Orjan Carlborg

Summary

Affiliation: Uppsala University
Country: Sweden

Publications

  1. ncbi Epistasis and the release of genetic variation during long-term selection
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Nat Genet 38:418-20. 2006
  2. ncbi Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice
    Orjan Carlborg
    Roslin Institute, Roslin, Midlothian, EH25 9PS, United Kingdom
    Mamm Genome 16:481-94. 2005
  3. ncbi Epistasis: too often neglected in complex trait studies?
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE 751 24 Uppsala, Sweden
    Nat Rev Genet 5:618-25. 2004
  4. pmc An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden
    Genetics 178:2315-26. 2008
  5. pmc How to perform meaningful estimates of genetic effects
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    PLoS Genet 4:e1000062. 2008
  6. pmc Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight
    Per Wahlberg
    Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden
    BMC Genomics 10:248. 2009
  7. ncbi Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth
    Orjan Carlborg
    Roslin Institute, Roslin, Midlothian, EH25 9PS, UK
    Genet Res 83:197-209. 2004
  8. pmc Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
    Genetics 179:1591-9. 2008
  9. doi How to deal with genotype uncertainty in variance component quantitative trait loci analyses
    Xia Shen
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genet Res (Camb) 93:333-42. 2011
  10. doi Defining the assumptions underlying modeling of epistatic QTL using variance component methods
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, SE 75124 Uppsala, Sweden
    J Hered 99:421-5. 2008

Detail Information

Publications32

  1. ncbi Epistasis and the release of genetic variation during long-term selection
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Nat Genet 38:418-20. 2006
    ..The interactions in this radial network mediate a considerably larger selection response than predicted by a single-locus model...
  2. ncbi Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice
    Orjan Carlborg
    Roslin Institute, Roslin, Midlothian, EH25 9PS, United Kingdom
    Mamm Genome 16:481-94. 2005
    ..Five of these patterns resembled previously published patterns of QTL interactions...
  3. ncbi Epistasis: too often neglected in complex trait studies?
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE 751 24 Uppsala, Sweden
    Nat Rev Genet 5:618-25. 2004
  4. pmc An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden
    Genetics 178:2315-26. 2008
    ..Extensions of FIA and its applications on other intercross populations including backcrosses, advanced intercross lines, and heterogeneous stocks are also discussed...
  5. pmc How to perform meaningful estimates of genetic effects
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    PLoS Genet 4:e1000062. 2008
    ..We also discuss further implementations leading to a completely general genotype-phenotype map...
  6. pmc Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight
    Per Wahlberg
    Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden
    BMC Genomics 10:248. 2009
    ..Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines...
  7. ncbi Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth
    Orjan Carlborg
    Roslin Institute, Roslin, Midlothian, EH25 9PS, UK
    Genet Res 83:197-209. 2004
    ....
  8. pmc Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
    Genetics 179:1591-9. 2008
    ..Our results demonstrate that the effects of many genes are dependent on genetic interactions with other loci and how their involvement in the domestication process relies on these interactions...
  9. doi How to deal with genotype uncertainty in variance component quantitative trait loci analyses
    Xia Shen
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genet Res (Camb) 93:333-42. 2011
    ..Our simulations show that the bias of variance component estimates using traditional expected IBD matrix can be adjusted by accounting for the distribution and that the calculations are computationally feasible for large pedigrees...
  10. doi Defining the assumptions underlying modeling of epistatic QTL using variance component methods
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, SE 75124 Uppsala, Sweden
    J Hered 99:421-5. 2008
    ..e., all marker alleles are unique in the base generation) is located between the loci. We discuss the need of developing a general algorithm to estimate the variance-covariance structure of the random epistatic effect for linked loci...
  11. pmc Phenotypic evolution from genetic polymorphisms in a radial network architecture
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    BMC Biol 5:50. 2007
    ..To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support...
  12. pmc Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    Genetics 176:1935-8. 2007
    ..The relative advantage of using our method increases with pedigree size, marker density, and linkage disequilibrium, indicating even greater improvements in the future...
  13. pmc Genetic architecture of tameness in a rat model of animal domestication
    Frank W Albert
    Department of Genetics and Pathology, Uppsala University, 75123 Uppsala, Sweden
    Genetics 182:541-54. 2009
    ..The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general...
  14. pmc A genetic algorithm based method for stringent haplotyping of family data
    Francois Besnier
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    BMC Genet 10:57. 2009
    ..It is therefore important to only use haplotypes that are strongly supported by the available data for IBD estimation, to avoid introducing new errors due to erroneous linkage phases...
  15. pmc A unified model for functional and statistical epistasis and its application in quantitative trait Loci analysis
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    Genetics 176:1151-67. 2007
    ..Furthermore, we use our theoretical foundations to conceptually clarify functional and statistical epistasis, discuss the advantages of NOIA over previous theory, and stress the importance of linking functional and statistical models...
  16. ncbi Use of randomization testing to detect multiple epistatic QTLs
    Orjan Carlborg
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, BMC, Box 597, S 751 24 Uppsala, Sweden
    Genet Res 79:175-84. 2002
    ..We believe that this method will facilitate the evaluation of the importance at epistatic interaction among QTLs controlling multifactorial traits and disorders...
  17. pmc Strong signatures of selection in the domestic pig genome
    Carl Johan Rubin
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE 751 23 Uppsala, Sweden
    Proc Natl Acad Sci U S A 109:19529-36. 2012
    ....
  18. pmc Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana
    Xia Shen
    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    PLoS Genet 8:e1002839. 2012
    ....
  19. ncbi Efficient algorithms for quantitative trait loci mapping problems
    Kajsa Ljungberg
    Department of Scientific Computing, Information Technology, Uppsala University, Box 337, SE 751 05 Uppsala, Sweden
    J Comput Biol 9:793-804. 2002
    ..For example, using the new algorithms, it is reasonable to perform permutation testing using exhaustive search on populations of 200 individuals using an epistatic two-QTL model...
  20. doi Whole-genome resequencing reveals loci under selection during chicken domestication
    Carl Johan Rubin
    Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE 75123 Uppsala, Sweden
    Nature 464:587-91. 2010
    ..This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research...
  21. pmc Separation of base allele and sampling term effects gives new insights in variance component QTL analysis
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE 75124 Uppsala, Sweden
    BMC Genet 8:1. 2007
    ..In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix)...
  22. pmc A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL
    Francois Besnier
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    BMC Bioinformatics 8:440. 2007
    ..Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values...
  23. ncbi Evolutionary potential of hidden genetic variation
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Biomedical Centre, Box 598, Uppsala University, SE 751 24 Uppsala, Sweden
    Trends Ecol Evol 23:33-7. 2008
    ..We introduce the 'genetic charge' concept, to describe how the architecture of a trait can be 'charged' with potential for evolutionary change that can later be 'discharged' in response to selection...
  24. pmc Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis
    Katarina Tengvall
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Genet 9:e1003475. 2013
    ..Our results may yield further insight into the genetics behind both canine and human AD...
  25. pmc Hierarchical likelihood opens a new way of estimating genetic values using genome-wide dense marker maps
    Xia Shen
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    BMC Proc 5:S14. 2011
    ..We propose the use of hierarchical likelihood to solve such problems...
  26. ncbi Epistatic regulation of behavioural and morphological traits in the zebrafish (Danio rerio)
    Dominic Wright
    Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
    Behav Genet 36:914-22. 2006
    ..These results provide novel insight into the genetic architecture of the regulation of behavioural as well as morphological phenotypes and call for more studies of epistasis for this group of traits...
  27. pmc Statistical epistasis is a generic feature of gene regulatory networks
    Arne B Gjuvsland
    Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N 1432 Aas, Norway
    Genetics 175:411-20. 2007
    ..This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation...
  28. ncbi Major growth QTLs in fowl are related to fearful behavior: possible genetic links between fear responses and production traits in a red junglefowl x white leghorn intercross
    Karin E Schütz
    Department of Animal Environment and Health, Section of Ethology, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Behav Genet 34:121-30. 2004
    ..The results show that loci affecting important production traits are located in the same chromosomal region as loci affecting different fear-related behaviors...
  29. pmc A global search reveals epistatic interaction between QTL for early growth in the chicken
    Orjan Carlborg
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, S 751 24 Uppsala, Sweden
    Genome Res 13:413-21. 2003
    ..Several of the detected loci affected either early or late growth but not both. Very few loci affected the entire growth process, which points out that early and late growth, at least to some extent, have different genetic regulation...
  30. ncbi QTL analysis of a red junglefowl x White Leghorn intercross reveals trade-off in resource allocation between behavior and production traits
    Karin Schutz
    Swedish University of Agricultural Sciences, Department of Animal Environment and Health, Section of Ethology, POB 234, SE 532 23 Skara, Sweden
    Behav Genet 32:423-33. 2002
    ..The results suggest a trade-off between energy-demanding behavior and high production and that some of this may be caused by genetic linkage or pleiotropic gene effects...
  31. ncbi Chicken genomics: feather-pecking and victim pigmentation
    Linda Keeling
    Department of Animal Environment and Health, Swedish University of Agricultural Sciences, PO Box 234, 53223 Skara, Sweden
    Nature 431:645-6. 2004
    ....
  32. ncbi The genetic dissection of immune response using gene-expression studies and genome mapping
    Dirk Jan de Koning
    The Roslin Institute, Roslin Biocentre, Roslin EH25 9PS, UK
    Vet Immunol Immunopathol 105:343-52. 2005
    ..Initial applications of this approach are critically reviewed and potential applications of this approach with regard to immune response are presented...