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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ftunivnantes:oai:HAL:halsde-00278842v1 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 https://hal.science/halsde-00278842 https://doi.org/10.1111/j.1365-294X.2004.02346.x en eng HAL CCSD Wiley info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1365-294X.2004.02346.x halsde-00278842 https://hal.science/halsde-00278842 doi:10.1111/j.1365-294X.2004.02346.x ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.science/halsde-00278842 Molecular Ecology, 2004, 13 (11), pp.3261-3273. ⟨10.1111/j.1365-294X.2004.02346.x⟩ [SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment info:eu-repo/semantics/article Journal articles 2004 ftunivnantes https://doi.org/10.1111/j.1365-294X.2004.02346.x 2023-02-08T05:57:20Z 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 Université de Nantes: HAL-UNIV-NANTES Molecular Ecology 13 11 3261 3273 |
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Université de Nantes: HAL-UNIV-NANTES |
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language |
English |
topic |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
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[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment Bonin, A. Bellemain, E. Eidesen, P. B. Pompanon, F. Brochmann, C. Taberlet, P. How to track and assess genotyping errors in population genetics studies |
topic_facet |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology [SDV.BID]Life Sciences [q-bio]/Biodiversity [SDV.EE]Life Sciences [q-bio]/Ecology environment |
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://hal.science/halsde-00278842 https://doi.org/10.1111/j.1365-294X.2004.02346.x |
genre |
Dwarf birch |
genre_facet |
Dwarf birch |
op_source |
ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.science/halsde-00278842 Molecular Ecology, 2004, 13 (11), pp.3261-3273. ⟨10.1111/j.1365-294X.2004.02346.x⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1365-294X.2004.02346.x halsde-00278842 https://hal.science/halsde-00278842 doi:10.1111/j.1365-294X.2004.02346.x |
op_doi |
https://doi.org/10.1111/j.1365-294X.2004.02346.x |
container_title |
Molecular Ecology |
container_volume |
13 |
container_issue |
11 |
container_start_page |
3261 |
op_container_end_page |
3273 |
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1766398678283583488 |