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    Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer.

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    Authors
    Kheirelseid, Elrasheid A H
    Chang, Kah Hoong
    Newell, John
    Kerin, Michael J
    Miller, Nicola
    Affiliation
    Department of Surgery, National University of Ireland, Galway, Ireland.
    Issue Date
    2010
    
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    Citation
    Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer. 2010, 11:12 BMC Mol. Biol.
    Journal
    BMC molecular biology
    URI
    http://hdl.handle.net/10147/93867
    DOI
    10.1186/1471-2199-11-12
    PubMed ID
    20122155
    Abstract
    BACKGROUND: Gene expression analysis has many applications in cancer diagnosis, prognosis and therapeutic care. Relative quantification is the most widely adopted approach whereby quantification of gene expression is normalised relative to an endogenously expressed control (EC) gene. Central to the reliable determination of gene expression is the choice of control gene. The purpose of this study was to evaluate a panel of candidate EC genes from which to identify the most stably expressed gene(s) to normalise RQ-PCR data derived from primary colorectal cancer tissue. RESULTS: The expression of thirteen candidate EC genes: B2M, HPRT, GAPDH, ACTB, PPIA, HCRT, SLC25A23, DTX3, APOC4, RTDR1, KRTAP12-3, CHRNB4 and MRPL19 were analysed in a cohort of 64 colorectal tumours and tumour associated normal specimens. CXCL12, FABP1, MUC2 and PDCD4 genes were chosen as target genes against which a comparison of the effect of each EC gene on gene expression could be determined. Data analysis using descriptive statistics, geNorm, NormFinder and qBasePlus indicated significant difference in variances between candidate EC genes. We determined that two genes were required for optimal normalisation and identified B2M and PPIA as the most stably expressed and reliable EC genes. CONCLUSION: This study identified that the combination of two EC genes (B2M and PPIA) more accurately normalised RQ-PCR data in colorectal tissue. Although these control genes might not be optimal for use in other cancer studies, the approach described herein could serve as a template for the identification of valid ECs in other cancer types.
    Language
    en
    ISSN
    1471-2199
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2199-11-12
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