Research Topics
| K W BromanSummaryAffiliation: Johns Hopkins Bloomberg School of Public Health Country: USA Publications
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Detail Information
Publications
Mapping quantitative trait loci in the case of a spike in the phenotype distributionKarl 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...- R/qtl: QTL mapping in experimental crossesKarl W Broman
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
Bioinformatics 19:889-90. 2003..AVAILABILITY: The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl... - Crossover interference in the mouseKarl 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... - Review of statistical methods for QTL mapping in experimental crossesK 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... - Estimation of allele frequencies with data on sibshipsK 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... - The genomes of recombinant inbred linesKarl W Broman
Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205 2179, USA
Genetics 169:1133-46. 2005.... - Characterization of human crossover interferenceK 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... - Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humainK 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... - Comprehensive human genetic maps: individual and sex-specific variation in recombinationK 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... - Method for constructing confidently ordered linkage mapsK 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... - Significance thresholds for quantitative trait locus mapping under selective genotypingAni 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... - Poor performance of bootstrap confidence intervals for the location of a quantitative trait locusAni 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... - Quantitative trait linkage analysis by generalized estimating equations: unification of variance components and Haseman-Elston regressionWei-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... - Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3U 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... - An initial linkage map of the West Nile Virus vector Culex tarsalisM 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... - The X chromosome in quantitative trait locus mappingKarl 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... - An extension of the regression of offspring on mid-parent to test for association and estimate locus-specific heritability: the revised ROMP methodM 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... - Comparison of human genetic and sequence-based physical mapsA 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... - Linkage of late-onset Fuchs corneal dystrophy to a novel locus at 13pTel-13q12.13Olof 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..The exceptional early onset of the disease observed in two children is unusual and might be the result of digenic interaction between FCD1 and an independent late-onset FCD mutation... - Power and robustness of linkage tests for quantitative traits in general pedigreesWei 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... - Two autoimmune diabetes loci influencing T cell apoptosis control susceptibility to experimental autoimmune myocarditisMehmet 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... - Inheritance of a novel COL8A2 mutation defines a distinct early-onset subtype of fuchs corneal dystrophyJohn 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)... - Extreme hyperopia is the result of null mutations in MFRP, which encodes a Frizzled-related proteinOlof 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... - SNP-specific array-based allele-specific expression analysisHans 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... - Interactions in hypoxic and hypercapnic breathing are genetically linked to mouse chromosomes 1 and 5Clarke 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... - Endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning (edict) syndrome maps to chromosome 15q22.1-q25.3Albert 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..Identification of the disease-causing gene in this region may yield insights into a broad range of disorders affecting the corneal stroma, endothelium, iris, and lens... - The recombinational anatomy of a mouse chromosomeKenneth 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... - Identification of susceptibility loci for skin disease in a murine psoriasis modelDaniel 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... - A common locus for late-onset Fuchs corneal dystrophy maps to 18q21.2-q21.32Olof 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..The incomplete penetrance and high phenocopy rate observed at FCD2 suggest that the origin of FCD in these three families is complex and also depends on other genetic loci or environmental factors... - Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysisJeremy 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... - Haplotype probabilities for multiple-strain recombinant inbred linesFriedrich 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)... - R/qtlDesign: inbred line cross experimental designSaunak 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 ... - A simple method for combining genetic mapping data from multiple crosses and experimental designsJeremy 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... - Crossover interference underlies sex differences in recombination ratesPetko 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... - The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolutionMatthew 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... - Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equationsBjarke Feenstra
Department of Natural Sciences, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
Genetics 173:2269-82. 2006.... - The Collaborative Cross, a community resource for the genetic analysis of complex traitsGary 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... - Discrete gene loci regulate neurodegeneration, lymphocyte infiltration, and major histocompatibility complex class II expression in the CNSOlle Lidman
Department of Clinical Neuroscience, Karolinska Institute, Karolinska Hospital, S 17176, Stockholm, Sweden
J Neurosci 23:9817-23. 2003.... - SNPs made routineKarl W Broman
Nat Methods 1:104-5. 2004 - Genome-wide linkage identifies novel modifier loci of aganglionosis in the Sox10Dom model of Hirschsprung diseaseSarah 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.... - High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila speciesVirginie 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... - Genetic control of X chromosome inactivation in mice: definition of the Xce candidate intervalLisa 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... - New loci regulating rat myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitisKristina 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... - A major locus conferring susceptibility to infection by Streptococcus pneumoniae in micePaul 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... - Simulation-based P values: response to North et alKarl W Broman
Am J Hum Genet 72:496. 2003 - 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... - Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineageMark 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.... - "Bias toward the null" means reduced powerSolveig K Sieberts
Am J Hum Genet 75:720-2; author reply 723-7. 2004 - Spectrum of heart disease associated with murine and human GATA4 mutationSatish 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... - Mapping expression in randomized rodent genomesKarl W Broman
Nat Genet 37:209-10. 2005 - Unknown biological mixtures evaluation using STR analytical quantificationSadeep 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... - Multiperson use of syringes among injection drug users in a needle exchange program: a gene-based molecular epidemiologic analysisSadeep 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... - Multiple polymorphic loci determine basal hepatic and splenic iron status in miceGemma 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... - Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykissKrista 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...