Magnusson Nils E, Cardozo Alessandra K, Kruhøffer Mogens, Eizirik Decio L, Ørntoft Torben F, Jensen Jens L
Department of Clinical Biochemistry, Aarhus University Hospital, Denmark.
BMC Bioinformatics. 2005 Dec 29;6:311. doi: 10.1186/1471-2105-6-311.
Type 1 diabetes mellitus (T1DM) is a autoimmune disease caused by a long-term negative balance between immune-mediated beta-cell damage and beta-cell repair/regeneration. Following immune-mediated damage the beta-cell fate depends on several genes up- or down-regulated in parallel and/or sequentially. Based on the information obtained by the analysis of several microarray experiments of beta-cells exposed to pro-apoptotic conditions (e.g. double stranded RNA (dsRNA) and cytokines), we have developed a spotted rat oligonucleotide microarray, the APOCHIP, containing 60-mer probes for 574 genes selected for the study of beta-cell apoptosis.
The APOCHIP was validated by a combination of approaches. First we performed an internal validation of the spotted probes based on a weighted linear regression model using dilution series experiments. Second we profiled expression measurements in ten dissimilar rat RNA samples for 515 genes that were represented on both the spotted oligonucleotide collection and on the in situ-synthesized 25-mer arrays (Affymetrix GeneChips). Internal validation showed that most of the spotted probes displayed a pattern of reaction close to that predicted by the model. By using simple rules for comparison of data between platforms we found strong correlations (rmedian= 0.84) between relative gene expression measurements made with spotted probes and in situ-synthesized 25-mer probe sets.
In conclusion our data suggest that there is a high reproducibility of the APOCHIP in terms of technical replication and that relative gene expression measurements obtained with the APOCHIP compare well to the Affymetrix GeneChip. The APOCHIP is available to the scientific community and is a useful tool to study the molecular mechanisms regulating beta-cell apoptosis.
1型糖尿病（T1DM）是一种自身免疫性疾病，由免疫介导的β细胞损伤与β细胞修复/再生之间长期的负平衡所致。免疫介导的损伤后，β细胞的命运取决于多个平行和/或顺序上调或下调的基因。基于对暴露于促凋亡条件（如双链RNA（dsRNA）和细胞因子）的β细胞的多个微阵列实验分析所获得的信息，我们开发了一种斑点大鼠寡核苷酸微阵列APOCHIP，其包含用于研究β细胞凋亡的574个基因的60聚体探针。
通过多种方法对APOCHIP进行了验证。首先，我们基于加权线性回归模型，利用稀释系列实验对斑点探针进行了内部验证。其次，我们对十个不同的大鼠RNA样本中515个基因的表达测量进行了分析，这些基因同时存在于斑点寡核苷酸集合和原位合成的25聚体阵列（Affymetrix基因芯片）上。内部验证表明，大多数斑点探针显示出与模型预测相近的反应模式。通过使用简单的平台间数据比较规则，我们发现用斑点探针和原位合成的25聚体探针集进行的相对基因表达测量之间存在强相关性（r中位数 = 0.84）。
总之，我们的数据表明，APOCHIP在技术重复方面具有高重现性，并且用APOCHIP获得的相对基因表达测量结果与Affymetrix基因芯片相比效果良好。APOCHIP可供科学界使用，是研究调节β细胞凋亡分子机制的有用工具。
