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Framework for DNA quantification and outlier detection using multidimensional standard curves
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Moniri, Ahmad, Rodriguez-Manzano, Jesus, Malpartida-Cardenas, Kenny, Yu, Ling-Shan, Didelot, Xavier, Holmes, Alison and Georgiou, Pantelis (2019) Framework for DNA quantification and outlier detection using multidimensional standard curves. Analytical Chemistry, 91 (11). pp. 7426-7434. doi:10.1021/acs.analchem.9b01466 ISSN 1520-6882.
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Official URL: https://doi.org/10.1021/acs.analchem.9b01466
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.
Item Type: | Journal Article | |||||||||||||||||||||
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Subjects: | Q Science > QP Physiology | |||||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||||||||||||||
SWORD Depositor: | Library Publications Router | |||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | DNA, Polymerase chain reaction | |||||||||||||||||||||
Journal or Publication Title: | Analytical Chemistry | |||||||||||||||||||||
Publisher: | American Chemical Society (ACS) | |||||||||||||||||||||
ISSN: | 1520-6882 | |||||||||||||||||||||
Official Date: | 6 May 2019 | |||||||||||||||||||||
Dates: |
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Volume: | 91 | |||||||||||||||||||||
Number: | 11 | |||||||||||||||||||||
Page Range: | pp. 7426-7434 | |||||||||||||||||||||
DOI: | 10.1021/acs.analchem.9b01466 | |||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||
Reuse Statement (publisher, data, author rights): | “This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see [insert ACS Articles on Request author-directed link to Published Work, see http://pubs.acs.org/page/policy/articlesonrequest/index.html].” | |||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||||||||
Date of first compliant deposit: | 22 May 2019 | |||||||||||||||||||||
Date of first compliant Open Access: | 6 May 2020 | |||||||||||||||||||||
RIOXX Funder/Project Grant: |
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