Framework for DNA quantification and outlier detection using multidimensional standard curves
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Published version
Supporting information
Author(s)
Type
Journal Article
Abstract
Real-time PCR is a highly sensitive and powerful technology for the quantification of DNA and has become the method of choice in microbiology, bioengineering, and molecular biology. Currently, the analysis of real-time PCR data is hampered by only considering a single feature of the amplification profile to generate a standard curve. The current “gold standard” is the cycle-threshold (Ct) method which is known to provide poor quantification under inconsistent reaction efficiencies. Multiple single-feature methods have been developed to overcome the limitations of the Ct method; however, there is an unexplored area of combining multiple features in order to benefit from their joint information. Here, we propose a novel framework that combines existing standard curve methods into a multidimensional standard curve. This is achieved by considering multiple features together such that each amplification curve is viewed as a point in a multidimensional space. Contrary to only considering a single-feature, in the multidimensional space, data points do not fall exactly on the standard curve, which enables a similarity measure between amplification curves based on distances between data points. We show that this framework expands the capabilities of standard curves in order to optimize quantification performance, provide a measure of how suitable an amplification curve is for a standard, and thus automatically detect outliers and increase the reliability of quantification. Our aim is to provide an affordable solution to enhance existing diagnostic settings through maximizing the amount of information extracted from conventional instruments.
Date Issued
2019-05-06
Date Acceptance
2019-05-06
Citation
Analytical Chemistry, 2019, 91 (11), pp.7426-7434
ISSN
0003-2700
Publisher
American Chemical Society (ACS)
Start Page
7426
End Page
7434
Journal / Book Title
Analytical Chemistry
Volume
91
Issue
11
Copyright Statement
© 2019 American Chemical Society. This is an open access article published under a Creative Commons Attribution (CC-BY)License, which permits unrestricted use, distribution and reproduction in any medium,provided the author and source are cited.
Sponsor
National Institute for Health Research
National Institute for Health Research
Grant Number
NF-SI-0617-10176
RDF04
Subjects
0301 Analytical Chemistry
0904 Chemical Engineering
0399 Other Chemical Sciences
Analytical Chemistry
Publication Status
Published
Article Number
acs.analchem.9b01466
Date Publish Online
2019-05-14