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Genotyping errors in a calibrated DNA register: implications for identification of individuals

Bergen Open Research Archive

Show simple item record Haaland, Øystein eng Glover, Kevin eng Seliussen, Bjørghild Breistein eng Skaug, Hans J. eng 2012-01-20T13:19:01Z 2012-01-20T13:19:01Z 2011-04-20 eng
dc.identifier.citation BMC Genetics 2011, 12:36 en
dc.identifier.issn 1471-2156 eng
dc.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 withinsample 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 genotyping platforms and in different laboratories. Although errors were detected, it is demonstrated that if the re-genotyping of individual samples is possible, these will have a minimal effect on the database’s primary purpose, i.e., to perform individual identification. en
dc.language.iso eng eng
dc.publisher BioMed Central eng
dc.rights Attribution CC BY eng
dc.rights.uri eng
dc.subject Calibration DNA register eng
dc.subject Genotyping error eng
dc.subject Microsatellite eng
dc.subject Minke whale eng
dc.subject Mixed logistic eng
dc.subject Regression eng
dc.title Genotyping errors in a calibrated DNA register: implications for identification of individuals eng
dc.type Peer reviewed eng
dc.type Journal article eng
dc.subject.nsi VDP::Medical disciplines: 700::Basic medical, dental and veterinary science disciplines: 710::Medical genetics: 714 eng
dc.rights.holder Copyright 2011 Haaland et al; licensee BioMed Central Ltd.
dc.type.version publishedVersion eng
bora.peerreviewed Peer reviewed eng
bora.cristinID 844899 eng
bibo.doi eng
dc.identifier.cristinID 844899 eng

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