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  • 1
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    Application of high-dimensional feature selection: evaluation for genomic prediction in man (2015)
    Springer Nature
    Details
    Publication Date: 2015-05-20
    Description: In this study, we investigated the effect of five feature selection approaches on the performance of a mixed model (G-BLUP) and a Bayesian (Bayes C) prediction method. We predicted height, high density lipoprotein cholesterol (HDL) and body mass index (BMI) within 2,186 Croatian and into 810 UK individuals using genome-wide SNP data. Using all SNP information Bayes C and G-BLUP had similar predictive performance across all traits within the Croatian data, and for the highly polygenic traits height and BMI when predicting into the UK data. Bayes C outperformed G-BLUP in the prediction of HDL, which is influenced by loci of moderate size, in the UK data. Supervised feature selection of a SNP subset in the G-BLUP framework provided a flexible, generalisable and computationally efficient alternative to Bayes C; but careful evaluation of predictive performance is required when supervised feature selection has been used. Scientific Reports 5 doi: 10.1038/srep10312
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 2
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    Genetic mapping of quantitative trait loci for growth and fatness in pigs (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-25
    Description: The European wild boar was crossed with the domesticated Large White pig to genetically dissect phenotypic differences between these populations for growth and fat deposition. The most important effects were clustered on chromosome 4, with a single region accounting for a large part of the breed difference in growth rate, fatness, and length of the small intestine. The study is an advance in genome analyses and documents the usefulness of crosses between divergent outbred populations for the detection and characterization of quantitative trait loci. The genetic mapping of a major locus for fat deposition in the pig could have implications for understanding human obesity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersson, L -- Haley, C S -- Ellegren, H -- Knott, S A -- Johansson, M -- Andersson, K -- Andersson-Eklund, L -- Edfors-Lilja, I -- Fredholm, M -- Hansson, I -- New York, N.Y. -- Science. 1994 Mar 25;263(5154):1771-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8134840" target="_blank"〉PubMed〈/a〉
    Keywords: Adipose Tissue/*anatomy & histology ; Animals ; *Chromosome Mapping ; Crosses, Genetic ; Disease Models, Animal ; Female ; *Genes ; Genetic Markers ; Humans ; Intestine, Small/anatomy & histology ; Likelihood Functions ; Male ; Obesity/genetics ; Phenotype ; Swine/anatomy & histology/*genetics/growth & development
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
    Electronic Resource
    Electronic Resource
    Are monozygotic twins similar due to genetic factors alone? (1982)
    [s.l.] : Nature Publishing Group
    Nature 295 (1982), S. 172-172 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] THE number of errors and inconsistencies in the paper by Gartner et al.1 raises doubts about the validity of their conclusions. In Table 1, the mean and standard deviation of 51-day-old monozygotic (MZ) males are incorrect and differ from the mean and standard deviation for the same data given in ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/295172b0
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  • 4
    Electronic Resource
    Electronic Resource
    Detection of putative quantitative trait loci in line crosses under infinitesimal genetic models (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 691-702 
    Details
    ISSN: 1432-2242
    Keywords: Quantitative trait locus ; Genetic mapping ; Significance threshold ; F2 population ; Infinitesimal model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Quantitative trait locus (QTL) mapping studies often employ segregating generations derived from a cross between genetically divergent inbred lines. In the analysis of such data it is customary to fit a single QTL and use a null hypothesis which assumes that the genomic region under study contributes no genetic variance. To explore the situation in which multiple linked genes contribute to the genetic variance, we simulated an F2-mapping experiment in which the genetic difference between the two original inbred strains was caused by a large number of loci, each having equal effect on the quantitative trait. QTLs were either in coupling, dispersion or repulsion phase in the base population of inbred lines, with the expected F2 genetic variance explained by the QTLs being equivalent in the three models. Where QTLs were in coupling phase, one inbred line was fixed for all plus alleles, and the other line was fixed for minus alleles. Where QTLs were in dispersion phase, they were assumed to be randomly fixed for one or other allele (as if the inbred lines had evolved from a common ancestor by random drift). Where QTLs were in repulsion phase alleles within an inbred line were alternating plus and minus at adjacent loci, and alternative alleles were fixed in the two inbred lines. In all these genetic models a standard interval mapping test statistic used to determine whether there is a QTL of large effect segregating in the population was inflated on average. Furthermore, the use of a threshold for QTL detection derived under the assumption that no QTLs were segregating would often lead to spurious conclusions regards the presence of genes of large effects (i.e. type I errors). The employment of an alternative model for the analysis, including linked markers as cofactors in the analysis of a single interval, reduced the problem of type I error rate, although test statistics were still inflated relative to the case of no QTLs. It is argued that in practice one should take into account the difference between the strains or the genetic variance in the F2 population when setting significance thresholds. In addition, tests designed to probe the adequacy of a single-QTL model or of an alternative infinitesimal coupling model are described. Such tests should be applied in QTL mapping studies to help dissect the true nature of genetic variation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224064
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  • 5
    Electronic Resource
    Electronic Resource
    Multiple marker mapping of quantitative trait loci in an outbred pedigree of loblolly pine (1997)
    Springer
    Theoretical and applied genetics 94 (1997), S. 810-820 
    Details
    ISSN: 1432-2242
    Keywords: Key words Quantitative trait loci ; Outcrossing ; Pinus taeda L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A multiple marker least squares approach is presented for the analysis of a single three-generation pedigree for quantitative trait locus (QTL) characterisation. It is an extension of the approach by Haley et al. (1994) to the situation where grandparents cannot be assumed to be homozygous at QTLs for the trait of interest. The method is applied to the analysis of wood specific gravity in loblolly pine (Pinus taeda L.). Within a similar framework, a series of preliminary analyses are carried out, followed by a more detailed search of the genome for one or more QTLs. The preliminary analyses provide information about whether the contribution from each linkage group appears to be polygenic, localised to a small region (e.g. a single QTL) or oligogenic (i.e. several QTLs). Significance levels are obtained using a permutation test that uses the observed phenotypes and marker genotypes. The conclusion of these analyses is that in this pedigree single QTLs with very large effect on wood specific gravity do not appear to be segregating, although there is evidence for QTLs with small effect. Finally, in order to assess the potential power of this pedigree, we simulated QTLs within the framework of the actual marker data. As expected, QTL effects would need to be large to be reliably detected in this study, and the power to detect QTLs varies at different positions in the genome depending on the level of information in the local markers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050482
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  • 6
    Electronic Resource
    Electronic Resource
    Methods for multiple-marker mapping of quantitative trait loci in half-sib populations (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 71-80 
    Details
    ISSN: 1432-2242
    Keywords: Key words QTL mapping  ;  Genetic mapping  ;   Animal breeding  ;  Half-sibs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we consider the detection of individual loci controlling quantitative traits of interest (quantitative trait loci or QTLs) in the large half-sib family structure found in some species. Two simple approaches using multiple markers are proposed, one using least squares and the other maximum likelihood. These methods are intended to provide a relatively fast screening of the entire genome to pinpoint regions of interest for further investigation. They are compared with a more traditional single-marker least-squares approach. The use of multiple markers is shown to increase power and has the advantage of providing an estimate for the location of the QTL. The maximum-likelihood and the least-squares approaches using multiple markers give similar power and estimates for the QTL location, although the likelihood approach also provides estimates of the QTL effect and sire heterozygote frequency. A number of assumptions have been made in order to make the likelihood calculations feasible, however, and computationally it is still more demanding than the least-squares approach. The least-squares approach using multiple markers provides a fast method that can easily be extended to include additional effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050249
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  • 7
    Electronic Resource
    Electronic Resource
    Methods for multiple-marker mapping of quantitative trait loci in half-sib populations (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 71-80 
    Details
    ISSN: 1432-2242
    Keywords: QTL mapping ; Genetic mapping ; Animal breeding ; Half-sibs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we consider the detection of individual loci controlling quantitative traits of interest (quantitative trait loci or QTLs) in the large half-sib family structure found in some species. Two simple approaches using multiple markers are proposed, one using least squares and the other maximum likelihood. These methods are intended to provide a relatively fast screening of the entire genome to pinpoint regions of interest for further investigation. They are compared with a more traditional single-marker least-squares approach. The use of multiple markers is shown to increase power and has the advantage of providing an estimate for the location of the QTL. The maximum-likelihood and the least-squares approaches using multiple markers give similar power and estimates for the QTL location, although the likelihood approach also provides estimates of the QTL effect and sire heterozygote frequency. A number of assumptions have been made in order to make the likelihood calculations feasible, however, and computationally it is still more demanding than the least-squares approach. The least-squares approach using multiple markers provides a fast method that can easily be extended to include additional effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225729
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  • 8
    Electronic Resource
    Electronic Resource
    Comparison between some approximate maximum-likelihood methods for quantitative trait locus detection in progeny test designs (1997)
    Springer
    Theoretical and applied genetics 95 (1997), S. 236-245 
    Details
    ISSN: 1432-2242
    Keywords: Key words QTL ; Genetic marker ; Likelihood ratiotest ; Segregation analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The power and efficiency of parameter estimation of four approximate maximum-likelihood segregation-analysis methods for QTL detection were numerically compared using Monte Carlo simulation. The approximations were designed to avoid the long computation required by exact maximum-likelihood segregation analysis for populations composed of large, independent half-sib families, as found in forest-tree and animal-breeding programs. The methods were compared both when information from a marker closely linked to the QTL was available and when it was not. Three of the approximations were from the literature: the Modal-Estimation method initially developed by Le Roy et al., an approximate Regressive Model from Demenais and Bonney, and the Within-Sire method used by Boichard et al. The fourth method was derived from this Within-Sire method by ignoring between-male-parent information and segregation within families due to the alleles inherited from the female parents. The relative advantages of the criteria are compared for various hypotheses concerning the characteristics of the QTL and the size of the population. No one method was clearly superior over all situations studied. The fourth, and simplest, method, however, performed sufficiently well when marker data were available, particularly in terms of power, for it to provide a tool for rapid preliminary screening of data from QTL mapping studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050554
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  • 9
    Electronic Resource
    Electronic Resource
    The PiGMaP consortium linkage map of the pig (Sus scrofa) (1995)
    Springer
    Mammalian genome 6 (1995), S. 157-175 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (∼16.5 Morgans) than the genetic map of the homogametic sex (female) (∼21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be ∼18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00293008
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  • 10
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    Validation of NO2 and NO from the Atmospheric Chemistry Experiment (ACE) (2008)
    In:  EPIC3Atmospheric Chemistry and Physics, 8, pp. 5801-5841
    Details
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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