Bioinformatics Advance Access published online on August 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth457
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Whitehead Institute for Biomedical Research, Cambridge, MA 02142
* To whom correspondence should be addressed. E-mail: jcbarret{at}broad.mit.edu.
Abstract: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. 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 interactive interface. Summary: A program for visualizing and analyzing LD and haplotype patterns in genotype data. Availability: http://www.broad.mit.edu/personal/jcbarret/haploview/.
Accepted July 23, 2004
Applications note
Haploview: analysis and visualization of LD and haplotype maps
2 MIT Media Lab, Cambridge, MA 02139
3 Whitehead Institute for Biomedical Research, Cambridge, MA 02142; Broad Institute of Harvard and MIT, Cambridge, MA
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M. Sikora, A. Ferrer-Admetlla, H. Laayouni, C. Menendez, A. Mayor, A. Bardaji, B. Sigauque, I. Mandomando, P. L. Alonso, J. Bertranpetit, et al. A variant in the gene FUT9 is associated with susceptibility to placental malaria infection Hum. Mol. Genet., August 15, 2009; 18(16): 3136 - 3144. [Abstract] [Full Text] [PDF]
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A. Malarstig, A. Buil, J. C. Souto, R. Clarke, F. Blanco-Vaca, J. Fontcuberta, J. Peden, M. Andersen, A. Silveira, S. Barlera, et al. Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study Blood, August 13, 2009; 114(7): 1417 - 1422. [Abstract] [Full Text] [PDF]
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A. Sabbagh, E. Pasmant, I. Laurendeau, B. Parfait, S. Barbarot, B. Guillot, P. Combemale, S. Ferkal, M. Vidaud, P. Aubourg, et al. Unravelling the genetic basis of variable clinical expression in neurofibromatosis 1 Hum. Mol. Genet., August 1, 2009; 18(15): 2768 - 2778. [Abstract] [Full Text] [PDF]
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N. Niu, V. Manickam, K. R. Kalari, I. Moon, L. L. Pelleymounter, B. W. Eckloff, E. D. Wieben, D. J. Schaid, and L. Wang Human Glucocorticoid Receptor {alpha} Gene (NR3C1) Pharmacogenomics: Gene Resequencing and Functional Genomics J. Clin. Endocrinol. Metab., August 1, 2009; 94(8): 3072 - 3084. [Abstract] [Full Text] [PDF]
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Y.-C. Cheng, W.-H. L. Kao, B. D. Mitchell, J. R. O'Connell, H. Shen, P. F. McArdle, Q. Gibson, K. A. Ryan, A. R. Shuldiner, and T. I. Pollin Genome-Wide Association Scan Identifies Variants near Matrix Metalloproteinase (MMP) Genes on Chromosome 11q21-22 Strongly Associated With Serum MMP-1 Levels Circ Cardiovasc Genet, August 1, 2009; 2(4): 329 - 337. [Abstract] [Full Text] [PDF]
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H. Ding, Y. Xu, X. Wang, Q. Wang, L. Zhang, Y. Tu, J. Yan, W. Wang, R. Hui, C.-Y. Wang, et al. 9p21 is a Shared Susceptibility Locus Strongly for Coronary Artery Disease and Weakly for Ischemic Stroke in Chinese Han Population Circ Cardiovasc Genet, August 1, 2009; 2(4): 338 - 346. [Abstract] [Full Text] [PDF]
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B Asling, J Jirholt, P Hammond, M Knutsson, A Walentinsson, G Davidson, L Agreus, A Lehmann, and M Lagerstrom-Fermer Collagen type III alpha I is a gastro-oesophageal reflux disease susceptibility gene and a male risk factor for hiatus hernia Gut, August 1, 2009; 58(8): 1063 - 1069. [Abstract] [Full Text] [PDF]
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A M Muise, T D Walters, W K Glowacka, A M Griffiths, B-Y Ngan, H Lan, W Xu, M S Silverberg, and D Rotin Polymorphisms in E-cadherin (CDH1) result in a mis-localised cytoplasmic protein that is associated with Crohn's disease Gut, August 1, 2009; 58(8): 1121 - 1127. [Abstract] [Full Text] [PDF]
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A. HELLQUIST, T. M. JARVINEN, S. KOSKENMIES, M. ZUCCHELLI, C. ORSMARK-PIETRAS, L. BERGLIND, J. PANELIUS, T. HASAN, H. JULKUNEN, M. D'AMATO, et al. Evidence for Genetic Association and Interaction Between the TYK2 and IRF5 Genes in Systemic Lupus Erythematosus J Rheumatol, August 1, 2009; 36(8): 1631 - 1638. [Abstract] [Full Text] [PDF]
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R. DIEGUEZ-GONZALEZ, S. AKAR, M. CALAZA, I. GONZALEZ-ALVARO, B. FERNANDEZ-GUTIERREZ, J. R. LAMAS, A. R. de la SERNA, R. CALIZ, F. J. BLANCO, D. PASCUAL-SALCEDO, et al. Lack of Association with Rheumatoid Arthritis of Selected Polymorphisms in 4 Candidate Genes: CFH, CD209, Eotaxin-3, and MHC2TA J Rheumatol, August 1, 2009; 36(8): 1590 - 1595. [Abstract] [Full Text] [PDF]
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A. E. Fry, A. Ghansa, K. S. Small, A. Palma, S. Auburn, M. Diakite, A. Green, S. Campino, Y. Y. Teo, T. G. Clark, et al. Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes Hum. Mol. Genet., July 15, 2009; 18(14): 2683 - 2692. [Abstract] [Full Text] [PDF]
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G. Orozco, A. Hinks, S. Eyre, X. Ke, L. J. Gibbons, J. Bowes, E. Flynn, P. Martin, Wellcome Trust Case Control Consortium, YEAR consortium, et al. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23 Hum. Mol. Genet., July 15, 2009; 18(14): 2693 - 2699. [Abstract] [Full Text] [PDF]
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A. -M. Wills, S. Cronin, A. Slowik, D. Kasperaviciute, M. A. Van Es, J. M. Morahan, P. N. Valdmanis, V. Meininger, J. Melki, C. E. Shaw, et al. A large-scale international meta-analysis of paraoxonase gene polymorphisms in sporadic ALS Neurology, July 7, 2009; 73(1): 16 - 24. [Abstract] [Full Text] [PDF]
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N. N. Hansel, L. Gao, N. M. Rafaels, R. A. Mathias, E. R. Neptune, C. Tankersley, A. V. Grant, J. Connett, T. H. Beaty, R. A. Wise, et al. Leptin receptor polymorphisms and lung function decline in COPD Eur. Respir. J., July 1, 2009; 34(1): 103 - 110. [Abstract] [Full Text] [PDF]
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X. Yang, S.-H. Liang, D. M. Weyant, P. Lazarus, C. J. Gallagher, and C. J. Omiecinski The Expression of Human Microsomal Epoxide Hydrolase Is Predominantly Driven by a Genetically Polymorphic Far Upstream Promoter J. Pharmacol. Exp. Ther., July 1, 2009; 330(1): 23 - 30. [Abstract] [Full Text] [PDF]
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G. Wang, K. L. Spencer, B. L. Court, L. M. Olson, W. K. Scott, J. L. Haines, and M. A. Pericak-Vance Localization of Age-Related Macular Degeneration-Associated ARMS2 in Cytosol, Not Mitochondria Invest. Ophthalmol. Vis. Sci., July 1, 2009; 50(7): 3084 - 3090. [Abstract] [Full Text] [PDF]
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A. Biyasheva, R. S. Legro, A. Dunaif, and M. Urbanek Evidence for Association between Polycystic Ovary Syndrome (PCOS) and TCF7L2 and Glucose Intolerance in Women with PCOS and TCF7L2 J. Clin. Endocrinol. Metab., July 1, 2009; 94(7): 2617 - 2625. [Abstract] [Full Text] [PDF]
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M. Urbanek, G. Nampiaparampil, J. D'Souza, E. Sefton, C. Ackerman, R. S. Legro, and A. Dunaif The Role of Genetic Variation in the Lamin A/C Gene in the Etiology of Polycystic Ovary Syndrome J. Clin. Endocrinol. Metab., July 1, 2009; 94(7): 2665 - 2669. [Abstract] [Full Text] [PDF]
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H.-L. Xu, W.-H. Xu, Q. Cai, M. Feng, J. Long, W. Zheng, Y.-B. Xiang, and X.-O. Shu Polymorphisms and Haplotypes in the Caspase-3, Caspase-7, and Caspase-8 Genes and Risk for Endometrial Cancer: A Population-Based, Case-Control Study in a Chinese Population Cancer Epidemiol. Biomarkers Prev., July 1, 2009; 18(7): 2114 - 2122. [Abstract] [Full Text] [PDF]
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L. Lu, J. Sun, S. D. Isaacs, K. E. Wiley, S. Smith, K. Pruett, Y. Zhu, Z. Zhang, F. Wiklund, H. Gronberg, et al. Fine-Mapping and Family-Based Association Analyses of Prostate Cancer Risk Variants at Xp11 Cancer Epidemiol. Biomarkers Prev., July 1, 2009; 18(7): 2132 - 2136. [Abstract] [Full Text] [PDF]
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H. Peterson, H. Laivuori, E. Kerkela, H. Jiao, L. Hiltunen, S. Heino, I. Tiala, S. Knuutila, V. Rasi, J. Kere, et al. ROCK2 allelic variants are not associated with pre-eclampsia susceptibility in the Finnish population Mol. Hum. Reprod., July 1, 2009; 15(7): 443 - 449. [Abstract] [Full Text] [PDF]
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R. A. Mason, E. V. Morlock, M. R. Karagas, K. T. Kelsey, C. J. Marsit, A. R. Schned, and A. S. Andrew EGFR pathway polymorphisms and bladder cancer susceptibility and prognosis Carcinogenesis, July 1, 2009; 30(7): 1155 - 1160. [Abstract] [Full Text] [PDF]
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