K W Broman

Summary

Affiliation: Johns Hopkins Bloomberg School of Public Health
Country: USA

Publications

  1. pmc Mapping quantitative trait loci in the case of a spike in the phenotype distribution
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 163:1169-75. 2003
  2. ncbi request reprint R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
  3. pmc Crossover interference in the mouse
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 160:1123-31. 2002
  4. ncbi request reprint Review of statistical methods for QTL mapping in experimental crosses
    K W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Lab Anim (NY) 30:44-52. 2001
  5. ncbi request reprint Estimation of allele frequencies with data on sibships
    K W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genet Epidemiol 20:307-15. 2001
  6. pmc The genomes of recombinant inbred lines
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205 2179, USA
    Genetics 169:1133-46. 2005
  7. pmc Characterization of human crossover interference
    K W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Am J Hum Genet 66:1911-26. 2000
  8. pmc Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain
    K W Broman
    Marshfield Medical Research Foundation, Marshfield, WI, USA
    Am J Hum Genet 65:1493-500. 1999
  9. pmc Comprehensive human genetic maps: individual and sex-specific variation in recombination
    K W Broman
    Marshfield Medical Research Foundation, Marshfield, WI 54449, USA
    Am J Hum Genet 63:861-9. 1998
  10. ncbi request reprint Method for constructing confidently ordered linkage maps
    K W Broman
    Center for Medical Genetics, Marshfield Medical Research Foundation, WI 54449, USA
    Genet Epidemiol 16:337-43. 1999

Detail Information

Publications54

  1. pmc Mapping quantitative trait loci in the case of a spike in the phenotype distribution
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 163:1169-75. 2003
    ..The procedures are further illustrated with data from an intercross experiment to identify QTL contributing to variation in survival of mice following infection with Listeria monocytogenes...
  2. ncbi request reprint R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ....
  3. pmc Crossover interference in the mouse
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 160:1123-31. 2002
    ..We further compared the observed numbers of crossovers to previous cytological observations on the numbers of chiasmata and evaluated evidence for the obligate chiasma hypothesis...
  4. ncbi request reprint Review of statistical methods for QTL mapping in experimental crosses
    K W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Lab Anim (NY) 30:44-52. 2001
    ..The author reviews the basic statistical methods for mapping QTLs in experimental crosses and comments on a number of the statistical issues to consider in the application of these methods...
  5. ncbi request reprint Estimation of allele frequencies with data on sibships
    K W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genet Epidemiol 20:307-15. 2001
    ..We used computer simulation to study the performance of methods 3 and 4, and showed that method 3 provides some improvement over method 2, while method 4 improves little on method 3...
  6. pmc The genomes of recombinant inbred lines
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205 2179, USA
    Genetics 169:1133-46. 2005
    ....
  7. pmc Characterization of human crossover interference
    K W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Am J Hum Genet 66:1911-26. 2000
    ..Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms...
  8. pmc Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain
    K W Broman
    Marshfield Medical Research Foundation, Marshfield, WI, USA
    Am J Hum Genet 65:1493-500. 1999
    ..Our results indicate that long homozygous segments are common in humans and that these segments could have a substantial impact on gene mapping and health...
  9. pmc Comprehensive human genetic maps: individual and sex-specific variation in recombination
    K W Broman
    Marshfield Medical Research Foundation, Marshfield, WI 54449, USA
    Am J Hum Genet 63:861-9. 1998
    ..The new linkage maps plus much additional information, including a query system for use in the construction of reliably ordered maps for selected subsets of markers, are available from the Marshfield Website...
  10. ncbi request reprint Method for constructing confidently ordered linkage maps
    K W Broman
    Center for Medical Genetics, Marshfield Medical Research Foundation, WI 54449, USA
    Genet Epidemiol 16:337-43. 1999
    ..We illustrate the approach using a short region of chromosome 7p...
  11. pmc Significance thresholds for quantitative trait locus mapping under selective genotyping
    Ani Manichaikul
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 177:1963-6. 2007
    ..A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals...
  12. pmc Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus
    Ani Manichaikul
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205 2179, USA
    Genetics 174:481-9. 2006
    ..Likelihood support intervals and approximate Bayes credible intervals, on the other hand, are shown to behave appropriately...
  13. ncbi request reprint Quantitative trait linkage analysis by generalized estimating equations: unification of variance components and Haseman-Elston regression
    Wei Min Chen
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genet Epidemiol 26:265-72. 2004
    ..Third, our general framework suggests important extensions to the Haseman-Elston approach which make more complete use of the data in extended pedigrees and allow a natural incorporation of environmental and other covariates...
  14. pmc Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3
    U Lichter-Konecki
    Center for Medical Genetics, Marshfield Medical Research Foundation, Marshfield, WI, USA
    Am J Hum Genet 68:264-8. 2001
    ..The identification of the gene and gene product altered in autosomal dominant renal Fanconi syndrome will allow the study of the physiology of proximal renal tubular transport...
  15. pmc An initial linkage map of the West Nile Virus vector Culex tarsalis
    M Venkatesan
    The W Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Insect Mol Biol 18:453-63. 2009
    ..This map will aid in identification of loci involved with variable phenotypes in C. tarsalis including WNV susceptibility...
  16. pmc The X chromosome in quantitative trait locus mapping
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Genetics 174:2151-8. 2006
    ..We found suggestive evidence of linkage to the X chromosome, which would be viewed as strong evidence of linkage if the X chromosome was treated as an autosome. Our methods have been implemented in the package R/qtl...
  17. ncbi request reprint An extension of the regression of offspring on mid-parent to test for association and estimate locus-specific heritability: the revised ROMP method
    M H Roy-Gagnon
    Genometrics Section, Inherited Disease Research Branch, National Human Genome Research Institute, NIH, Baltimore, MD 21224, USA
    Ann Hum Genet 72:115-25. 2008
    ..The ROMP(rev) method provides a computationally fast and simple way of testing for association and obtaining accurate estimates of locus-specific heritability while minimizing the genotyping required...
  18. ncbi request reprint Comparison of human genetic and sequence-based physical maps
    A Yu
    Center for Medical Genetics, Marshfield Medical Research Foundation, Wisconsin 54449, USA
    Nature 409:951-3. 2001
    ..Linkage disequilibrium was much more common and extended for greater distances in the deserts than in the jungles...
  19. ncbi request reprint Linkage of late-onset Fuchs corneal dystrophy to a novel locus at 13pTel-13q12.13
    Olof H Sundin
    Center for Corneal Genetics, Cornea and External Disease Service, The Johns Hopkins University, Baltimore, Maryland, USA
    Invest Ophthalmol Vis Sci 47:140-5. 2006
    ..To identify the gene locus underlying the inheritance of late-onset Fuchs corneal dystrophy (FCD) in a large white kindred...
  20. ncbi request reprint Power and robustness of linkage tests for quantitative traits in general pedigrees
    Wei Min Chen
    Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
    Genet Epidemiol 28:11-23. 2005
    ..While we have not yet examined the performance of our procedures in the context of selective sampling via computer simulations, the proposed tests satisfy all of the other qualities of an ideal quantitative trait linkage analysis method...
  21. ncbi request reprint Two autoimmune diabetes loci influencing T cell apoptosis control susceptibility to experimental autoimmune myocarditis
    Mehmet L Guler
    Department of Pathology, The Johns Hopkins University, Baltimore, MD 21205, USA
    J Immunol 174:2167-73. 2005
    ..SW mice demonstrate the same characteristics in apoptosis. These results suggest that common pathogenetic mechanisms involving apoptosis of both thymic and peripheral T cells are shared by multiple autoimmune diseases...
  22. ncbi request reprint Inheritance of a novel COL8A2 mutation defines a distinct early-onset subtype of fuchs corneal dystrophy
    John D Gottsch
    Center for Corneal Genetics, Cornea and External Disease Service, The Wilmer Eye Institute, John Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Invest Ophthalmol Vis Sci 46:1934-9. 2005
    ..To characterize the genetic basis and phenotype of inherited Fuchs corneal dystrophy (FCD)...
  23. pmc Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related protein
    Olof H Sundin
    Laboratory of Developmental Genetics, The Johns Hopkins University, Baltimore, MD 21287, USA
    Proc Natl Acad Sci U S A 102:9553-8. 2005
    ..MFRP appears primarily devoted to regulating axial length of the eye. It remains to be determined whether natural variation in its activity plays a role in common refractive errors...
  24. pmc SNP-specific array-based allele-specific expression analysis
    Hans T Bjornsson
    Department of Medicine and Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 18:771-9. 2008
    ..The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples...
  25. ncbi request reprint Interactions in hypoxic and hypercapnic breathing are genetically linked to mouse chromosomes 1 and 5
    Clarke G Tankersley
    Department of Environmental Health Sciences, The Johns Hopkins University, Baltimore, MD 21205, USA
    J Appl Physiol 97:77-84. 2004
    ..7) in a region between 7 and 29 cM (i.e., centered at D5Mit66). In conclusion, these results support the hypothesis that a minimum of two significant genes modulate the interactive effects of hypoxia and hypercapnia in this genetic model...
  26. ncbi request reprint Endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning (edict) syndrome maps to chromosome 15q22.1-q25.3
    Albert S Jun
    Center for Corneal Genetics, Cornea and External Disease Service, The Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
    Am J Ophthalmol 134:172-6. 2002
    ..To localize a gene causing a newly described autosomal dominant anterior segment dysgenesis characterized by corneal endothelial dystrophy, iris hypoplasia, congenital cataracts, and corneal stromal thinning (EDICT syndrome)...
  27. pmc The recombinational anatomy of a mouse chromosome
    Kenneth Paigen
    Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
    PLoS Genet 4:e1000119. 2008
    ..It appears that the regulation of mammalian recombination is a complex, dynamic process involving multiple factors reflecting species, sex, individual variation within species, and the properties of individual hotspots...
  28. ncbi request reprint Identification of susceptibility loci for skin disease in a murine psoriasis model
    Daniel Kess
    Department of Dermatology and Allergic Diseases, University of Ulm, Maienweg 12, D 89081 Ulm, Germany
    J Immunol 177:4612-9. 2006
    ..The identification of gene regions associated with psoriasis in this mouse model might contribute to the understanding of genetic causes of psoriasis in patients and pathological mechanisms involved in development of disease...
  29. ncbi request reprint A common locus for late-onset Fuchs corneal dystrophy maps to 18q21.2-q21.32
    Olof H Sundin
    Center for Corneal Genetics, Cornea and External Disease Service, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, MD 21287, USA
    Invest Ophthalmol Vis Sci 47:3919-26. 2006
    ..To identify the genetic basis of late-onset Fuchs corneal dystrophy (FCD)...
  30. pmc Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis
    Jeremy L Peirce
    Center for Neuroscience, Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
    PLoS ONE 3:e1977. 2008
    ..The critical problem with naïve mapping approaches in AIL populations is that the individual is not an exchangeable unit...
  31. pmc Haplotype probabilities for multiple-strain recombinant inbred lines
    Friedrich Teuscher
    Research Unit Genetics and Biometry, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
    Genetics 175:1267-74. 2007
    ..We also extend the two-point results for the case of additional generations of intermating, including the case of 2(n)-way intermated recombinant inbred populations (IRIP)...
  32. pmc R/qtlDesign: inbred line cross experimental design
    Saunak Sen
    Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
    Mamm Genome 18:87-93. 2007
    ..We give examples of software usage in real-life settings. The software is available at http://www.biostat.ucsf.edu/sen/software.html ...
  33. pmc A simple method for combining genetic mapping data from multiple crosses and experimental designs
    Jeremy L Peirce
    Center for Neuroscience, Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
    PLoS ONE 2:e1036. 2007
    ..Many phenotypes are now associated with enough mapping data that meta-analysis could help refine locations of known QTLs and detect many novel QTLs...
  34. ncbi request reprint Crossover interference underlies sex differences in recombination rates
    Petko M Petkov
    Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Trends Genet 23:539-42. 2007
    ..However, the interference distance is the same in terms of bivalent length. We propose a model in which the interference distance in the two sexes reflects the compaction of chromosomes at the pachytene stage of meiosis...
  35. pmc The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
    Matthew M Hill
    Department of Pathology, SUMC, Stanford, CA 94305 5324, USA
    Genome Res 18:1369-79. 2008
    ..These results, when considered in light of the neutral theory, suggest fundamentally different modes of evolution of animal species with large versus small population sizes...
  36. pmc Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations
    Bjarke Feenstra
    Department of Natural Sciences, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
    Genetics 173:2269-82. 2006
    ....
  37. ncbi request reprint The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
    Nat Genet 36:1133-7. 2004
    ..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...
  38. ncbi request reprint Discrete gene loci regulate neurodegeneration, lymphocyte infiltration, and major histocompatibility complex class II expression in the CNS
    Olle Lidman
    Department of Clinical Neuroscience, Karolinska Institute, Karolinska Hospital, S 17176, Stockholm, Sweden
    J Neurosci 23:9817-23. 2003
    ....
  39. ncbi request reprint SNPs made routine
    Karl W Broman
    Nat Methods 1:104-5. 2004
  40. ncbi request reprint Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung disease
    Sarah E Owens
    Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, 529 Light Hall, 2215 Garland Avenue, Nashville, TN 37232 0275, USA
    Hum Mol Genet 14:1549-58. 2005
    ....
  41. pmc High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila species
    Virginie Orgogozo
    Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08544, USA
    Genetics 173:197-205. 2006
    ..the absence of the QTL3b D. sechellia allele. This property of QTL3a allows us to reconstruct the probable order of fixation of the QTL alleles during evolution...
  42. pmc Genetic control of X chromosome inactivation in mice: definition of the Xce candidate interval
    Lisa Helbling Chadwick
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Genetics 173:2103-10. 2006
    ..This study provides a foundation for future analyses into the genetic control of X chromosome inactivation and defines a 1.85-Mb interval encompassing all the major elements of the Xce locus...
  43. ncbi request reprint New loci regulating rat myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis
    Kristina Becanovic
    Neuroimmunology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
    J Immunol 170:1062-9. 2003
    ..Furthermore, we detected a locus-specific parent-of-origin effect with suggestive linkage in Eae17. Further genetic and functional dissection of these loci may disclose critical disease-regulating molecular mechanisms...
  44. ncbi request reprint A major locus conferring susceptibility to infection by Streptococcus pneumoniae in mice
    Paul Denny
    MRC UK Mouse Genome Centre and Mammalian Genetics Unit, Harwell, Oxon, OX11 0RD, UK
    Mamm Genome 14:448-53. 2003
    ..Linkage analysis of the F(2) generation from a cross between resistant BALB/cO1aHsd and susceptible CBA/CaO1aHsd strains allowed us to map a major locus controlling the development of bacteremia and survival after intranasal infection...
  45. pmc Simulation-based P values: response to North et al
    Karl W Broman
    Am J Hum Genet 72:496. 2003
  46. ncbi request reprint Quasi-linkage: a confounding factor in linkage analysis of complex diseases?
    Sinthuja Sivagnanasundaram
    The Krembil Family Epigenetics Research Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, M5T 1R8 Canada
    Hum Genet 114:588-93. 2004
    ..51. In conclusion, although complex disease relevant markers did not produce high QL lod scores, the general phenomenon of QL in humans cannot be excluded and potentially can be a confounding factor in genetic studies of complex traits...
  47. pmc Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage
    Mark W Neff
    Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 101:11725-30. 2004
    ....
  48. pmc "Bias toward the null" means reduced power
    Solveig K Sieberts
    Am J Hum Genet 75:720-2; author reply 723-7. 2004
  49. pmc Spectrum of heart disease associated with murine and human GATA4 mutation
    Satish K Rajagopal
    Department of Cardiology, Children s Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
    J Mol Cell Cardiol 43:677-85. 2007
    ..Additional studies will be required to determine the degree to which GATA4 mutation contributes to human CHD characterized by ECD or RV hypoplasia...
  50. ncbi request reprint Mapping expression in randomized rodent genomes
    Karl W Broman
    Nat Genet 37:209-10. 2005
  51. ncbi request reprint Unknown biological mixtures evaluation using STR analytical quantification
    Sadeep Shrestha
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Electrophoresis 27:409-15. 2006
    ..4 and 97.4%, respectively. The newly validated approach of using multiple STRs as highly informative biomarkers in unknown sample mixture analyses has potential applications in genetics, forensic science, and epidemiological studies...
  52. ncbi request reprint Multiperson use of syringes among injection drug users in a needle exchange program: a gene-based molecular epidemiologic analysis
    Sadeep Shrestha
    Laboratory of Genomic Diversity, National Cancer Institute, NCI Frederick, MD 21702, USA
    J Acquir Immune Defic Syndr 43:335-43. 2006
    ..Testing of STRs represents a promising approach to examining and accessing complex behavioral data, including syringe sharing...
  53. ncbi request reprint Multiple polymorphic loci determine basal hepatic and splenic iron status in mice
    Gemma R Grant
    MRC Toxicology Unit, University of Leicester, Leicester, UK
    Hepatology 44:174-85. 2006
    ..In conclusion, the findings show the location of polymorphic genes that determine basal iron status in wild-type mice. Human equivalents may be pertinent in predisposition to hepatic and other disorders...
  54. pmc Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss
    Krista M Nichols
    School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164 4236, USA
    Genetics 175:335-47. 2007
    ..Both MCE and QTL x MCE effects contribute to variability in development rate, but QTL x MCE were minor and detected only at small-effect QTL...