How To Perform Meaningful Estimates of Genetic Effects
Publication Date
May 02, 2008
Journal
PLOS Genetics
Authors
José M. Álvarez Castro, Arnaud Le Rouzic & Örjan Carlborg
Volume
4
Issue
5
Pages
e1000062
DOI
https://dx.plos.org/10.1371/journal.pgen.1000062
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000062
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18451979
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2320976
Europe PMC
http://europepmc.org/abstract/MED/18451979
Web of Science
000256869100021
Scopus
44449116784
Mendeley
http://www.mendeley.com/research/perform-meaningful-estimates-genetic-effects
Events
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Mendeley | Further Information

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/932323"], "description"=>"<p>The variance decomposition was performed for the same cases as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000062#pgen-1000062-g001\" target=\"_blank\">Figure 1</a>. V<sub>P</sub> is the phenotypic variance, which (in absence of environmental variance) is equal to V<sub>G</sub>, the genetic variance. V<sub>A</sub> is the additive variance, V<sub>D</sub> is the dominance variance and V<sub>I</sub> is the epistatic (interaction) variance.</p>", "links"=>[], "tags"=>["departures", "hwp", "variance"], "article_id"=>602768, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_of_departures_from_the_HWP_on_the_variance_components_/602768", "title"=>"Effects of departures from the HWP on the variance components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-02 00:46:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/460050"], "description"=>"<div><p>Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F<sub>2</sub> or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map.</p></div>", "links"=>[], "tags"=>["estimates", "effects"], "article_id"=>150642, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/How_To_Perform_Meaningful_Estimates_of_Genetic_Effects/150642", "title"=>"How To Perform Meaningful Estimates of Genetic Effects", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-02 00:10:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/932374"], "description"=>"<p>Genotype-phenotype map of the two-locus system used in the simulated populations to evaluate the effect of departures from HWP on genetic effects estimated using the F<sub>2</sub>, G2A and NOIA models.</p>", "links"=>[], "tags"=>["two-locus", "simulated", "populations", "departures", "hwp", "g2a", "noia"], "article_id"=>602819, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062.t001", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotype_phenotype_map_of_the_two_locus_system_used_in_the_simulated_populations_to_evaluate_the_effect_of_departures_from_HWP_on_genetic_effects_estimated_using_the_F_2_G2A_and_NOIA_models_/602819", "title"=>"Genotype-phenotype map of the two-locus system used in the simulated populations to evaluate the effect of departures from HWP on genetic effects estimated using the F<sub>2</sub>, G2A and NOIA models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-02 00:46:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/932198"], "description"=>"<p>The genetic effects were obtained using the F<sub>2</sub>, G2A and NOIA models in a two locus genetic system that was simulated in nine F<sub>2</sub> populations with departures from HWP ranging from zero to 97% (see text for details).</p>", "links"=>[], "tags"=>["departures", "hwp"], "article_id"=>602645, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_of_departures_from_the_HWP_on_genetic_effects_/602645", "title"=>"Effects of departures from the HWP on genetic effects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-02 00:44:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/932412"], "description"=>"1<p>QTL on chromosome 2 (486 cM).</p>2<p>QTL on chromosome 3 (117 cM).</p>", "links"=>[], "tags"=>["genotype", "deviations", "epistatic", "qtl", "leghorn", "intercross"], "article_id"=>602856, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062.t003", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_functional_genetic_effects_from_the_reference_of_genotype_A_1_A_1_B_1_B_1_G_1111_177_963_G_1111_8202_8202_265_18_177_8_35_grams_and_their_standard_deviations_for_an_epistatic_QTL_pair_for_growth_rate_in_a_Red_junglefowl_215_White_leghorn_int/602856", "title"=>"Estimates of functional genetic effects from the reference of genotype <i>A</i><sub>1</sub><i>A</i><sub>1</sub><i>B</i><sub>1</sub><i>B</i><sub>1</sub>, <i>G</i><sub>1111</sub>±σ<i><sub>G</sub></i><sub>1111</sub> = 265.18±8.35 grams, and their standard deviations for an epistatic QTL pair for growth rate in a Red junglefowl×White leghorn intercross [21].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-02 00:47:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/932446"], "description"=>"1<p>The variances in this column are the total genetic variances computed as the sum of the components of variance given in the rest of the columns.</p>", "links"=>[], "tags"=>["components", "variance", "epistatic", "qtl", "leghorn", "intercross"], "article_id"=>602890, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["José M. Álvarez-Castro", "Arnaud Le Rouzic", "Örjan Carlborg"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000062.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_statistical_genetic_effects_to_the_left_of_each_cell_and_components_of_the_genetic_variance_to_the_right_for_an_epistatic_QTL_for_growth_rate_pair_in_a_Red_junglefowl_White_leghorn_layer_intercross_21_using_four_different_models_/602890", "title"=>"Estimates of statistical genetic effects (to the left of each cell) and components of the genetic variance (to the right) for an epistatic QTL for growth rate pair in a Red junglefowl×White leghorn layer intercross [21] using four different models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-02 00:48:10"}

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