A5078084607- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Gene expression and cancer classification
- Genetics and Plant Breeding
- Genetic Associations and Epidemiology
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genomics and Chromatin Dynamics
- Wheat and Barley Genetics and Pathology
- Scientific Computing and Data Management
- Gut microbiota and health
- Data Analysis with R
- Prenatal Screening and Diagnostics
- Immune Cell Function and Interaction
- Genomic variations and chromosomal abnormalities
- DNA Repair Mechanisms
- Advanced Proteomics Techniques and Applications
- Microtubule and mitosis dynamics
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- T-cell and B-cell Immunology
- Pancreatic function and diabetes
- Bioinformatics and Genomic Networks
University of Wisconsin–Madison
2016-2025
Johns Hopkins University
2002-2014
Washington State University
2004-2014
Johns Hopkins Medicine
2012-2014
University of Pennsylvania
2012
University of Groningen
2010-2012
Cancer Genetics (United States)
2012
George Washington University
2012
National Cancer Institute
2012
European Bioinformatics Institute
2012
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It implemented as add-on package the freely-available statistical software, R, and includes functions estimating genetic maps, identifying genotyping errors, performing single-QTL two-dimensional, two-QTL genome scans by multiple methods, with possible inclusion of covariates.The freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.
Recent research has emphasized the importance of metabolic cluster, which includes glucose intolerance, dyslipidemia, and high blood pressure, as a strong predictor obesity-related morbidities premature mortality. Fundamental to this association, commonly referred syndrome, is close interaction between abdominal fat patterning, total body adiposity, insulin resistance. As initial step in identifying major genetic loci influencing these phenotypes, we performed genomewide scan by using...
Position-effect variegation (PEV) describes the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin. Using FISH, we have tested whether variegated expression eye-color brown in Drosophila is influenced by its nuclear localization. In embryonic nuclei, heterochromatic insertion at locus always spatially isolated from other However, during larval development this physically associates with regions on same chromosome manner. These observations indicate that...
R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The expands the scope of widely used R/qtl package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, MAGIC plant designed handle modern high-density genotyping data high-dimensional molecular phenotypes, including gene expression proteomics. includes ability perform...
Abstract Motivation: R/qtl is free and powerful software for mapping exploring quantitative trait loci (QTL). provides a fully comprehensive range of methods wide experimental cross types. We recently added multiple QTL (MQM) to R/qtl. MQM adds higher statistical power detect disentangle the effects linked unlinked compared with many other methods. new features including improved handling missing data, analysis 10 000 s molecular traits, permutation determining significance thresholds hot...
The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that being developed as resource for mammalian systems genetics. Here we describe an experiment uses partially CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis incipient strains reveals high diversity, balanced allele frequencies, dense, evenly distributed recombination sites—all ideal qualities genetics We map discrete, complex, biomolecular traits contrast two...
Genetic dissection of complex, polygenic trait variation is a key goal medical and evolutionary genetics. Attempts to identify genetic variants underlying complex traits have been plagued by low mapping resolution in traditional linkage studies, an inability that cumulatively explain the bulk standing genome-wide association studies (GWAS). Thus, much heritability remains unexplained for most traits. Here we describe novel, freely available resource Drosophila community consisting two sets...
Genetic mapping studies in the mouse and other model organisms are used to search for genes underlying complex phenotypes. Traditional genetic that employ single-generation crosses have poor resolution limit discovery loci polymorphic between two parental strains. Multiparent outbreeding populations address these shortcomings by increasing density of recombination events introducing allelic variants from multiple founder However, multiparent present new analytical challenges require...
Summary We consider the problem of identifying genetic loci (called quantitative trait (QTLs)) contributing to variation in a trait, with data on an experimental cross. A large number different statistical approaches this have been described; most make use multiple tests hypotheses, and many models allowing only single QTL. feel that is best viewed as one model selection. discuss selection ideas identify QTLs crosses. focus back-cross experiment, strictly additive QTLs, concentrate...
We describe a postgenomic in silico approach for identifying genes that are likely to be essential and estimate their proportion haploid genomes. With the knowledge of all sites eligible mutagenesis an experimentally determined partial list nonessential from genome mutagenesis, Bayesian statistical method provides reasonable predictions with subsaturation level random mutagenesis. For transposon such as Himar1 is suitable it inserts randomly into TA sites. All possible insertion may priori...
SummaryUsing genotypes from nearly 8,000 short tandem-repeat polymorphisms typed in eight of the reference families Centre d'Étude du Polymorphisme Humain (CEPH), we identified numerous long chromosomal segments marker homozygosity many CEPH individuals. These are likely to represent autozygosity, result mating related Confidence that complete segment is homozygous gained only with markers high density. The longest spanned 77 cM and included 118 markers. All individuals family 884 showed at...
The genetic architecture of complex traits underlying physiology and disease in most organisms remains elusive. We still know little about the number genes that underlie these traits, magnitude their effects, or extent to which they interact. Chromosome substitution strains (CSSs) enable statistically powerful studies based on testing engineered inbred have single, unique, nonoverlapping differences, thereby providing measures phenotypic effects are attributable individual chromosomes. Here,...
Genetic maps provide a means to estimate the probability of co-inheritance linked loci as they are transmitted across generations in both experimental and natural populations. However, age whole-genome sequences, physical distances measured base pairs DNA standard coordinates for navigating myriad features genomes. Although genetic colinear, there well-characterized sometimes dramatic heterogeneities average frequency meiotic recombination events that occur along extent chromosomes. There...
Abstract Purebred strains, pronounced phenotypic variation, and a high incidence of heritable disease make the domestic dog uniquely suited to complement genetic analyses in humans mice. A comprehensive linkage map would afford many opportunities dogs, ranging from positional cloning genes dissection quantitative differences size, shape, behavior. Here we report canine with number mapped loci expanded 276 10-cM coverage extended 75–90% genome. Most 38 autosomes are likely represented...
Abstract The identification of quantitative trait loci (QTL) and their interactions is a crucial step toward the discovery genes responsible for variation in experimental crosses. problem best viewed as one model selection, most important aspect comparison models different sizes. We present penalized likelihood approach, with penalties on QTL pairwise chosen to control false positive rates. This extends work Broman Speed allow among QTL. A conservative version our LOD score provides strict...
To characterize the genetic basis and phenotype of inherited Fuchs corneal dystrophy (FCD).DNA from blood was used for genome-wide linkage scans with tandem repeat polymorphisms. Mutation detection involved sequencing PCR-amplified exons. Families FCD were clinically evaluated graded on Krachmer severity scale. Confocal specular microscopy visualized morphology endothelial guttae, small protrusions Descemet's membrane that are characteristic FCD.Linkage obtained to 1p34.3-p32 autosomal...
Human immunodeficiency virus (HIV) production continues in patients receiving highly active antiretroviral therapy (HAART) with undetectable (<50 copies/mL) loads. Our initial cross-sectional study showed that this viremia is composed of viruses lack new resistance mutations to the HAART regimen. Here we describe a longitudinal, clonal genotypic analysis plasma loads treated adults who had We document continuous 8 HIV-1-infected maintained suppression for up 15 months. Using analytical...
A surprising diversity of mechanisms controls sex determination vertebrate organisms, even among closely related species. Both genetic and temperature-dependent systems have been described in teleost fish. In the common zebrafish model organism, heteromorphic chromosomes are not observed, potential role a component remains largely unknown. Here we report genome-wide linkage study using novel SNP map. We identified loci on 5 (LOD score 7.9) 16 9.3) governing as complex trait, rather than an...