Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA
Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA
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DOI：
10.1093/nar/gnh072
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发表时间：
2004-05-01
影响因子：
14.9
通讯作者：
Lau, CC
中科院分区：
文献类型：
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作者：
Wong, KK;Tsang, YTM;Lau, CC
除了用于mRNA表达谱外，寡核苷酸微阵列还应用于单核苷酸多态性（SNP）和杂合性缺失（LOH）或等位基因失衡的研究。在这篇报告中，我们评估了使用全基因组扩增DNA进行分析的可靠性，用含有11 560个snp的寡核苷酸微阵列来检测等位基因失衡和染色体拷贝数异常。用从骨肉瘤组织和患者匹配血液中提取的DNA进行全基因组SNP分析。然后由Affymetrix((R)) GeneChip((R)) DNA分析软件生成SNP呼叫。在两例骨肉瘤病例中，使用未扩增的DNA，我们分别鉴定了793和1070个等位基因不平衡的SNP位点。在扩增DNA的平行实验中，检测到这些等位基因不平衡的SNP位点的78%和83%。平均假阳性率为13.8%。此外，使用Affymetrix((R)) GeneChip（(R)）染色体拷贝数工具分析SNP阵列数据，我们能够在细胞带分辨率下检测扩增和未扩增DNA的相同染色体区域的增益或损失。
Besides their use in mRNA expression profiling, oligonucleotide microarrays have also been applied to single-nucleotide polymorphism (SNP) and loss of heterozygosity (LOH) or allelic imbalance studies. In this report, we evaluate the reliability of using whole genome amplified DNA for analysis with an oligonucleotide microarray containing 11 560 SNPs to detect allelic imbalance and chromosomal copy number abnormalities. Whole genome SNP analyses were performed with DNA extracted from osteosarcoma tissues and patient-matched blood. SNP calls were then generated by Affymetrix((R)) GeneChip((R)) DNA Analysis Software. In two osteosarcoma cases, using unamplified DNA, we identified 793 and 1070 SNP loci with allelic imbalance, respectively. In a parallel experiment with amplified DNA, 78% and 83% of these SNP loci with allelic imbalance was detected. The average false-positive rate is 13.8%. Furthermore, using the Affymetrix((R)) GeneChip((R)) Chromosome Copy Number Tool to analyze the SNP array data, we were able to detect identical chromosomal regions with gain or loss in both amplified and unamplified DNA at cytoband resolution.