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Contaminations contaminate common databases

The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contam...

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Autores principales: Bensch, Staffan, Inumaru, Mizue, Sato, Yukita, Lee Cruz, Larisa, Cunningham, Andrew A., Goodman, Simon J., Levin, Iris I., Parker, Patricia G., Casanueva, Patricia, Hernández, Maria‐Angeles, Moreno‐Rueda, Gregorio, Rojo, Maria‐Angeles
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820996/
https://www.ncbi.nlm.nih.gov/pubmed/33037786
http://dx.doi.org/10.1111/1755-0998.13272
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author Bensch, Staffan
Inumaru, Mizue
Sato, Yukita
Lee Cruz, Larisa
Cunningham, Andrew A.
Goodman, Simon J.
Levin, Iris I.
Parker, Patricia G.
Casanueva, Patricia
Hernández, Maria‐Angeles
Moreno‐Rueda, Gregorio
Rojo, Maria‐Angeles
author_facet Bensch, Staffan
Inumaru, Mizue
Sato, Yukita
Lee Cruz, Larisa
Cunningham, Andrew A.
Goodman, Simon J.
Levin, Iris I.
Parker, Patricia G.
Casanueva, Patricia
Hernández, Maria‐Angeles
Moreno‐Rueda, Gregorio
Rojo, Maria‐Angeles
author_sort Bensch, Staffan
collection PubMed
description The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR‐based identifications, not just of parasites and pathogens.
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spelling pubmed-78209962021-01-26 Contaminations contaminate common databases Bensch, Staffan Inumaru, Mizue Sato, Yukita Lee Cruz, Larisa Cunningham, Andrew A. Goodman, Simon J. Levin, Iris I. Parker, Patricia G. Casanueva, Patricia Hernández, Maria‐Angeles Moreno‐Rueda, Gregorio Rojo, Maria‐Angeles Mol Ecol Resour News and Views The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR‐based identifications, not just of parasites and pathogens. John Wiley and Sons Inc. 2020-10-31 2021-02 /pmc/articles/PMC7820996/ /pubmed/33037786 http://dx.doi.org/10.1111/1755-0998.13272 Text en © 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle News and Views
Bensch, Staffan
Inumaru, Mizue
Sato, Yukita
Lee Cruz, Larisa
Cunningham, Andrew A.
Goodman, Simon J.
Levin, Iris I.
Parker, Patricia G.
Casanueva, Patricia
Hernández, Maria‐Angeles
Moreno‐Rueda, Gregorio
Rojo, Maria‐Angeles
Contaminations contaminate common databases
title Contaminations contaminate common databases
title_full Contaminations contaminate common databases
title_fullStr Contaminations contaminate common databases
title_full_unstemmed Contaminations contaminate common databases
title_short Contaminations contaminate common databases
title_sort contaminations contaminate common databases
topic News and Views
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820996/
https://www.ncbi.nlm.nih.gov/pubmed/33037786
http://dx.doi.org/10.1111/1755-0998.13272
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