Genotyping errors in a calibrated DNA register: implications for identification of individuals
Abstract Background The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and f...
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ftdoajarticles:oai:doaj.org/article:6ce479565c7240babca52cd0dbbad7c1 2023-05-15T17:12:50+02:00 Genotyping errors in a calibrated DNA register: implications for identification of individuals Seliussen Bjørghild B Glover Kevin A Haaland Øystein A Skaug Hans J 2011-04-01T00:00:00Z https://doi.org/10.1186/1471-2156-12-36 https://doaj.org/article/6ce479565c7240babca52cd0dbbad7c1 EN eng BMC http://www.biomedcentral.com/1471-2156/12/36 https://doaj.org/toc/1471-2156 doi:10.1186/1471-2156-12-36 1471-2156 https://doaj.org/article/6ce479565c7240babca52cd0dbbad7c1 BMC Genetics, Vol 12, Iss 1, p 36 (2011) Calibration DNA register genotyping error microsatellite minke whale mixed logistic regression wildlife Genetics QH426-470 article 2011 ftdoajarticles https://doi.org/10.1186/1471-2156-12-36 2022-12-31T02:55:02Z Abstract Background The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR) contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors. Results The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote) and three false heterozygotes (i.e., the true genotype was a homozygote). Conclusions To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and genotyping consistency, despite analyses being conducted on different ... Article in Journal/Newspaper minke whale Directory of Open Access Journals: DOAJ Articles BMC Genetics 12 1 36 |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Calibration DNA register genotyping error microsatellite minke whale mixed logistic regression wildlife Genetics QH426-470 |
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Calibration DNA register genotyping error microsatellite minke whale mixed logistic regression wildlife Genetics QH426-470 Seliussen Bjørghild B Glover Kevin A Haaland Øystein A Skaug Hans J Genotyping errors in a calibrated DNA register: implications for identification of individuals |
topic_facet |
Calibration DNA register genotyping error microsatellite minke whale mixed logistic regression wildlife Genetics QH426-470 |
description |
Abstract Background The use of DNA methods for the identification and management of natural resources is gaining importance. In the future, it is likely that DNA registers will play an increasing role in this development. Microsatellite markers have been the primary tool in ecological, medical and forensic genetics for the past two decades. However, these markers are characterized by genotyping errors, and display challenges with calibration between laboratories and genotyping platforms. The Norwegian minke whale DNA register (NMDR) contains individual genetic profiles at ten microsatellite loci for 6737 individuals captured in the period 1997-2008. These analyses have been conducted in four separate laboratories for nearly a decade, and offer a unique opportunity to examine genotyping errors and their consequences in an individual based DNA register. We re-genotyped 240 samples, and, for the first time, applied a mixed regression model to look at potentially confounding effects on genotyping errors. Results The average genotyping error rate for the whole dataset was 0.013 per locus and 0.008 per allele. Errors were, however, not evenly distributed. A decreasing trend across time was apparent, along with a strong within-sample correlation, suggesting that error rates heavily depend on sample quality. In addition, some loci were more error prone than others. False allele size constituted 18 of 31 observed errors, and the remaining errors were ten false homozygotes (i.e., the true genotype was a heterozygote) and three false heterozygotes (i.e., the true genotype was a homozygote). Conclusions To our knowledge, this study represents the first investigation of genotyping error rates in a wildlife DNA register, and the first application of mixed models to examine multiple effects of different factors influencing the genotyping quality. It was demonstrated that DNA registers accumulating data over time have the ability to maintain calibration and genotyping consistency, despite analyses being conducted on different ... |
format |
Article in Journal/Newspaper |
author |
Seliussen Bjørghild B Glover Kevin A Haaland Øystein A Skaug Hans J |
author_facet |
Seliussen Bjørghild B Glover Kevin A Haaland Øystein A Skaug Hans J |
author_sort |
Seliussen Bjørghild B |
title |
Genotyping errors in a calibrated DNA register: implications for identification of individuals |
title_short |
Genotyping errors in a calibrated DNA register: implications for identification of individuals |
title_full |
Genotyping errors in a calibrated DNA register: implications for identification of individuals |
title_fullStr |
Genotyping errors in a calibrated DNA register: implications for identification of individuals |
title_full_unstemmed |
Genotyping errors in a calibrated DNA register: implications for identification of individuals |
title_sort |
genotyping errors in a calibrated dna register: implications for identification of individuals |
publisher |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1471-2156-12-36 https://doaj.org/article/6ce479565c7240babca52cd0dbbad7c1 |
genre |
minke whale |
genre_facet |
minke whale |
op_source |
BMC Genetics, Vol 12, Iss 1, p 36 (2011) |
op_relation |
http://www.biomedcentral.com/1471-2156/12/36 https://doaj.org/toc/1471-2156 doi:10.1186/1471-2156-12-36 1471-2156 https://doaj.org/article/6ce479565c7240babca52cd0dbbad7c1 |
op_doi |
https://doi.org/10.1186/1471-2156-12-36 |
container_title |
BMC Genetics |
container_volume |
12 |
container_issue |
1 |
container_start_page |
36 |
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1766069719795761152 |