linkage disequilibrium


Summary: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.

Top Publications

  1. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
  2. pmc Common SNPs explain a large proportion of the heritability for human height
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 42:565-9. 2010
  3. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
  4. ncbi TASSEL: software for association mapping of complex traits in diverse samples
    Peter J Bradbury
    United States Department of Agriculture Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
    Bioinformatics 23:2633-5. 2007
  5. pmc SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
    Andrew D Johnson
    The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
    Bioinformatics 24:2938-9. 2008
  6. ncbi Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families
    E H Corder
    Department of Medicine, Joseph and Kathleen Bryan Alzheimer s Disease Research Center, Duke University Medical Center, Durham, NC 27710
    Science 261:921-3. 1993
  7. ncbi PowerMarker: an integrated analysis environment for genetic marker analysis
    Kejun Liu
    Bioinformatics Research Center, North Carolina State University Raleigh, 27695 7566, USA
    Bioinformatics 21:2128-9. 2005
  8. ncbi Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
    S Purcell
    Social, Genetics and Developmental Psychiatry Research Centre, Institute of Psychiatry, King s College London, De Crespigny Park, UK
    Bioinformatics 19:149-50. 2003
  9. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
  10. pmc Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
    Gosia Trynka
    Genetics Department, University Medical Center and University of Groningen, The Netherlands
    Nat Genet 43:1193-201. 2011

Detail Information

Publications360 found, 100 shown here

  1. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
    ..Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and ..
  2. pmc Common SNPs explain a large proportion of the heritability for human height
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 42:565-9. 2010
    ..We provide evidence that the remaining heritability is due to incomplete linkage disequilibrium between causal variants and genotyped SNPs, exacerbated by causal variants having lower minor allele ..
  3. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
    ..Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers...
  4. ncbi TASSEL: software for association mapping of complex traits in diverse samples
    Peter J Bradbury
    United States Department of Agriculture Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
    Bioinformatics 23:2633-5. 2007
    ..For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically...
  5. pmc SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
    Andrew D Johnson
    The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
    Bioinformatics 24:2938-9. 2008
    The interpretation of genome-wide association results is confounded by linkage disequilibrium between nearby alleles...
  6. ncbi Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families
    E H Corder
    Department of Medicine, Joseph and Kathleen Bryan Alzheimer s Disease Research Center, Duke University Medical Center, Durham, NC 27710
    Science 261:921-3. 1993
    ..Thus APOE-epsilon 4 gene dose is a major risk factor for late onset AD and, in these families, homozygosity for APOE-epsilon 4 was virtually sufficient to cause AD by age 80...
  7. ncbi PowerMarker: an integrated analysis environment for genetic marker analysis
    Kejun Liu
    Bioinformatics Research Center, North Carolina State University Raleigh, 27695 7566, USA
    Bioinformatics 21:2128-9. 2005
    ..It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker...
  8. ncbi Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
    S Purcell
    Social, Genetics and Developmental Psychiatry Research Centre, Institute of Psychiatry, King s College London, De Crespigny Park, UK
    Bioinformatics 19:149-50. 2003
    ..A website for performing power calculations for the design of linkage and association genetic mapping studies of complex traits...
  9. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  10. pmc Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
    Gosia Trynka
    Genetics Department, University Medical Center and University of Groningen, The Netherlands
    Nat Genet 43:1193-201. 2011
    ..HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions...
  11. pmc Reconstructing Indian population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 461:489-94. 2009
    ..We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically...
  12. ncbi SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci
    Yong Yong Shi
    Bio X Life Science Research Center, Shanghai Jiao Tong University, Shanghai, China
    Cell Res 15:97-8. 2005
    ..genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples ..
  13. pmc Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci
    John B Harley
    Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
    Nat Genet 40:204-10. 2008
    ..Our results show that numerous genes, some with known immune-related functions, predispose to SLE...
  14. pmc A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other
    Dale R Nyholt
    Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Am J Hum Genet 74:765-9. 2004, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between ..
  15. pmc Complement factor H polymorphism in age-related macular degeneration
    Robert J Klein
    Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 308:385-9. 2005
    ..4 (95% confidence interval 2.9 to 19). Resequencing revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402...
  16. ncbi Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum
    T J Anderson
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford, England
    Mol Biol Evol 17:1467-82. 2000
    ..These data reveal dramatic differences in parasite population structure in different locations. Strong linkage disequilibrium (LD) was observed in six of nine populations...
  17. pmc Genome-wide association studies for agronomical traits in a world wide spring barley collection
    Raj K Pasam
    Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Corrensstr, 3, 06466 Gatersleben, Germany
    BMC Plant Biol 12:16. 2012
    Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits...
  18. pmc The impact of genetic relationship information on genome-assisted breeding values
    D Habier
    Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011, USA
    Genetics 177:2389-97. 2007
    ..from both simulations and practical applications have to be evaluated for this potential, which requires linkage disequilibrium (LD) between markers and QTL...
  19. pmc Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data
    Bingshan Li
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Am J Hum Genet 83:311-21. 2008
    ..The CMC method can be applied to either candidate-gene or whole-genome sequence data...
  20. ncbi Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum
    John C Wootton
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 6075, USA
    Nature 418:320-3. 2002
    ..genetic diversity varies substantially among different regions of the parasite genome, revealing extensive linkage disequilibrium surrounding the key CQR gene pfcrt and at least four CQR founder events...
  21. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended ..
  22. ncbi Complement factor H variant increases the risk of age-related macular degeneration
    Jonathan L Haines
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Science 308:419-21. 2005
    ..45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults...
  23. pmc A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping
    Tom Druet
    Unit of Animal Genomics, GIGA Research and Department of Animal Production, Faculty of Veterinary Medicine, University of Liege, Belgium
    Genetics 184:789-98. 2010
    ..In human genetics, phasing most often exploits population information (linkage disequilibrium), while in animal genetics the primary source of information is familial (Mendelian segregation and ..
  24. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  25. pmc Global variation in copy number in the human genome
    Richard Redon
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 444:444-54. 2006
    ..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations...
  26. pmc Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars
    Flavio Breseghello
    Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 172:1165-77. 2006
    Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding...
  27. ncbi An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing
    L A Pennacchio
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 294:169-73. 2001
    ..These findings indicate that APOAV is an important determinant of plasma triglyceride levels, a major risk factor for coronary artery disease...
  28. pmc Calibrating a coalescent simulation of human genome sequence variation
    Stephen F Schaffner
    Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02139, USA
    Genome Res 15:1576-83. 2005
    ..More specifically, models are used to compare empirical measures of sequence variation, linkage disequilibrium (LD), and selection to expectations under a "null" distribution...
  29. pmc Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE) study
    Logan Dumitrescu
    Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
    PLoS Genet 7:e1002138. 2011
    ..For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.
  30. pmc Deregressing estimated breeding values and weighting information for genomic regression analyses
    Dorian J Garrick
    Department of Animal Science, Iowa State University, Ames, IA 50011, USA
    Genet Sel Evol 41:55. 2009
    ..The literature indicates that researchers are inconsistent in their approach to using EBV or deregressed data, and as to using the appropriate methods for weighting some data sources to account for heterogeneous variance...
  31. pmc High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L
    Régine Delourme
    INRA, UMR1349 IGEPP, BP35327, 35653, Le Rheu Cedex, France
    BMC Genomics 14:120. 2013
    ..Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern.
  32. ncbi LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis
    B Haubold
    Max Planck Institut für Chemische Okologie, Carl Zeiss Promenade 10, D 07745 Jena, Germany
    Bioinformatics 16:847-8. 2000
    ..LIAN incorporates both a Monte Carlo method as well as a novel algebraic method to carry out the hypothesis test. The program further returns the genetic diversity of the sample and the pairwise distances between its members...
  33. pmc Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis
    Rafael de Cid
    Genes and Disease Programme, Centre for Genomic Regulation CRG and Public Health and Epidemiology Network Biomedical Research Center CIBERESP, 08003 Barcelona, Spain
    Nat Genet 41:211-5. 2009
    ..LCE expression can be induced in normal epidermis by skin barrier disruption and is strongly expressed in psoriatic lesions, suggesting that compromised skin barrier function has a role in psoriasis susceptibility...
  34. ncbi A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians
    Yoichiro Kamatani
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
    Nat Genet 41:591-5. 2009
    ..52 and 0.57, respectively). Our findings show that genetic variants in the HLA-DP locus are strongly associated with risk of persistent infection with hepatitis B virus...
  35. ncbi Structure of linkage disequilibrium in plants
    Sherry A Flint-Garcia
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Annu Rev Plant Biol 54:357-74. 2003
    ..Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome...
  36. ncbi Sequence variants at the TERT-CLPTM1L locus associate with many cancer types
    Thorunn Rafnar
    deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
    Nat Genet 41:221-7. 2009
    ..However, neither variant could fully account for the association of the other. rs2736098 corresponds to A305A in the telomerase reverse transcriptase (TERT) protein and rs401681 is in an intron of the CLPTM1L gene...
  37. ncbi Efficiency and power in genetic association studies
    Paul I W de Bakker
    Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
    Nat Genet 37:1217-23. 2005
    ..Power is robust to the completeness of the reference panel from which tags are selected. These findings have implications for prioritizing tag SNPs and interpreting association studies...
  38. pmc A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma
    Maria Teresa Landi
    Division of Cancer Epidemiology, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
    Am J Hum Genet 85:679-91. 2009
    ..In conclusion, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma...
  39. pmc Structure of linkage disequilibrium and phenotypic associations in the maize genome
    D L Remington
    Department of Genetics, North Carolina State University, Raleigh, NC 27695 7614, USA
    Proc Natl Acad Sci U S A 98:11479-84. 2001
    Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation...
  40. ncbi Complement factor H polymorphism and age-related macular degeneration
    Albert O Edwards
    Department of Ophthalmology and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center UTSWMC, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Science 308:421-4. 2005
    ..Possession of at least one histidine at amino acid position 402 increased the risk of AMD 2.7-fold and may account for 50% of the attributable risk of AMD...
  41. ncbi The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm
    Anna Helgadottir
    deCODE Genetics, Sturlugata 8, IS 101 Reykjavik, Iceland
    Nat Genet 40:217-24. 2008
    ..These findings extend our insight into the role of the sequence variant tagged by rs10757278-G and show that it is not confined to atherosclerotic diseases...
  42. pmc Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    Sergey Nejentsev
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
    Science 324:387-9. 2009
    ..This finding firmly establishes the role of IFIH1 in T1D and demonstrates that resequencing studies can pinpoint disease-causing genes in genomic regions initially identified by GWASs...
  43. pmc Newly identified genetic risk variants for celiac disease related to the immune response
    Karen A Hunt
    Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK
    Nat Genet 40:395-402. 2008
    ..Type 1 diabetes and celiac disease share HLA-DQ, IL2-IL21, CCR3 and SH2B3 risk regions. Thus, this extensive genome-wide association follow-up study has identified additional celiac disease risk variants in relevant biological pathways...
  44. ncbi A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
    Donald F Conrad
    Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
    Nat Genet 38:1251-60. 2006
    ..Although the extent of linkage disequilibrium (LD) varies markedly across populations, considerable sharing of haplotype structure exists, and inferred ..
  45. pmc A data-adaptive sum test for disease association with multiple common or rare variants
    Fang Han
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Hum Hered 70:42-54. 2010
    ..for common variants, which aims to strike a balance between utilizing information on multiple markers in linkage disequilibrium and reducing the cost of large degrees of freedom or of multiple testing adjustment...
  46. ncbi A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms
    Xiaoyi Gao
    Center for Genetic Epidemiology and Statistical Genetics, Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
    Genet Epidemiol 32:361-9. 2008
    ..studies using large numbers of single nucleotide polymorphism (SNP) markers, many of which exhibit linkage disequilibrium (LD)...
  47. ncbi Genome-wide association studies for common diseases and complex traits
    Joel N Hirschhorn
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nat Rev Genet 6:95-108. 2005
    ..Genome-wide association studies will soon become possible, and could open new frontiers in our understanding and treatment of disease. However, the execution and analysis of such studies will require great care...
  48. ncbi The effects of artificial selection on the maize genome
    Stephen I Wright
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Science 308:1310-4. 2005
    ..If we assume that our sample of genes is representative, approximately 1200 genes throughout the maize genome have been affected by artificial selection...
  49. ncbi A functional polymorphism in the 5' UTR of GDF5 is associated with susceptibility to osteoarthritis
    Yoshinari Miyamoto
    Laboratory for Bone and Joint Diseases, SNP Research Center, RIKEN, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nat Genet 39:529-33. 2007
    ..Our findings implicate GDF5 as a susceptibility gene for osteoarthritis and suggest that decreased GDF5 expression is involved in the pathogenesis of osteoarthritis...
  50. pmc Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle
    A P W de Roos
    CRV, 6800 AL Arnhem, The Netherlands
    Genetics 179:1503-12. 2008
    When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed...
  51. pmc Inferring admixture histories of human populations using linkage disequilibrium
    Po Ru Loh
    Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Genetics 193:1233-54. 2013
    ..An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance...
  52. pmc Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    Chris C A Spencer
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000477. 2009
    ..but this fails to properly account for the effects of sample size, the genetic model of the disease, and linkage disequilibrium between SNPs...
  53. pmc Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
    B Mangin
    INRA, UR875 Unité de Biométrie et Intelligence Artificielle, Chemin de Borde Rouge, Castanet Tolosan, France
    Heredity (Edinb) 108:285-91. 2012
    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure...
  54. pmc Estimation of linkage disequilibrium in four US pig breeds
    Yvonne M Badke
    Department of Animal Science, Michigan State University, East Lansing, MI, USA
    BMC Genomics 13:24. 2012
    The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent and degree of LD is essential...
  55. pmc HAPGEN2: simulation of multiple disease SNPs
    Zhan Su
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
    Bioinformatics 27:2304-5. 2011
    ..based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data...
  56. pmc Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 44:369-75, S1-3. 2012
    ..use summary-level statistics from a meta-analysis of genome-wide association studies (GWAS) and estimated linkage disequilibrium (LD) from a reference sample with individual-level genotype data...
  57. pmc Genome-wide and fine-resolution association analysis of malaria in West Africa
    Muminatou Jallow
    MRC Laboratories, Fajara, Banjul, Gambia
    Nat Genet 41:657-65. 2009
    ..also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD)...
  58. pmc Tissue-specific genetic control of splicing: implications for the study of complex traits
    Erin L Heinzen
    Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina, USA
    PLoS Biol 6:e1. 2008
  59. pmc Variation near complement factor I is associated with risk of advanced AMD
    Jesen A Fagerness
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
    Eur J Hum Genet 17:100-4. 2009
    ..Sequencing was performed on coding exons in linkage disequilibrium with the detected association...
  60. pmc Common variants near MC4R are associated with fat mass, weight and risk of obesity
    Ruth J F Loos
    MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
    Nat Genet 40:768-75. 2008
  61. pmc Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer
    Clare Turnbull
    Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, UK
    Nat Genet 42:604-7. 2010
    ..Finally, we identified a locus on chromosome 9 (rs755383, OR=1.37, P=1.12x10(-23)), containing the sex determination gene DMRT1, which has been linked to teratoma susceptibility in mice...
  62. pmc Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers
    Jianbing Yan
    Genetic Resources Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
    PLoS ONE 4:e8451. 2009
    ..b>Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by ..
  63. pmc Variants in nicotinic receptors and risk for nicotine dependence
    Laura Jean Bierut
    Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Ave, St Louis, MO 63110, USA
    Am J Psychiatry 165:1163-71. 2008
  64. pmc Genetic structure of Europeans: a view from the North-East
    Mari Nelis
    Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
    PLoS ONE 4:e5472. 2009
    ..Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS)...
  65. ncbi A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis
    J N Feder
    Mercator Genetics, Inc, Menlo Park, California 94025, USA
    Nat Genet 13:399-408. 1996
    ..A role of this gene in haemochromatosis is supported by the frequency and nature of the major mutation and prior studies implicating MHC class I-like proteins in iron metabolism...
  66. pmc Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)
    Shiaoman Chao
    USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
    BMC Genomics 11:727. 2010
    ..Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from ..
  67. ncbi A genome-wide association study identifies novel risk loci for type 2 diabetes
    Robert Sladek
    Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal H3A 1A4, Canada
    Nature 445:881-5. 2007 the zinc transporter SLC30A8, which is expressed exclusively in insulin-producing beta-cells, and two linkage disequilibrium blocks that contain genes potentially involved in beta-cell development or function (IDE-KIF11-HHEX and ..
  68. ncbi Genetic association mapping and genome organization of maize
    Jianming Yu
    Institute for Genomic Diversity and United States Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, USA
    Curr Opin Biotechnol 17:155-60. 2006
    Association mapping, a high-resolution method for mapping quantitative trait loci based on linkage disequilibrium, holds great promise for the dissection of complex genetic traits...
  69. pmc Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 76:449-62. 2005
    ..exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers...
  70. pmc Common variants on chromosome 6p22.1 are associated with schizophrenia
    Jianxin Shi
    Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94304, USA
    Nature 460:753-7. 2009
    ..8,008 cases, 19,077 controls), significant association with schizophrenia was observed in a region of linkage disequilibrium on chromosome 6p22.1 (P = 9.54 x 10(-9))...
  71. ncbi A comprehensive evaluation of SNP genotype imputation
    Michael Nothnagel
    Institute of Medical Informatics and Statistics, Christian Albrechts University, Kiel, Germany
    Hum Genet 125:163-71. 2009
    ..We nevertheless recommend either MACH or BEAGLE for practical use because these two programs are more user-friendly and generally require less memory than IMPUTE...
  72. ncbi MSX1 and TGFB3 contribute to clefting in South America
    A R Vieira
    Departments of Pediatrics, 2613 JCP, University of Iowa, Iowa City, 52242 1083, USA
    J Dent Res 82:289-92. 2003
    ..These results suggest that MSX1 and TGFB3 mutations make a contribution to clefts in South American populations...
  73. pmc Genetic mapping in human disease
    David Altshuler
    Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Science 322:881-8. 2008
  74. pmc Genome-wide linkage and association analyses to identify genes influencing adiponectin levels: the GEMS Study
    Hua Ling
    Department of Epidemiology and Preventive Medicine, University of Maryland, Baltimore, Maryland, USA
    Obesity (Silver Spring) 17:737-44. 2009
    ..These two SNPs were in high linkage disequilibrium (r(2) = 0.98) and located within ADIPOQ...
  75. ncbi Linkage disequilibrium and association studies in higher plants: present status and future prospects
    Pushpendra K Gupta
    Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch Charan Singh University, Meerut 250 004 UP, India
    Plant Mol Biol 57:461-85. 2005
    ..Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis...
  76. ncbi Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes
    K Kizilkaya
    Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
    J Anim Sci 88:544-51. 2010
    ..Panels that excluded the QTL and relied on markers in linkage disequilibrium (LD) to predict QTL effects performed more poorly than marker panels with QTL...
  77. ncbi Recombination and linkage disequilibrium in Arabidopsis thaliana
    Sung Kim
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 39:1151-5. 2007
    b>Linkage disequilibrium (LD) is a major aspect of the organization of genetic variation in natural populations...
  78. pmc Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits
    Angelo Scuteri
    Unità Operativa Geriatria, Istituto per la Patologia Endocrina e Metabolica, Rome, Italy
    PLoS Genet 3:e115. 2007
    ..These changes could have a significant impact on the risk of obesity-related morbidity in the general population...
  79. pmc Genotype-imputation accuracy across worldwide human populations
    Lucy Huang
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Am J Hum Genet 84:235-50. 2009
    ..By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and tested for ..
  80. pmc The impact of genetic relationship information on genomic breeding values in German Holstein cattle
    David Habier
    Institute of Animal Breeding and Husbandry, Christian Albrechts University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
    Genet Sel Evol 42:5. 2010
    ..However, this impact and the accuracy of GEBVs due to linkage disequilibrium (LD), which is fairly persistent over generations, must be known to implement future breeding programs.
  81. ncbi Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population
    Ryo Takata
    Laboratory for Biomarker Development, Center of Genomic Medicine, RIKEN, Tokyo, Japan
    Nat Genet 42:751-4. 2010
    ..6 x 10(-8)). These findings advance our understanding of the genetic basis of prostate carcinogenesis and also highlight the genetic heterogeneity of prostate cancer susceptibility among different ethnic populations...
  82. ncbi Human genetic variation and its contribution to complex traits
    Kelly A Frazer
    Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Rev Genet 10:241-51. 2009
    ..Technological advances, such as the ability to detect rare and structural variants, and a clear understanding of the challenges in linking different types of variation with phenotype, will be essential for future progress...
  83. pmc Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    Ben J Hayes
    Victorian Institute of Animal Science, Department of Natural Resources and Environment, Attwood, Victoria, 3049, Australia
    Genome Res 13:635-43. 2003
    b>Linkage disequilibrium (LD) between densely spaced, polymorphic genetic markers in humans and other species contains information about historical population size...
  84. ncbi Linkage disequilibrium--understanding the evolutionary past and mapping the medical future
    Montgomery Slatkin
    Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
    Nat Rev Genet 9:477-85. 2008
    b>Linkage disequilibrium--the nonrandom association of alleles at different loci--is a sensitive indicator of the population genetic forces that structure a genome...
  85. pmc Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae
    Bradley J White
    Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
    Mol Ecol 19:925-39. 2010
    ..Genotyping of 517 female M and S mosquitoes revealed nearly complete linkage disequilibrium between the centromeres of the three independently assorting chromosomes...
  86. ncbi Genetic association studies: design, analysis and interpretation
    Cathryn M Lewis
    Division of Medical and Molecular Genetics, Guy s Hospital, London, UK
    Brief Bioinform 3:146-53. 2002
    ..The transmission disequilibrium test is provided as an alternative family-based test, which is robust to population stratification. The relative benefits of each analysis are summarised...
  87. ncbi The pattern of linkage disequilibrium in German Holstein cattle
    S Qanbari
    Animal Breeding and Genetics Group, Department of Animal Sciences, Georg August University, 37075 Gottingen, Germany
    Anim Genet 41:346-56. 2010
    This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far...
  88. pmc Copy number, linkage disequilibrium and disease association in the FCGR locus
    Heather A Niederer
    Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke s Hospital, Hills Road, Cambridge CB2 0XY, UK
    Hum Mol Genet 19:3282-94. 2010
    ..There was no association of FCGR3B CNV with vasculitis, nor with malarial or bacterial infection. Linkage disequilibrium (LD) between multi-allelic FCGR3B CNV and SLE-associated SNPs in the FCGR locus was defined for the first ..
  89. pmc Characteristics of linkage disequilibrium in North American Holsteins
    Jarmila Bohmanova
    Centre for Genetic Improvement of Livestock, Animal and Poultry Science, Department, University of Guelph, Guelph, Ontario, Canada
    BMC Genomics 11:421. 2010
    Effectiveness of genomic selection and fine mapping is determined by the level of linkage disequilibrium (LD) across the genome...
  90. pmc Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study
    Marie France Hivert
    General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
    Diabetes 57:3353-9. 2008
    ..Using comprehensive linkage disequilibrium mapping, we genotyped single nucleotide polymorphisms (SNPs) in ADIPOQ to evaluate the association of ..
  91. pmc Replication of genome-wide association studies (GWAS) loci for fasting plasma glucose in African-Americans
    E Ramos
    Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD 20892, USA
    Diabetologia 54:783-8. 2011
    ..Thus, it is important to conduct replication analyses in populations with non-European ancestry to identify shared loci associated with FPG across populations...
  92. ncbi Patterns of molecular variation in a species-wide germplasm set of Brassica napus
    Anja Bus
    Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, 50829 Cologne, Germany
    Theor Appl Genet 123:1413-23. 2011
    ..napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B...
  93. pmc Transferability and fine-mapping of genome-wide associated loci for adult height across human populations
    Daniel Shriner
    Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 4:e8398. 2009
    ..However, when we comprehensively evaluated all HapMap variants in linkage disequilibrium (r(2) > or = 0.3) with the reported variants, the transferability rate increased to 54.1%...
  94. ncbi Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans
    Michael Nothnagel
    Institute of Medical Informatics and Statistics, Christian Albrechts University, 24105 Kiel, Germany
    Hum Mol Genet 19:2927-35. 2010
    ..contained ROHs at considerable frequency, thereby forming 'ROH islands' that were not explicable by high linkage disequilibrium alone...
  95. pmc Comprehensive approach to analyzing rare genetic variants
    Thomas J Hoffmann
    Department of Epidemiology and Biostatistics and Institute of Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13584. 2010
    ..This agnostic approach allows one to efficiently analyze the association between rare variants and disease while avoiding assumptions required by other approaches for grouping such variants...
  96. pmc Defining the role of the MHC in autoimmunity: a review and pooled analysis
    Michelle M A Fernando
    Section of Molecular Genetics and Rheumatology, Faculty of Medicine, Imperial College London, London, United Kingdom
    PLoS Genet 4:e1000024. 2008
    ..MHC for the majority of these diseases has remained difficult due to the great variability and extensive linkage disequilibrium (LD) that exists among alleles throughout this locus, coupled with inadequate study design whereby only a ..
  97. pmc Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease
    Minerva M Carrasquillo
    Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224, USA
    Nat Genet 41:192-8. 2009
    ..0 x 10(-7)) and 1.26 (95% CI = 1.05-1.51) for female heterozygotes (P = 0.01) compared to female noncarriers. For male hemizygotes (P = 0.07) compared to male noncarriers, the odds ratio was 1.18 (95% CI = 0.99-1.41)...
  98. ncbi Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power
    David Paetkau
    Department of Zoology and Entomology, University of Queensland, St Lucia, QLD 4072, Australia
    Mol Ecol 13:55-65. 2004
    ..The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set ..
  99. ncbi An imbalance of human complement regulatory proteins CFHR1, CFHR3 and factor H influences risk for age-related macular degeneration (AMD)
    Lars G Fritsche
    Institute of Human Genetics, University of Regensburg, Franz Josef Strauss Allee 11, Regensburg, Germany
    Hum Mol Genet 19:4694-704. 2010
    ..Our findings allude to a critical balance between the complement regulators CFHR3, CFHR1 and factor H and further emphasize the central role of complement regulation in AMD pathology...
  100. pmc Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus
    Indra Adrianto
    Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
    Nat Genet 43:253-8. 2011
    ..These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE...
  101. ncbi A genome-wide association study identifies IL23R as an inflammatory bowel disease gene
    Richard H Duerr
    Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, University of Pittsburgh Medical Center Presbyterian, Mezzanine Level, C Wing, 200 Lothrop Street, Pittsburgh, PA 15213, USA
    Science 314:1461-3. 2006
    ..These results and previous studies on the proinflammatory role of IL-23 prioritize this signaling pathway as a therapeutic target in inflammatory bowel disease...

Research Grants69

  1. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..studies assays shall be designed to capture >90% of the variation in human DNA when taking human linkage disequilibrium into account. This measure should be calculated for each of the three major human ancestral groups. 6...
  2. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2013
    ..We hypothesize that Bphse and Shs reside within a functional linkage disequilibrium (LD)-domain linked to Hrh1 and may contain genes related to H1R folding, trafficking, or signaling...
  3. Impacts of surface receptors [Toll like receptor (TLRs) and Fc gamma receptors (F
    Collins Ouma; Fiscal Year: 2012
    ..Fc3RIIIa gene is located proximate to Fc3RIIa and Fc3RIIIb, and the three genes have been shown to be in linkage disequilibrium. A recent report on a dimorphism within the Fc3RIIIa at position 176 (F/V) demonstrated that variation at ..
  4. The Role of Carboxypeptidase B and its Substrates in Rheumatoid Arthritis
    William H Robinson; Fiscal Year: 2013
    ..The non- synonymous C1064T CPB SNP is in strong linkage disequilibrium with rs1409433, and the C1064T variant encoding CPB Thr325Ile has been reported to possess a longer half-..
  5. Prolylcarboxypeptidase is a Risk Factor for Cardiovascular Disease
    Alvin H Schmaier; Fiscal Year: 2013
    ..Other SNPs are chosen because they are evolutionary conserved or in linkage disequilibrium with a functional SNP...
  6. Genetic Interactions and Synthetic Population Biology
    Michael B Elowitz; Fiscal Year: 2013
    ..will be used to analyze key population genetic phenomena, including maintenance of genetic variation, linkage disequilibrium, and outbreeding depression...
  7. Functional consequences of autophagy mutations in Crohn's disease.
    David L Boone; Fiscal Year: 2012
    ..The SNP in IRGM is in perfect linkage disequilibrium with a 20 kB deletion that may affect the regulation of IRGM expression...
    GEORGIRENE VLADUTIU; Fiscal Year: 2012
    ..Statistical analyses for power, effect size and patterns of linkage disequilibrium will be central to the validation of our findings...
  9. Human Population Diversity in Leukocyte Receptors
    PETER R PARHAM; Fiscal Year: 2013
    ..method will be used to study the world's populations, to define LRC haplotypes and to analyze the linkage disequilibrium between alleles at the different genes...
  10. Discovering More Juvenile Myoclonic Epilepsy Genes by a Consortium
    Antonio V Delgado-Escueta; Fiscal Year: 2013
    ..the Illumina Human 1 M Bead chip (includes 1 M SNPs and 56K CNV probes) for joint analysis of linkage and linkage disequilibrium in Year 5...
  11. The Genetics of Polycystic Ovary Syndrom
    Corrine K Welt; Fiscal Year: 2013
    ..In addition, the exons and promoter regions of genes in linkage disequilibrium with the associated variant will be sequenced in large numbers to identify rare variants that may affect ..
  12. Genetic analysis fo metabolic syndrome by admixture mapping in African Americans
    Ludmila Pawlikowska; Fiscal Year: 2012
    ..Admixture loci share linkage disequilibrium with ancestry-informative markers across large genomic segments and can be mapped using relatively few ..
  13. Polymorphism affecting water balance
    David M Cohen; Fiscal Year: 2013
    ..haplotype block in which this polymorphism is embedded, to establish that no other polymorphism in tight linkage disequilibrium with our known variant accounts for the effect of this allele...
    Craig P Hersh; Fiscal Year: 2013
    ..The information gained may eventually allow physicians to predict which COPD patients are most likely to benefit or most likely to be harmed by long-term oxygen therapy. ..
  15. Identification of Psoriatic Arthritis Genes
    JAMES TILFORD ELDER; Fiscal Year: 2013
    ..these results, we now hypothesize that there are two determinants of PsA susceptibility in the MHC, one in linkage disequilibrium (LD) with MICA*002, and one in LD with HLA-Cw6...
  16. HLA and schizophrenia: a high-throughput sequencing study
    ..SNP odds ratios are modest and localization is difficult due to extensive linkage disequilibrium (LD)...
  17. Functional characterization of a novel gene for non-alcoholic fatty liver disease
    ALEXIS L GORDEN; Fiscal Year: 2011
    ..We hypothesize that rs2228603 or a SNP in linkage disequilibrium is the most likely functional variant that promotes NAFLD...
  18. Comprehensive studies of novel SNPs affecting warfarin dose in African Americans
    Minoli Perera; Fiscal Year: 2012
    ..By looking at htSNPs we can genotype just one SNP in the haplotype and capture the variation in linkage disequilibrium (LD) with that SNP...
  19. Molecular analysis of bipolar and schizophrenia candidate genes
    Herbert M Lachman; Fiscal Year: 2012
    ..SNPs identified in GWAS are usually not functional variants on their own, but are presumably in linkage disequilibrium (LD) with bona fide disease-causing functional mutations...
  20. Molecular characterization of novel loci for orofacial clefting using canine mode
    Danika L Bannasch; Fiscal Year: 2013
    ..Due to the relatively large extent of linkage disequilibrium (LD) within individual dog breeds, many fewer SNPs and fewer DNA samples are needed compared to human ..
  21. Genetics of Nicotine Dependence
    Wade H Berrettini; Fiscal Year: 2013
    ..Because of strong linkage disequilibrium across the CHRNA3 and the adjacent CHRNA5 gene, additional genotyping is unlikely to identify causal ..
  22. H3Africa Kidney Disease Research Network
    Akinlolu O Ojo; Fiscal Year: 2013
    ..Advanced genome-based analysis strategies, such as Mapping by Admixture Linkage Disequilibrium (MALD) in African Americans, have identified a strong association between single gene variants (e.g...
  23. Genetics of Hypertension Risk Factors and Sequela in African Americans
    Yan Sun; Fiscal Year: 2010
    ..The population genetics (eg. linkage disequilibrium and allele frequencies) of African Americans are appreciably different from either of their ancestries...
  24. High-throughput screening and stem cell modeling of causal eQTL variants
    Kiran Musunuru; Fiscal Year: 2013
    ..These observations suggest that causal SNPs in linkage disequilibrium (LD) with the tag SNPs directly influence the expression of causal genes that are responsible for changes ..
    Ming You; Fiscal Year: 2013
    ..In Aim 2, we will conduct haplotype and whole-genome linkage disequilibrium analyses to guide discover new QTLs and guide and inform which loci to target in Aim 3...
  26. Role of HLA class II genes in demyelination
    Chella S David; Fiscal Year: 2013
    ..has been difficult to understand the contribution of HLA-DQ alleles in disease pathogenesis, due to strong linkage disequilibrium. Population studies have indicated that DQ alleles may play a modulatory role in progression of MS...
    Kenneth Kidd; Fiscal Year: 2009
    ..Our new haplotype analyses of the ADH gene cluster show significant linkage disequilibrium and attribute the effect on alcoholism in the Chinese sample analyzed to only one haplotype...
  28. Identification of maternal and fetal genetic factors in preterm birth
    Jeffrey C Murray; Fiscal Year: 2010
    ..II. Candidate gene evaluation. III. Genome-wide scans using both linkage and linkage disequilibrium. IV. Fine-mapping for gene identification...
  29. Ethnic difference in prostate cancer
    Timothy R Rebbeck; Fiscal Year: 2010
    ..identification of haplotype tag SNPs (htSNPs) and haplotypes, as well as characterization of linkage disequilibrium blocks. In Specific Aim 2...
  30. Cortical Excitability: Biomarker and Endophenotype in Combat Related PTSD
    Zhewu Wang; Fiscal Year: 2013
    ..Pairwise linkage disequilibrium (LD) will be estimated...
  31. Admixture mapping in African American Asthmatic Children
    TESFAYE BAYE MERSHA; Fiscal Year: 2013
    ..admixed populations and develop procedures and methods for utilizing this information and SNP markers for linkage disequilibrium admixture mapping to localize asthma liability genes...
    FRANCIS SESSIONS COLE; Fiscal Year: 2013
    ..2-0.8). Low frequencies of functional variants, allelic heterogeneity, low linkage disequilibrium in pulmonary surfactant metabolic network genes (SFTPB, SFTPC, and ABCA3), and natural selection against ..
  33. Genetics of high serum triglycerides and related metabolic traits in Mexicans
    Paivi Pajukanta; Fiscal Year: 2013
    ..Furthermore, no information about genome-wide linkage disequilibrium (LD) structure is available in Mexicans, as the publicly available HapMap data cannot be directly applied ..
  34. Design and Interpretation of SNP Association Studies of Addiction
    FRANK SCOTT SACCONE; Fiscal Year: 2013
    ..Even if a single nucleotide polymorphism (SNP) has a statistically significant association, linkage disequilibrium (LD) with other SNPs causes ambiguity that cannot be resolved statistically...
  35. Functional Genomics of Psoriasis
    JAMES TILFORD ELDER; Fiscal Year: 2013
    ..This will be accomplished by (a) applying multiple rounds of conditional analysis and preferential linkage disequilibrium (PLD) analysis to GWAS-IChip meta-analysis, targeted resequencing, PsA GWAS, and exome array datasets;(b) ..
    Shelley A Cole; Fiscal Year: 2011
    ..The use of new Bayesian methods will enable us to distinguish functional genes from polymorphisms in linkage disequilibrium with them and will greatly reduce the amount of time-consuming molecular genetic analysis that would ..
  37. Genomic Organization of Recombination Hot Spots
    Kenneth Paigen; Fiscal Year: 2013
    ..activity in humans and mice (our principal mammalian research model organism) determine patterns of linkage disequilibrium and the possibilities for closely linked genes to be coinherited, important issues in efforts to identify ..
  38. Molecular Mechanisms of Social Behavior
    Anna V Kukekova; Fiscal Year: 2010
    ..Combined linkage and linkage disequilibrium mapping will be applied to define the critical regions of the fox genome in which quantitative trait loci ..
  39. Evolution and Ancestral Functions of a Human MHC Class I Pseudogene, HLA-Y
    ANA S GOYOS; Fiscal Year: 2012 different modern HLA-A alleles, presumably obtained by recombination, partially due to the strong linkage disequilibrium between HLA-Y and HLA-A...
  40. Genome Wide Haplotype Association Analysis
    Nianjun Liu; Fiscal Year: 2012
    b>Linkage disequilibrium (LD, the non-random association of alleles at two or more loci) provides valuable information for detecting genetic variations that are responsible for complex human diseases such as hypertension, diabetes, obesity, ..
  41. Rare Variant Associations With Severe Obesity in Utah Pedigrees
    Steven C Hunt; Fiscal Year: 2013
    ..The first barrier is that rare variants are not likely to be in high linkage disequilibrium with the common variants used in GWAS...
  42. Schizophrenia-associated long non-coding RNAs in neurons derived from iPS cells
    Herbert M Lachman; Fiscal Year: 2013
    ..a subgroup of patients, presumably caused by genetic variation within these non-coding genes that are in linkage disequilibrium with associated SNPs...
  43. Immune Response Gene Polymorphisms and AMD: Examining HLA-KIR Epistasis
    Gregory J Tranah; Fiscal Year: 2013
    ..employ unique laboratory and statistical methods developed for HLA and KIR that account for the extensive linkage disequilibrium (LD) within these regions...
  44. Genomics of natural populations
    ALAN OLAV BERGLAND; Fiscal Year: 2013
    ..We predict that cyclic population boom-busts will cause changes in heterozygosity, linkage disequilibrium and signatures of population structure through the growing season...
  45. Genome Wide Association Study of Latent Autoimmune Diabetes in Adults
    Struan F A Grant; Fiscal Year: 2013
    ..that are successfully replicated will then be refined in an African American (AA) cohort, as the degree of linkage disequilibrium (LD) is lower in this ethnic group...
  46. Genome Wide Association Study of Bone Mineral Accretion During Childhood
    Babette S Zemel; Fiscal Year: 2013
    ..successfully replicated will then be refined in the African-American (AA) sample (n=435), as the degree of linkage disequilibrium is lower in this group...
  47. QTLs in Drosophila
    Eric A Stone; Fiscal Year: 2012
    ..traits using genome wide association (GWA) mapping, because high levels of molecular polymorphism and low linkage disequilibrium in Drosophila facilitate the identification of not only genes associated with complex traits, but actual ..
  48. Identification of regulatory cancer risk SNPs for chemoprevention discovery
    Robert J Klein; Fiscal Year: 2013
    ..Regulatory SNPs in linkage disequilibrium with known cancer risk loci will be identified and tested for association with cancer through statistical ..
  49. Role of SOCS-1 in Regulation of IgE
    Paul B Rothman; Fiscal Year: 2010
    ..Analysis demonstrated that this SNP was in linkage disequilibrium with a SNP at position -820 of the SOCS-1 promoter...
  50. Genetic Association Studies in African American Colorectal Cancer Patients
    SONIA KUPFER; Fiscal Year: 2013
    ..are an ideal population in whom to identify functional variants because their genomes exhibit less linkage disequilibrium. To this end, I propose three specific aims: 1) Validate candidate CRC-associated regions in African ..
  51. Genome-wide association studies in outbred mice
    Abraham A Palmer; Fiscal Year: 2013
    ..We will utilize outbred CD-1 mice because linkage disequilibrium breaks down over short physical distances in these mice compared to other commonly studied mouse ..
  52. GWAS for Sleep Apnea and Endothelial Function Among Mexican Americans
    Craig L Hanis; Fiscal Year: 2013
    ..including the Hispanic Health Cohort;and 4) to distinguish causal polymorphisms from those simply in linkage disequilibrium for identified genes through deep re-sequencing and analyses that exploit network theory and evolutionary ..
  53. IBD Gene Mapping by Clinical and Population Subset
    Steven R Brant; Fiscal Year: 2013
    ..those in linkage disequilibrium. Comparing association patterns across populations and evaluating function of associated SNPs that map to ..
  54. A Genetic Study of Schizophrenia Endophenotypes in Sub-Saharan Africans
    Ikwunga Wonodi; Fiscal Year: 2012
    ..The advantages of the Nigerian site include, small linkage disequilibrium (LD) blocks ideal for gene mapping in an old population (similar to the Yoruba in the International HapMap ..
  55. Genomic Patterns of Polymorphism in Primates
    Jeffrey D Wall; Fiscal Year: 2012
    ..Establishing baseline levels of neutral polymorphism and linkage disequilibrium in these species will facilitate the proper design and analysis of both candidate gene studies and genome-..
  56. Expression and proteomic characterization of risk loci in type 1 diabetes
    Patrick Concannon; Fiscal Year: 2009
    ..Based on consideration of the decay of linkage disequilibrium around the most strongly associated SNPs in these T1D associated regions, the median number of genes in a ..
  57. Pharmacogenetics of Warfarin in Puerto Rican Patients using a Physiogenomics Appr
    Jorge Duconge; Fiscal Year: 2013
    ..structure of Puerto Ricans and create a reference database of individual admixture, allele frequencies, linkage disequilibrium (LD) and haplotypes for pharmacogenetics studies...
  58. Inherited genetic factors in breast cancer predisposition and tumor presentation
    Julie Dutil; Fiscal Year: 2013
    ..susceptibility to hormonal receptor-negative tumors in breast cancer patients using mapping by admixture linkage disequilibrium. This method takes advantage of the differences in the frequency of genetic variants between populations ..
  59. Comprehensive Mapping of a Blood Pressure QTL on Chromosome 17
    Kari E North; Fiscal Year: 2010
    ..contains one or more polymorphic variants that account for the linkage signal by performing comprehensive linkage disequilibrium mapping of the region in the SHFS samples...
  60. Studies of HLA Region Genomics in Systemic Sclerosis and Ankylosing Spondyilitis
    Xiaodong Zhou; Fiscal Year: 2013
    ..However, because of the extensive linkage disequilibrium (LD) between genes within the HLA region, some of observed disease associations may be due to LD...
  61. How Genetic Variation in Protein Kinases Affects Drug Response
    EDWARD E HARLOW; Fiscal Year: 2010
    ..with diseases are often functionally neutral, correlated with a particular phenotype only due to linkage disequilibrium. By contrast, insight into disease mechanism is primarily provided by knowledge of the functional variant...
  62. Identifying and Analyzing Genes Linked to Autoimmune Thyroid Diseases
    Yaron Tomer; Fiscal Year: 2010
    ..patients;(2) To identify the AITD susceptibility genes in the 2 major replicated loci on 12q &14q by linkage disequilibrium mapping, haplotype analysis, and gene sequencing...
    LAWRENCE LAYMAN; Fiscal Year: 2001
    ..The third aim will be to use linkage analysis, linkage disequilibrium analysis, and association to identify candidate genes which might be involved in the pathogenesis of IHH...
  64. Pharmacogenetics and Cardiovascular Events
    Bruce Psaty; Fiscal Year: 2006
    ..SNP) per gene in each of a few candidate genes-an approach that ignores the complexity of the underlying linkage disequilibrium or haplotype structure of candidate genes. Aims...
    Edmond Yunis; Fiscal Year: 1991
    ..genes in the Class II region of chromosome 6p and to better define the extent of non-random association (linkage disequilibrium) of genes in the extended haplotypes...
    Joseph Felsenstein; Fiscal Year: 2001
    ..b>Linkage disequilibrium mapping uses individuals sampled from a large population...
    Henry Erlich; Fiscal Year: 2003
    ..Family based material allows the analysis of haplotype sharing, transmission ratios, and linkage disequilibrium patterns as well as stratification analysis to see whether some of the associated alleles at DPB1, or any ..
  68. Comprehensive genomic approach to rare hearing disorders and ataxia
    Margit Burmeister; Fiscal Year: 2010
    ..In some situations, linkage disequilibrium analysis can further narrow a region. Recently, global analysis of gene expression has become a reality...
  69. A Genome-Wide Association Study of Ischemic Brain Vascular Injury
    Myriam Fornage; Fiscal Year: 2010
    ..sciences afford new opportunities to identify genes for ischemic brain vascular injury through genome-wide linkage disequilibrium mapping...