Table of Contents
Computational Biology Journal
Volume 2015, Article ID 601504, 6 pages
http://dx.doi.org/10.1155/2015/601504
Research Article

Simplified Algorithms for Determining Cycle Shift between qPCR Fluorescence Curves

1Department of Anæsthesia and Pain Management and Department of Anatomy, Flinders University, Bedford Park, SA 5042, Australia
2Department of Surgery, Flinders University, Bedford Park, SA 5042, Australia

Received 16 September 2014; Revised 31 December 2014; Accepted 13 January 2015

Academic Editor: Andre Fujita

Copyright © 2015 Michael E. Jones et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The polymerase chain reaction is a central component of current molecular biology. It is a cyclic process, in each early cycle of which the template DNA approximately doubles. An indicator which fluoresces when bound to DNA quantifies the DNA present at the end of each cycle, giving rise to a fluorescence curve which is characteristically sigmoid in shape. The fluorescence curve quantifies the amount of DNA initially present; the more the initial DNA, the earlier the rise in the fluorescence. Accordingly the amount of DNA initially present in two samples can be compared: the sample with the less DNA gives rise to a relatively delayed fluorescence curve and the ratio of the DNAs can be deduced from the separation of the curves. There is, however, a second determinant of this separation, the fold increase in DNA per cycle: ideally a twofold increase but frequently less. Current guidelines recommend that this be determined experimentally by carrying out PCR on a series of dilutions. If the value of the fold increase is known, then the algorithm for determining the separation can be reduced to a relatively simple computation, rather than employing a multidimensional nonlinear optimization such as the Marquardt-Levenberg as currently employed.