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  • Review Article
  • Published:

Genotyping errors: causes, consequences and solutions

Nature Reviews Genetics volume 6, pages 847–859 (2005)Cite this article

Key Points

  • Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected.

  • Genotyping errors can result from very diverse, complex, and sometimes cryptic origins and are linked to the primary DNA sequence itself, the low quality or quantity of the DNA sample, biochemical artefacts or human factors.

  • Although several estimates of genotyping error rates are commonly used, the error rate per locus is considered to be the most universal metric, as it allows comparisons to be made between studies and different types of markers.

  • Even low rates of genotyping error can markedly affect linkage and association studies, individual identification and population genetic studies.

  • The optimal strategies to limit the occurrence and the impact of genotyping errors are case-specific and will be determined by several factors (for example, biological question, tolerable error rate, equipment and technical skills locally available).

  • General recommendations are provided to help researchers to build their own procedure to face genotyping errors by limiting the production of errors during genotyping, cleaning the dataset after genotyping and analysing data taking into account the errors.

  • Providing information about the methods for error detection and error rate estimation in published work would make it possible to assign a quality index to each genotype, and would allow the scientific community to critically assess unexpected results.

Abstract

Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.

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Figure 1: The recent increase in the number of papers that deal with genotyping errors.
Figure 2: Flow chart that shows the important steps in a genotyping process for limiting the occurrence and effect of genotyping errors.
Figure 3: The use of blind replicates to estimate the error rate.

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Acknowledgements

The authors are grateful to G. Luikart for fruitful discussions and comments on the manuscript and to the persons from the Scandinavian Brown Bear Research Project who provided the bear samples. They thank three anonymous reviewers for providing references and helpful comments.

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Authors and Affiliations

  1. Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, B.P. 53, Grenoble, 38041, Cedex 9, France

    François Pompanon, Aurélie Bonin, Eva Bellemain & Pierre Taberlet

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  1. François Pompanon
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  2. Aurélie Bonin
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  3. Eva Bellemain
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  4. Pierre Taberlet
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Correspondence to François Pompanon.

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FURTHER INFORMATION

An alphabetical list of genetic analysis software

DNA Advisory Board Quality Assurance Standards for Forensic DNA Testing Laboratories

European Molecular Genetics Quality Network

ISI Web of Science

Minimum Information About a Microarray Experiment

PARENTE

Programs useful for detecting genotyping and pedigree errors

UCLA Human Genetics Software Distribution

Glossary

PATERNITY EXCLUSION

The elimination of a male as the potential father of a given offspring, owing to incompatibility between the multilocus genotypes of the two individuals concerned.

NON-INVASIVE GENOTYPING

Genotyping from samples that are collected without capturing the animal (such as hair or faeces).

AMPLIFIED FRAGMENT-LENGTH POLYMORPHISMS

A PCR-based DNA fingerprinting technique that reveals polymorphisms in restriction-enzyme recognition sites by generating dozens of dominant marker bands.

MICROSATELLITE

A class of repetitive DNA that is made up of repeats that are 2–8 nucleotides in length. They can be highly polymorphic and are frequently used as molecular markers in population genetics studies.

SIZE HOMOPLASY

The generation of alleles that are the same size which are not the result of common ancestry (not homologous), but arose independently in different ancestors by parallel or convergent mutations.

ALLELIC DROPOUTS

The stochastic non-amplification of an allele; that is, amplification of only one of the two alleles present at a heterozygous locus.

FALSE ALLELE

An allele-like artefact that is generated by PCR.

ALLELE CALLING

The determination of an allele from an electropherogram or a fluorescent profile.

REPLICATED GENOTYPES

Genotypes that are produced from different (preferentially independent) samples from the same individual.

STUTTER BANDS

Artefacts that occur during the PCR amplification of microsatellites.

HAPLOTYPE

The combination of alleles found at neighbouring loci on a single chromosome or haploid DNA molecule.

FST ESTIMATES

Statistics that were first defined by Sewall Wright to describe the genetic structure at different hierarchical levels (individuals, subpopulations and total populations).

POPULATION BOTTLENECK

A marked reduction in population size that often results in the loss of genetic variation and more frequent matings among closely related individuals.

HARDY–WEINBERG TEST

A test that assesses whether the frequency of each diploid genotype at a locus equals that expected from the random union of alleles.

MAXIMUM LIKELIHOOD APPROACH

A statistical approach that is used to make inferences about the combination of parameter values that gives the greatest probability of obtaining the observed data.

POPULATION ADMIXTURE

A process that leads to a composite gene pool in which at least some individuals come from more than one population.

LIKELIHOOD RATIO TEST

A method for hypothesis testing. The maximum of the likelihood that the data fit a full model of the data is compared with the maximum of the likelihood that the data fit a restricted model and the likelihood ratio (LR) test statistic is computed. If the LR is significant, the full model provides a better fit to the data than does the restricted model.

SHORT-ALLELE DOMINANCE

The preferential PCR amplification of the shorter allele from a heterozygote individual. This is equivalent to a long-allele dropout.

PROBABILITY OF IDENTITY

The overall probability that two individuals drawn at random from a given population share identical genotypes at all typed loci.

EFFECTIVE POPULATION SIZE

The size of the ideal population in which the effects of random drift would be the same as those seen in the actual population.

DIRECTED-ERROR MODEL

A model postulating that there is a greater probability for a particular allele to be consistently incorrectly genotyped.

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Pompanon, F., Bonin, A., Bellemain, E. et al. Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6, 847–859 (2005). https://doi.org/10.1038/nrg1707

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