How to track and assess genotyping errors in population genetics studies

By Aurélie Bonin, E. Bellemain, P. B. Eidesen, F. Pompanon, C. Brochmann, P. Taberlet. Molecular Ecology, 2004

1,452 citations recorded by the source corpus.

Subfields: Genetics, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/f288ab36da80da4867294b5a0ca35ef966447ac7

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In Genetics

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Citations in the corpus

Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference (2015, background): “These potentially inaccurate inferences can be mitigated and accounted for if error rates are reported (Bonin et al. 2004; Pompanon et al. 2005; Pool et al. 2010; Davey et al. 2011) or incorporated into data analysis (Gompert & Buerkle 2011; Niel-sen et al. 2011; Gautier et al. 2013a).”
Genotyping errors: causes, consequences and solutions (2005, background): “A genotyping error occurs when the observed genotype of an individual does not correspond to the true genotyp”
Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets (2010, background): “Molecular ecologists are keenly aware of those errors and their consequences (Bonin et al. 2004; Miller et al. 2002; Morin et al. 2001; Valiere et al. 2002).”
Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers (2008, methodology): “We used three selective primer combinations (Bonin et al. 2004): EcoRI 5′-GACT GCGTACCAATTCAGT-3′/MseI 5′-GATGAGTCCTGAG TAACTC-3′, EcoRI 5′-GACTGCGTACCAATTCATG-3′/ MseI 5′-GATGAGTCCTGAGTAACAC-3′, and EcoRI 8 5′-GACTGCGTACCAATTCATG-3′/MseI 5′-GATG AGTCCTGAGTAACAA-3′.”
Highly accurate SNP genotyping from historical and low‐quality samples (2007, background): “Although the potential application of SNPs to degraded, historical, and ancient samples has been discussed in the literature (Surridge et al . 2002; Noonan et al . 2005; Asher & Hofreiter 2006; Poinar et al . 2006; Rompler et al . 2006b), there are few examples to date (Rompler et al . 2006b).”
Repeatedly out of Beringia: Cassiope tetragona embraces the Arctic (2007, methodology): “Based on the 23 duplicated individuals, an error rate was calculated according to Bonin et al. (2004).”
Inter-simple sequence repeat (ISSR) markers: are we doing it right? (2015, background): “37 with at least 5–10% of random samples can also be used to assess reproducibility (Bonin et al. 2004), whereas data points (DNA bands) that are not reproducible should be left out of the study.”
Break zones in the distributions of alleles and species in alpine plants (2011, methodology): “All laboratories used replicates to conduct internal quality checks, following Bonin et al. (2004).”
Introgression between invasive saltcedars (Tamarix chinensis and T. ramosissima) in the USA (2009, background): “AFLP error rates Knowledge of error rate in AFLP analysis is important as errors can bias final conclusions (Bonin et al. 2004).”
Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugium (2011, methodology): “The error rate (according to Bonin et al., 2004) before the exclusion of unreliable characters was 0.7%.”
Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer (2006, neutral): “Taberlet et al. (1996) Ursus arctos Faeces 1 53% (P) Bonin et al. (2004) Ursus arctos Faeces 6 1% (A) 0.13% (A) Garnier et al. (2001) Diceros bicornis Faeces 10 30% (P) 0% (P) Parsons (2001) Tursiops truncatus Faeces 3 0% (P) 0.97% (P) Piggot et al. (2004) Petrogale penicilata Faeces 6 0.92% (P) 3”
An evaluation of field and noninvasive genetic methods for estimating Eurasian otter population size (2009, background): “The quality of data needs to be thoroughly monitored in order to detect and eliminate genotyping errors and, therefore, calculations of error rates and probability of identity values should be meticulously reported in all studies based on NGS (Waits et al. 2001; Bonin et al. 2004; Broquet and Peti”
Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome (2006, background): “from the data (Bonin et al. 2004).”
Evolutionary ecology of social and sexual systems : crustaceans as model organisms (2007, background): “Errors in genotyping appear to be higher for AFLPs than for microsatellites (Bonin et al. 2004), and the dominance of AFLP bands makes it impossible to detect artifacts or bands produced by contaminating organisms as departures from Hardy-Weinberg proportions.”
Genetics and conservation of European brown bears Ursus arctos (2011, background): “Brown bear research has provided field precautions and laboratory methods to deal with these challenges (Bellemain & Taberlet 2004, Bonin et al. 2004, Piggott et al. 2004, Murphy et al. 2007, De Barba & Waits 2009).”
Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. (2006, background): “Homoplasy dampens the visible allelic diversity of populations and may inflate estimates of gene flow when mutation rate is high (Garza & Freimer 1996; Rousset 1996; Viard et al. 1998; Blankenship et al. 2002; Epperson 2005).”
Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs (2011, background): “The error rate per reaction, calculated following Bonin et al. (2004) as the number of mismatching genotypes divided by the number of polymorphic bands compared, was 2.1% (111 diVerences observed out of 5,217 comparisons).”