A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.
A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.
复制标题
DOI：
10.1371/journal.pone.0005157
复制
发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Kohane IS
中科院分区：
文献类型：
--
作者：
Tian Z;Palmer N;Schmid P;Yao H;Galdzicki M;Berger B;Wu E;Kohane IS
虽然微阵列技术已成为研究全球基因表达的最常用方法，但整个实验中的大量技术因素导致使用外周全血进行基因组基因表达谱分析的变量。为了获得可靠的、可重复的数据，以满足生物标志物研究的临床需求，需要建立一个实用的平台。我们应用了珠蛋白减少的外周全血样品，并使用Illumina BeadChips进行全基因组转录组分析。实时PCR随后被用来评估阵列数据的质量，并阐明血红蛋白干扰基因表达谱的模式。我们证明，当应用于标准微阵列处理程序的背景下，珠蛋白减少的结果在一个一致的和显着的提高微珠阵列数据的质量。当与其珠蛋白减少前的对应物相比时，珠蛋白减少后的样品显示出改进的检测统计、降低的方差和增加的灵敏度。更重要的是，性别基因分离在珠蛋白减少后的样品中比在珠蛋白减少前的样品中明显更清楚。我们的研究表明，从珠蛋白减少前样品获得的差的数据是来自红细胞的高浓度血红蛋白干扰靶mRNA结合或给出假结合背景信号的结果。因此，我们建议将外周全血样本中的珠蛋白mRNA减少和Illumina BeadChips上的杂交相结合作为生物标志物研究的实用方法。
Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study. We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal. We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.
登录
查看更多内容
影响因子：
7
作者：
Kuhn, K;Baker, SC;Chee, MS
通讯作者：
Chee, MS
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
通过定量实时PCR评估寡核苷酸阵列数据的方法。
影响因子：
3
作者：
Qin, LX;Beyer, RP;Hudson, FN;Linford, NJ;Morris, DE;Kerr, KF
通讯作者：
Kerr, KF
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
11.5
作者：
Osman, I;Bajorin, DF;Liew, CC
通讯作者：
Liew, CC