Open Access Research article

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

Øystein A Haaland1, Kevin A Glover2, Bjørghild B Seliussen2 and Hans J Skaug12*

Author Affiliations

1 Department of Mathematics, University of Bergen, Johannes Brunsgate 12, 5008 Bergen, Norway

2 Institute of Marine Research. P.O. Box 1870, Nordnes. N- 5817 Bergen, Norway

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BMC Genetics 2011, 12:36  doi:10.1186/1471-2156-12-36

Published: 20 April 2011

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 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.

Keywords:
Calibration; DNA register; genotyping error; microsatellite; minke whale; mixed logistic regression; wildlife