单核苷酸多态性影响顺式和反式表达数量性状基因座。
Single nucleotide polymorphisms affect both cis- and trans-eQTLs.
作者信息
Chen Lang, Page Grier P, Mehta Tapan, Feng Rui, Cui Xiangqin
机构信息
Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, AL 35209, USA.
出版信息
Genomics. 2009 Jun;93(6):501-8. doi: 10.1016/j.ygeno.2009.01.011. Epub 2009 Feb 25.
Single nucleotide polymorphisms (SNPs) between microarray probes and RNA targets can affect the performance of expression array by weakening the hybridization. In this paper, we examined the effect of the SNPs on Affymetrix GeneChip probe set summaries and the expression quantitative trait loci (eQTL) mapping results in two eQTL datasets, one from mouse and one from human. We showed that removing SNP-containing probes significantly changed the probe set summaries and the more SNP-containing probes we removed the greater the change. Comparison of the eQTL mapping results between with and without SNP-containing probes showed that less than 70% of the significant eQTL peaks were concordant regardless of the significance threshold. These results indicate that SNPs do affect both probe set summaries and eQTLs (both cis and trans), thus SNP-containing probes should be filtered out to improve the performance of eQTL mapping.
微阵列探针与RNA靶标之间的单核苷酸多态性（SNP）可通过削弱杂交来影响表达阵列的性能。在本文中，我们在两个表达定量性状位点（eQTL）数据集中研究了SNP对Affymetrix基因芯片探针集汇总以及eQTL定位结果的影响，其中一个数据集来自小鼠，另一个来自人类。我们发现，去除含SNP的探针会显著改变探针集汇总，且去除的含SNP探针越多，变化就越大。对含与不含SNP探针的eQTL定位结果进行比较表明，无论显著性阈值如何，不到70%的显著eQTL峰是一致的。这些结果表明，SNP确实会影响探针集汇总和eQTL（顺式和反式），因此应滤除含SNP的探针以提高eQTL定位的性能。
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