A new genome wide expression array and its application to eQTL mapping, synergy to other platforms

The study of gene expression as an intermediate phenotype in associating genotype to disease is growing rapidly. The success of this approach depends heavily on the availability of accurate, high throughput platforms for assaying expression levels of genome-wide gene sets. We evaluated a new platform for gene expression, Phalanx Human OneArray (HOA), in 90 HapMap cell lines (CEU panel) for which Illumina BeadChip data were available (Stranger et al. 2007, PMID: 17873874). We found high reproducibility between technical HOA replicates (R = 0.99) and strong inter-platform correlation based on 2,458 sequence-matched probes (R = 0.87). We next performed an association analysis between gene expression levels and HapMap SNPs in the 60 unrelated CEU parents [SNP data downloaded directly from HapMap project (http://www.hapmap.org/)(HapMap phase II/Rel # 22)]. Among the 4356 genes (HOA array) showing variable expression, 122 (2.8%) had a significant cis association (p-value < 0.001) with at least one SNP. Of the 1751 genes showing variable expression on both platforms, 84 had a significant cis association with 36.9% of the genes (31/84) present in both data sets, 39.3 % (33/84) only in HOA, and 23.8% (20/84) only in Illumina. A subset of these 84 eQTLs overlap or are in strong linkage disequilibrium (LD) with reported complex disease/trait susceptibility loci. Combining the results of the two platforms provides a more comprehensive eQTL database (30% increase), which may help to accelerate our understanding of the molecular basis of quantitative traits and diseases. We quantified gene expression levels in the 90 HapMap cell lines (CEU panel) using Phalanx HOA for which Illumina BeadChip data were available (Stranger et al. 2007). We used the same set of RNA samples employed in Stranger et al 2007 (see GEO Series GSE6536, CEU panel; raw data were re-analyzed, ie, re-normalized, thereby generating new values) which allowed us to undertake a detailed comparison to the Illumina expression platform and profiled the 60 parent samples at Industrial Technology Research Institute (ITRI), Taiwan and the 30 children samples at Wellcome Trust Sanger Institute (WTSI), United Kingdom. We performed two in vitro transcription (IVT) reactions for each RNA sample and three technical replicates per IVT with exception of seven samples (15CP, 33CP, 43CP, 44CP, 48CP, 56CP, 60CP) that had two technical replicates for one of the two IVT reactions. *** This Series represents the Phalanx HOA data. *** File "info.pass.parent.txt" (a description of the relationship between an array and a sample and its replicates) is linked below as a supplementary file.

将基因表达作为基因型与疾病关联的中间表型的研究正快速发展。该研究路径的成功高度依赖于可精准检测全基因组基因集表达水平的高通量平台。我们针对一款新型基因表达检测平台——Phalanx Human OneArray（HOA）进行了评估，实验样本为90株HapMap细胞系（CEU群组），这些样本已有Illumina BeadChip检测数据（Stranger等人，2007年，PMID: 17873874）。
我们发现，HOA平台的技术重复样本之间具有极高的重现性（相关系数R=0.99）；基于2458个序列匹配探针的跨平台相关性分析结果显示，二者相关性较强（R=0.87）。随后，我们针对60株无关CEU亲本细胞系的基因表达水平与HapMap SNP数据开展了关联分析（SNP数据直接下载自HapMap项目官网http://www.hapmap.org/，HapMap第二阶段/发布版本#22）。
在4356个在HOA芯片上呈现表达差异的基因中，有122个（占比2.8%）与至少一个SNP存在显著的顺式关联（p值<0.001）。在两个平台上均呈现表达差异的1751个基因中，有84个存在显著顺式关联：其中36.9%（31/84）的基因在两组数据中均有检出，39.3%（33/84）仅在HOA平台检出，23.8%（20/84）仅在Illumina平台检出。这84个表达数量性状位点（expression quantitative trait locus, eQTL）中有一部分与已报道的复杂疾病/性状易感位点存在重叠或处于强连锁不平衡（LD）状态。
整合两个平台的分析结果可得到更全面的eQTL数据库（数据量提升30%），这将有助于加速我们对数量性状与疾病的分子机制的理解。我们使用Phalanx HOA平台对90株已有Illumina BeadChip检测数据的HapMap CEU群组细胞系进行了基因表达定量（Stranger等人，2007年）。本次实验采用了Stranger等人2007年研究中使用的同一批RNA样本（详见基因表达综合数据库（Gene Expression Omnibus, GEO）系列数据集GSE6536，CEU群组；原始数据经重新分析，即重新标准化，得到新的表达值），这使得我们能够与Illumina表达平台进行细致的对比；其中60株亲本样本的基因表达谱检测在台湾工业技术研究院（Industrial Technology Research Institute, ITRI）完成，30株子代样本的检测在英国惠康桑格研究所（Wellcome Trust Sanger Institute, WTSI）完成。
我们对每一份RNA样本进行了两次体外转录（in vitro transcription, IVT）反应，且每一次IVT反应设置3次技术重复；但有7个样本（15CP、33CP、43CP、44CP、48CP、56CP、60CP）仅在其中一次IVT反应中设置了2次技术重复。
***本系列数据集代表Phalanx HOA平台的检测数据。***
补充文件附带有"info.pass.parent.txt"，该文件用于说明芯片、样本及其重复之间的对应关系。