA.
Cancer Epidemiol Biomarkers Prev. 2008 Dec;17(12):3499-508. doi: 10.1158/1055-9965.EPI-08-0482.
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.
在基于高密度单核苷酸多态性（SNP）基因分型芯片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。我们研究了在此类平台上使用多重置换扩增（MDA）全基因组扩增（WGA）方法的可行性。Affymetrix早期访问Mendel Nsp 250K基因芯片用于对28个DNA样本进行每个样本224,940个SNP的基因分型。我们比较了14个gDNA样本及其相应的14个WGA样本的分型一致性。gDNA和相应WGA样本的总体平均基因型分型率相当，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）。以重复样本的一致性计算的平台重现性为99.45%。gDNA和WGA样本之间97.74%（95% CI，97.03 - 98.44）的SNP总体基因型一致。当分析限于表现良好的SNP（在>90%的样本中gDNA和WGA成功基因分型）时，平均99.11%（95% CI，98.80 - 99.42）的SNP一致，总体上一个SNP在0.92%（95% CI，0.90 - 0.94）的配对样本中显示分型不一致。在一对gDNA和WGA DNA中，类似的一致性在Illumina的Infinium 610 Quad平台上也可重现。尽管拷贝数分析在6条染色体中总共发现7个小的端粒区域存在拷贝数缺失，但估计的基因组代表性为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产生可重现的数据，且MDA - WGA DNA产物可有效地用于全基因组SNP基因分型分析。
