SNPinProbe_1.0

The Affymetrix GeneChip(R) Human Exon 1.0 ST array (exon array) is designed to measure both gene-level and exon-level expression in human samples. This exon array contains approximately 1.4 million probesets consisting of approximately 5.4 million probes and profiles over 17,000 well-annotated gene transcripts in the human genome. As with all expression arrays, the exon array is vulnerable to SNPs within probes, because these SNPs can affect the hybridization of the probes and thus produce misleading expression values. In some cases, this could result in dramatic fluctuations of the exon-level expression. For this reason, we performed a genome-wide search for SNPs within regions that hybridize to probes by evaluating approximately 18 million SNPs in dbSNP (Build 129) and about 5.4 million probes in the exon array. We identified 597,068 probes within 350,382 probe sets that hybridized to regions containing SNPsAffymetrix GeneChip®人类外显子1.0 ST阵列（外显子芯片）专为检测人类样本中的基因水平与外显子水平的基因表达量而设计。该外显子芯片包含约140万个探针组，总计约540万个探针，可对人类基因组中超过17000条已精准注释的基因转录本进行表达谱分析。与所有表达阵列芯片类似，该外显子芯片易受探针内单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的影响：此类SNP会干扰探针的核酸杂交过程，进而生成误导性的表达量检测结果。在部分场景下，这可能会导致外显子水平的表达量出现剧烈波动。基于此，我们针对探针结合区域开展了全基因组范围的SNP筛查：通过评估dbSNP数据库（版本129）中约1800万个SNP，以及该外显子芯片上的约540万个探针，完成了此项筛查。最终我们在350382个探针组中鉴定出597068个探针，这些探针的杂交区域均包含SNP。

搜集汇总

背景与挑战

背景概述

该数据集基于Affymetrix GeneChip Human Exon 1.0 ST阵列，覆盖约540万探针和超过1.7万个基因转录本，旨在评估SNP对探针杂交的影响。通过分析dbSNP中的约1800万SNP，识别出涉及约35万个探针集的59.7万多个受SNP影响的探针。