Related Experiment Video
Updated: Jul 8, 2026
10:28
Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
Published on: April 14, 2015
TaqMan low density array is roughly right for gene expression quantification in colorectal cancer
Bingjian Lü1, Jing Xu, Jian Chen
1Department of Pathology, School of Medicine, Zhejiang University, PR China.
Summary
TaqMan low density array (LDA) shows good reproducibility for most gene expression in colorectal cancer. However, caution is advised for low copy genes due to decreased reliability.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- TaqMan low density array (LDA) enables high-throughput gene expression analysis.
- Assessing the reproducibility and reliability of LDA in functional genomics is crucial.
Purpose of the Study:
- To evaluate the reproducibility and reliability of LDA for measuring mRNA expression of 95 gastrointestinal differentiation genes in colorectal cancer.
- To compare LDA with conventional quantitative PCR (Q-PCR) for detecting differentially expressed genes.
Main Methods:
- Applied LDA to 27 colorectal cancer samples and matched normal mucosa.
- Utilized conventional Q-PCR for 18 differentially expressed genes in an additional 22 colorectal cancer samples.
- Analyzed intra-assay agreement and gene expression levels (Ct values).
Main Results:
- LDA achieved high amplification success (97.2%) with excellent intra-assay agreement (CCC=0.952).
- Seventy-nine genes demonstrated perfect or substantial agreement between intra-LDA tests.
- LDA and SYBR Green Q-PCR showed consistent directional changes for 18 genes.
- Reproducibility was higher for genes with low Ct values (<30 cycles).
Conclusions:
- LDA is a robust method for gene quantification in colorectal cancer.
- Reproducibility of LDA decreases for low copy genes.
- Recommend careful analysis of LDA results for low copy genes.
