Open AccessReal-time cdPCR opens a window into events occurring in the first few PCR amplification cycles
Author(s) -
David L. Duewer,
Margaret C. Kline,
Erica L. Romsos
Publication year - 2015
Publication title -
analytical and bioanalytical chemistry/analytical and bioanalytical chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.86
H-Index - 166
eISSN - 1618-2650
pISSN - 1618-2642
DOI - 10.1007/s00216-015-9073-8
Subject(s) - amplicon , digital polymerase chain reaction , polymerase chain reaction , computer science , biological system , computational biology , real time polymerase chain reaction , biology , genetics , gene
Polymerase chain reaction (PCR) end-point limiting dilution techniques, collectively termed "digital PCR (dPCR)", have been proposed as providing a potentially primary method for DNA quantification. We are evaluating several commercially available dPCR systems for use in certifying mass concentration in human genomic DNA reference materials. To better understand observed anomalies among results from chamber- and droplet-dPCR (cdPCR and ddPCR) systems, we have developed a graphical tool for evaluating and documenting the performance of PCR assays in real-time cdPCR systems: the ogive plot, the cumulative distribution of crossing threshold values. The ogive structure appears to embed information about early amplification events. We have successfully simulated ogives observed with different assays and reaction conditions using a four-stage amplification model parameterized by the probability of creating an intact 1) first generation "long" amplicon of indeterminate length from an original DNA target, 2) second generation defined-length amplicon from a long amplicon, and 3) defined-length amplicon from another defined-length amplicon. We are using insights from this model to optimize dPCR assay design and reaction conditions and to help validate assays proposed for use in value-assigning DNA reference materials.