title: A comparison of the effects of PCR inhibition in quantitative PCR and forensic STR analysis.
abstract: In this paper we compare the effects of three representative PCR inhibitors using quantitative PCR (qPCR) and multiplex STR amplification in order to determine the effect of inhibitor concentration on allele dropout and to develop better ways to interpret forensic DNA data. We have used humic acid, collagen and calcium phosphate at different concentrations to evaluate the profiles of alleles inhibited in these amplifications. These data were correlated with previously obtained results from quantitative PCR including melt curve effects, efficiency changes and cycle threshold (Ct) values. Overall, the data show that there are two competing processes that result from PCR inhibition. The first process is a general loss of larger alleles. This appears to occur with all inhibitors. The second process is more sequence specific and occurs when the inhibitor binds DNA, altering the cycle threshold and the melt curve. This sequence-specific inhibition results in patterns of allele loss that occur in addition to the overall loss of larger alleles. The data demonstrate the applicability of utilizing real-time PCR results to predict the presence of certain types of PCR inhibition in STR analysis.
authors.affiliation: International Forensic Research Institute, Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
authors.forename: Maribel E
authors.initials: ME
authors.lastname: Funes-Huacca
authors.forename: Kerry
authors.initials: K
authors.lastname: Opel
authors.forename: Robyn
authors.initials: R
authors.lastname: Thompson
authors.forename: Bruce R
authors.initials: BR
authors.lastname: McCord
mesh_terms: D002130:Calcium Phosphates; D003094:Collagen; D004247:DNA / Q000032:analysis*; D053803:Forensic Genetics / Q000379:methods* / Q000592:standards; D006801:Humans; D006812:Humic Substances; D008297:Male; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000592:standards
chemical_list: D002130:Calcium Phosphates; D006812:Humic Substances; D003094:Collagen; D004247:DNA; C020243:calcium phosphate