原创力文档an adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories一个适应性强的方法使用人类混合组织比率计控制基准性能在临床实验室基因表达微阵列.pdfVIP
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an adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories一个适应性强的方法使用人类混合组织比率计控制基准性能在临床实验室基因表达微阵列
Pine et al. BMC Biotechnology 2011, 11:38
/1472-6750/11/38
METHODOLOGY ARTICLE Open Access
An adaptable method using human mixed tissue
ratiometric controls for benchmarking
performance on gene expression microarrays in
clinical laboratories
P Scott Pine1,2, Barry A Rosenzweig1 and Karol L Thompson1*
Abstract
Background: Molecular biomarkers that are based on mRNA transcripts are being developed for the diagnosis and
treatment of a number of diseases. DNA microarrays are one of the primary technologies being used to develop
classifiers from gene expression data for clinically relevant outcomes. Microarray assays are highly multiplexed
measures of comparative gene expression but have a limited dynamic range of measurement and show
compression in fold change detection. To increase the clinical utility of microarrays, assay controls are needed that
benchmark performance using metrics that are relevant to the analysis of genomic data generated with biological
samples.
Results: Ratiometric controls were prepared from commercial sources of high quality RNA from human tissues
with distinctly different expression profiles and mixed in defined ratios. The samples were processed using six
different target labeling protocols and replicate datasets were generated on high density gene expression
microarrays. The area under the curve from receiver operating characteristic plots was calculated to measure
diagnostic performance. The reliable region of the dynamic range was derived from log2 ratio deviation plots
made for each dataset. Small but statistically significant differences in diagnostic performance were observed
between standardized assays available from the array manufacturer and alternative methods for target generation.
Assay performance using the reliable range of comparative measurement as a metric was i
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