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A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts

PCR inhibition remains a consistent problem for PCR amplification, particular in situations when the target DNA is in low-abundance or heavily degraded. Here we report an analysis on the identification of PCR inhibition and some recommendations to circumvent/alleviate inhibition in degraded samples.

Sep 11, 2009

Authors: C. King, R. Debruyne, M. Kuch, C. Schwarz, H. Poinar
 
BioTechniques, Vol 47, No. 5. September 2011. DOI:10.2144/000113244

Abstract

Inhibition is problematic in many applications of PCR, particularly those involving degraded or low amounts of template DNA, when simply diluting the extract is undesirable. Two basic approaches to monitoring inhibition in such samples using real-time or quantitative PCR (qPCR) have been proposed. The first method analyzes the quantification cycle (Cq) deviation of a spiked internal positive control. The second method considers variations in reaction efficiency based on the slopes of individual amplification plots. In combining these methods, we observed increased Cq values together with reduced amplification efficiencies in some samples, as expected; however, deviations from this pattern in other samples support the use of both measurements. Repeat inhibition testing enables optimization of PCR facilitator combinations and sample dilution such that DNA yields and/or quantitative accuracy can be maximized in subsequent PCR runs. Although some trends were apparent within sample types, differences in inhibition levels, optimal reactions conditions, and expected recovery of DNA under these conditions suggest that all samples be routinely tested with this approach.

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