How to track and assess genotyping errors in population genetics studies
Times Cited: 124 International audience Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a tab...
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fttriple:oai:gotriple.eu:10670/1.3an7zw 2023-05-15T16:03:02+02:00 How to track and assess genotyping errors in population genetics studies Bonin, A. Bellemain, E. Eidesen, P. B. Pompanon, F. Brochmann, C. Taberlet, P. Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) Department of Ecology and Natural Resource Management Norwegian University of Life Sciences (NMBU) National Centre for Biosystematics (NCB) University of Oslo (UiO) 2004-01-01 https://doi.org/10.1111/j.1365-294X.2004.02346.x https://hal.archives-ouvertes.fr/halsde-00278842 en eng HAL CCSD Wiley halsde-00278842 doi:10.1111/j.1365-294X.2004.02346.x 10670/1.3an7zw https://hal.archives-ouvertes.fr/halsde-00278842 undefined Hyper Article en Ligne - Sciences de l'Homme et de la Société ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology Molecular Ecology, Wiley, 2004, 13 (11), pp.3261-3273. ⟨10.1111/j.1365-294X.2004.02346.x⟩ anthro-se envir Journal Article https://vocabularies.coar-repositories.org/resource_types/c_6501/ 2004 fttriple https://doi.org/10.1111/j.1365-294X.2004.02346.x 2023-01-22T18:41:40Z Times Cited: 124 International audience Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies. Article in Journal/Newspaper Dwarf birch Unknown Molecular Ecology 13 11 3261 3273 |
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anthro-se envir Bonin, A. Bellemain, E. Eidesen, P. B. Pompanon, F. Brochmann, C. Taberlet, P. How to track and assess genotyping errors in population genetics studies |
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anthro-se envir |
description |
Times Cited: 124 International audience Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies. |
author2 |
Laboratoire d'Ecologie Alpine (LECA) Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS) Department of Ecology and Natural Resource Management Norwegian University of Life Sciences (NMBU) National Centre for Biosystematics (NCB) University of Oslo (UiO) |
format |
Article in Journal/Newspaper |
author |
Bonin, A. Bellemain, E. Eidesen, P. B. Pompanon, F. Brochmann, C. Taberlet, P. |
author_facet |
Bonin, A. Bellemain, E. Eidesen, P. B. Pompanon, F. Brochmann, C. Taberlet, P. |
author_sort |
Bonin, A. |
title |
How to track and assess genotyping errors in population genetics studies |
title_short |
How to track and assess genotyping errors in population genetics studies |
title_full |
How to track and assess genotyping errors in population genetics studies |
title_fullStr |
How to track and assess genotyping errors in population genetics studies |
title_full_unstemmed |
How to track and assess genotyping errors in population genetics studies |
title_sort |
how to track and assess genotyping errors in population genetics studies |
publisher |
HAL CCSD |
publishDate |
2004 |
url |
https://doi.org/10.1111/j.1365-294X.2004.02346.x https://hal.archives-ouvertes.fr/halsde-00278842 |
genre |
Dwarf birch |
genre_facet |
Dwarf birch |
op_source |
Hyper Article en Ligne - Sciences de l'Homme et de la Société ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology Molecular Ecology, Wiley, 2004, 13 (11), pp.3261-3273. ⟨10.1111/j.1365-294X.2004.02346.x⟩ |
op_relation |
halsde-00278842 doi:10.1111/j.1365-294X.2004.02346.x 10670/1.3an7zw https://hal.archives-ouvertes.fr/halsde-00278842 |
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op_doi |
https://doi.org/10.1111/j.1365-294X.2004.02346.x |
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Molecular Ecology |
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13 |
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11 |
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