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    • ENG: Bioinformatics: Scholarly Papers
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    •   OpenBU
    • College of Engineering
    • Bioinformatics
    • ENG: Bioinformatics: Scholarly Papers
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    Simultaneous Quantitative and Allele-Specific Expression Analysis with Real Competitive PCR

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    Date Issued
    2004-5-5
    Publisher Version
    10.1186/1471-2156-5-8
    Author(s)
    Ding, Chunming
    Maier, Esther
    Roscher, Adelbert A
    Braun, Andreas
    Cantor, Charles R
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    Permanent Link
    https://hdl.handle.net/2144/3196
    Citation (published version)
    Ding, Chunming, Esther Maier, Adelbert A Roscher, Andreas Braun, Charles R Cantor. "Simultaneous quantitative and allele-specific expression analysis with real competitive PCR" BMC Genetics 5:8. (2004)
    Abstract
    BACKGROUND. For a diploid organism such as human, the two alleles of a particular gene can be expressed at different levels due to X chromosome inactivation, gene imprinting, different local promoter activity, or mRNA stability. Recently, imbalanced allelic expression was found to be common in human and can follow Mendelian inheritance. Here we present a method that employs real competitive PCR for allele-specific expression analysis. RESULTS. A transcribed mutation such as a single nucleotide polymorphism (SNP) is used as the marker for allele-specific expression analysis. A synthetic mutation created in the competitor is close to a natural mutation site in the cDNA sequence. PCR is used to amplify the two cDNA sequences from the two alleles and the competitor. A base extension reaction with a mixture of ddNTPs/dNTP is used to generate three oligonucleotides for the two cDNAs and the competitor. The three products are identified and their ratios are calculated based on their peak areas in the MALDI-TOF mass spectrum. Several examples are given to illustrate how allele-specific gene expression can be applied in different biological studies. CONCLUSIONS. This technique can quantify the absolute expression level of each individual allele of a gene with high precision and throughput.
    Rights
    Copyright 2004 Ding et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
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    • ENG: Bioinformatics: Scholarly Papers [101]
    • Center for Advanced Biotechnology Papers [9]


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