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BMC Res Notes. 2008 Jul 28;1:54. doi: 10.1186/1756-0500-1-54.

A new approach to primer design for the control of PCR bias in methylation studies.

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Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St, Andrews Place, East Melbourne, Vic 3002, Australia.


Primer design for PCR-based methylation analysis following bisulfite conversion of DNA is considerably more complex than primer design for regular PCR. The choice of the optimal primer set is critical to the performance and correct interpretation of the results. Most methodologies in methylation analysis utilize primers that theoretically amplify methylated and unmethylated templates at the same time. The proportional amplification of all templates is critical but difficult to achieve due to PCR bias favouring the amplification of the unmethylated template. The focus of this brief communication is to point out the important criteria needed for the successful choice of primers that will enable the control of PCR bias in bisulfite based methylation-screening protocols.

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