Microsatellites behaving badly: empirical evaluation of genotyping errors and subsequent impacts on population studies

Kelly, Amy C.; Mateus‐Pinilla, Nohra E.; Douglas, Michael E.; Shelton, Paul; Novakofski, J.

doi:10.4238/2011.october.19.1

Cited by 31 publications

(32 citation statements)

References 41 publications

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“…They require a large investment of time and laboratorial effort due to the genotyping step [108]. Moreover, they require a species-specific marker, where there is a high potential for null alleles and imperfect repeats due to polymerase slippage during replication, and genotyping errors that impact population studies by providing unreliable genetic information for conservation biology, molecular ecology and population genetic research [132].…”

Section: Microsatellitesmentioning

confidence: 99%

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Mastrochirico-Filho¹,

Freitas²,

Ariede³

et al. 2018

Biological Resources of Water

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Neotropical fish correspond to approximately 30% of all fish species worldwide. The diversity of fish species found in Neotropical basins reflects variations in life-history strategies and exhibition of particular morphological, physiological and ecological attributes. These attributes are mainly related to different forms of feeding, life maintenance and reproduction. Today, fish populations are being threatened by anthropogenic actions that are having a visible impact on the natural state of continental aquatic ecosystems. The main causes are overfishing, non-native species introduction, reservoir-dam systems, mining, pollution and deforestation. The biology and population dynamics of the species are still unclear due to lack of research. Genetic tools can be useful resources for the conservation of Neotropical fish species in several ways. Molecular genetic markers are considered powerful tools to identify cryptic and hybrid fish and also allow the evaluation of the genetic variability and structure of populations of Neotropical ichthyofauna. Several analyses of molecular markers have been performed on Neotropical fish, including allozyme analysis, restriction fragment length polymorphisms in regions of DNA (RFLP), randomly amplified polymorphic DNA (AFLP), randomly amplified polymorphic DNA (RAPD), microsatellites, single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) markers. In order to analyse a high number of markers, next generation sequencing has allowed researchers to generate a large amount of genomic information that can be applied to the conservation of Neotropical fish.Keywords: molecular markers, genetic conservation, Neotropical ichthyofauna, overfishing, dam © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rivers of the Neotropical regionThe distribution of freshwater fish around the world was mediated by historical climatic and geological events at different time points. Today, each global region has distinct patterns of distribution due to physical barriers obstructing species dispersion, representing different tolerances to environmental variables [1]. The tropics of the American continent are well known for their high biodiversity. This is due to habitat heterogeneity and a complex geological history. The Neotropical region is a biogeographic region that comprises Central America (including the southern part of Mexico and the peninsula of Baja California), the south of Florida, the Caribbean and South America. The origin and evolution of the Neotropical region arose through a process of synergism between its fauna that experienced local rainfall variations and gradual climate change resulting in a mosaic of habitats controlled by river migrations, sea-level fluctuations, local dryness and local uplifts [2,3].Regional geo...

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Section: Microsatellitesmentioning

confidence: 99%

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Mastrochirico-Filho¹,

Freitas²,

Ariede³

et al. 2018

Biological Resources of Water

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“…In fact, empirical estimates showed that about two‐thirds of all genotyping errors can originate from the presence of null alleles and imperfect repetitions (Kelly et al . ).…”

Section: Introductionmentioning

confidence: 97%

Historical and non‐invasive samples: a study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

Clozato

Moraes‐Barros

Santos

et al. 2014

Molecular Ecology Resources

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Tamandua tetradactyla (Pilosa), the lesser anteater, is a medium-size mammal from South America. Its wide distribution through different landscapes, solitary and nocturnal habits, and the difficulty to capture and contain specimens limit the amount of individuals and populations sampled during fieldworks. These features along with the lack of specific molecular markers for the lesser anteater might be the causes for paucity in population genetic studies for the species. Historical samples from museum specimens, such as skins, and non-invasive samples, such as plucked hair, can be supplementary sources of DNA samples. However, the DNA quantity and quality of these samples may be limiting factors in molecular studies. In this study, we describe nine microsatellite loci for T. tetradactyla and test the amplification success, data reliability and estimate errors on both historical and non-invasive sample sets. We tested nine polymorphic microsatellites and applied the quality index approach to evaluate the relative performance in genotype analysis of 138 historical samples (study skin) and 19 non-invasive samples (plucked hair). The observed results show a much superior DNA quality of non-invasive over historical samples and support the quality index analysis as a practical tool to exclude samples with doubtful performance in genetic studies. We also found a relationship between the age of non-invasive samples and DNA quality, but lack of evidence of this pattern for historical samples.

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“…Genotyping errors due to uncharacterized sequence variation have been observed in microsatellite genotyping (termed "null alleles") and were recently subjected to systematic analysis [9,10], however they have gone largely unaddressed in SNP genotyping studies. In this study, we investigated the effect and extent of OTVs in a diverse collection of inbred strains and intercrossed mice using the Mouse Diversity Array.…”

Section: Introductionmentioning

confidence: 99%

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

et al. 2012

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BackgroundHigh-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs.ResultsWe identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains.ConclusionThe problems of ascertainment bias and missing information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses.

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Microsatellites behaving badly: empirical evaluation of genotyping errors and subsequent impacts on population studies

Cited by 31 publications

References 41 publications

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Historical and non‐invasive samples: a study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

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