Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2005 21(2):263-265; doi:10.1093/bioinformatics/bth457
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.
Haploview: analysis and visualization of LD and haplotype maps
1 Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
2 MIT Media Lab Cambridge, MA 02139, USA
3 Broad Institute of Harvard and MIT Cambridge, MA, USA
*To whom correspondence should be addressed.
Summary: 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.
Availability: http://www.broad.mit.edu/mpg/haploview/
Contact: jcbarret{at}broad.mit.edu
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L. M. Morton, M. P. Purdue, T. Zheng, S. S. Wang, B. Armstrong, Y. Zhang, I. Menashe, N. Chatterjee, S. Davis, Q. Lan, et al. Risk of Non-Hodgkin Lymphoma Associated with Germline Variation in Genes that Regulate the Cell Cycle, Apoptosis, and Lymphocyte Development Cancer Epidemiol. Biomarkers Prev., April 1, 2009; 18(4): 1259 - 1270. [Abstract] [Full Text] [PDF] |
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J. P. Breyer, M. E. Sanders, D. C. Airey, Q. Cai, B. L. Yaspan, P. A. Schuyler, Q. Dai, F. Boulos, M. G. Olivares, K. M. Bradley, et al. Heritable Variation of ERBB2 and Breast Cancer Risk Cancer Epidemiol. Biomarkers Prev., April 1, 2009; 18(4): 1252 - 1258. [Abstract] [Full Text] [PDF] |
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Y. Zha, K. H. Leung, K. K. Lo, W. Y. Fung, P. W. Ng, M.-g. Shi, M. K. H. Yap, and S. P. Yip TGFB1 as a Susceptibility Gene for High Myopia: A Replication Study With New Findings Arch Ophthalmol, April 1, 2009; 127(4): 541 - 548. [Abstract] [Full Text] [PDF] |
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S. K. Park, G. Andreotti, L. C. Sakoda, Y.-T. Gao, A. Rashid, J. Chen, B. E. Chen, P. S. Rosenberg, M.-C. Shen, B.-S. Wang, et al. Variants in hormone-related genes and the risk of biliary tract cancers and stones: a population-based study in China Carcinogenesis, April 1, 2009; 30(4): 606 - 614. [Abstract] [Full Text] [PDF] |
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J. S. Danik, G. Pare, D. I. Chasman, R. Y.L. Zee, D. J. Kwiatkowski, A. Parker, J. P. Miletich, and P. M Ridker Novel Loci, Including Those Related to Crohn Disease, Psoriasis, and Inflammation, Identified in a Genome-Wide Association Study of Fibrinogen in 17 686 Women: The Women's Genome Health Study Circ Cardiovasc Genet, April 1, 2009; 2(2): 134 - 141. [Abstract] [Full Text] [PDF] |
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J. G. Smith, O. Melander, H. Lovkvist, B. Hedblad, G. Engstrom, P. Nilsson, J. Carlson, G. Berglund, B. Norrving, and A. Lindgren Common Genetic Variants on Chromosome 9p21 Confers Risk of Ischemic Stroke: A Large-Scale Genetic Association Study Circ Cardiovasc Genet, April 1, 2009; 2(2): 159 - 164. [Abstract] [Full Text] [PDF] |
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W. C. Leung, S. Hessel, C. Meplan, J. Flint, V. Oberhauser, F. Tourniaire, J. E. Hesketh, J. von Lintig, and G. Lietz Two common single nucleotide polymorphisms in the gene encoding {beta}-carotene 15,15'-monoxygenase alter {beta}-carotene metabolism in female volunteers FASEB J, April 1, 2009; 23(4): 1041 - 1053. [Abstract] [Full Text] [PDF] |
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F.-C. Hsu, J. Sun, F. Wiklund, S. D. Isaacs, K. E. Wiley, L. D. Purcell, Z. Gao, P. Stattin, Y. Zhu, S.-T. Kim, et al. A Novel Prostate Cancer Susceptibility Locus at 19q13 Cancer Res., April 1, 2009; 69(7): 2720 - 2723. [Abstract] [Full Text] [PDF] |
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N. D. Shephard, R. Abo, S. H. Rigas, B. Frank, W.-Y. Lin, I. W. Brock, A. Shippen, S. P. Balasubramanian, M. W. R. Reed, C. R. Bartram, et al. A Breast Cancer Risk Haplotype in the Caspase-8 Gene Cancer Res., April 1, 2009; 69(7): 2724 - 2728. [Abstract] [Full Text] [PDF] |
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T. Lencz, R. H. Lipsky, P. DeRosse, K. E. Burdick, J. M. Kane, and A. K. Malhotra Molecular differentiation of schizoaffective disorder from schizophrenia using BDNF haplotypes The British Journal of Psychiatry, April 1, 2009; 194(4): 313 - 318. [Abstract] [Full Text] [PDF] |
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C. Wang, C. Hu, R. Zhang, Y. Bao, X. Ma, J. Lu, W. Qin, X. Shao, J. Lu, J. Xu, et al. Common Variants of Hepatocyte Nuclear Factor 1{beta} Are Associated With Type 2 Diabetes in a Chinese Population Diabetes, April 1, 2009; 58(4): 1023 - 1027. [Abstract] [Full Text] [PDF] |
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M. M. Gray, J. M. Granka, C. D. Bustamante, N. B. Sutter, A. R. Boyko, L. Zhu, E. A. Ostrander, and R. K. Wayne Linkage Disequilibrium and Demographic History of Wild and Domestic Canids Genetics, April 1, 2009; 181(4): 1493 - 1505. [Abstract] [Full Text] [PDF] |
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P. L. De Jager, C. Baecher-Allan, L. M. Maier, A. T. Arthur, L. Ottoboni, L. Barcellos, J. L. McCauley, S. Sawcer, A. Goris, J. Saarela, et al. The role of the CD58 locus in multiple sclerosis PNAS, March 31, 2009; 106(13): 5264 - 5269. [Abstract] [Full Text] [PDF] |
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L. L.E. Koskinen, E. Einarsdottir, E. Dukes, G. A. R. Heap, P. Dubois, I. R. Korponay-Szabo, K. Kaukinen, K. Kurppa, F. Ziberna, S. Vatta, et al. Association study of the IL18RAP locus in three European populations with coeliac disease Hum. Mol. Genet., March 15, 2009; 18(6): 1148 - 1155. [Abstract] [Full Text] [PDF] |
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H.-D. Song, J. Liang, J.-Y. Shi, S.-X. Zhao, Z. Liu, J.-J. Zhao, Y.-D. Peng, G.-Q. Gao, J. Tao, C.-M. Pan, et al. Functional SNPs in the SCGB3A2 promoter are associated with susceptibility to Graves' disease Hum. Mol. Genet., March 15, 2009; 18(6): 1156 - 1170. [Abstract] [Full Text] [PDF] |
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S. Han, X. Kim-Howard, H. Deshmukh, Y. Kamatani, P. Viswanathan, J. M. Guthridge, K. Thomas, K. M. Kaufman, J. Ojwang, A. Rojas-Villarraga, et al. Evaluation of imputation-based association in and around the integrin-{alpha}-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE) Hum. Mol. Genet., March 15, 2009; 18(6): 1171 - 1180. [Abstract] [Full Text] [PDF] |
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M. H. Sohn, J. H. Lee, K. W. Kim, S. W. Kim, S. H. Lee, K.-E. Kim, K. H. Kim, C. G. Lee, J. A. Elias, and M. G. Lee Genetic Variation in the Promoter Region of Chitinase 3-Like 1 Is Associated with Atopy Am. J. Respir. Crit. Care Med., March 15, 2009; 179(6): 449 - 456. [Abstract] [Full Text] [PDF] |
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W. Liu, J. Sun, G. Li, Y. Zhu, S. Zhang, S.-T. Kim, J. Sun, F. Wiklund, K. Wiley, S. D. Isaacs, et al. Association of a Germ-Line Copy Number Variation at 2p24.3 and Risk for Aggressive Prostate Cancer Cancer Res., March 15, 2009; 69(6): 2176 - 2179. [Abstract] [Full Text] [PDF] |
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M. C. Aldrich, S. Selvin, H. M. Hansen, L. F. Barcellos, M. R. Wrensch, J. D. Sison, K. T. Kelsey, P. A. Buffler, C. P. Quesenberry Jr., M. F. Seldin, et al. CYP1A1/2 Haplotypes and Lung Cancer and Assessment of Confounding by Population Stratification Cancer Res., March 15, 2009; 69(6): 2340 - 2348. [Abstract] [Full Text] [PDF] |
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J. M. Schildkraut, E. L. Goode, M. A. Clyde, E. S. Iversen, P. G. Moorman, A. Berchuck, J. R. Marks, J. Lissowska, L. Brinton, B. Peplonska, et al. Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer Cancer Res., March 15, 2009; 69(6): 2349 - 2357. [Abstract] [Full Text] [PDF] |
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M. E. Sehl, L. R. Langer, J. C. Papp, L. Kwan, J. L. Seldon, G. Arellano, J. Reiss, E. F. Reed, S. Dandekar, Y. Korin, et al. Associations between Single Nucleotide Polymorphisms in Double-Stranded DNA Repair Pathway Genes and Familial Breast Cancer Clin. Cancer Res., March 15, 2009; 15(6): 2192 - 2203. [Abstract] [Full Text] [PDF] |
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Y. H. Park, S. K. Sohn, J. G. Kim, M.-H. Lee, H. S. Song, M. K. Kim, J. S. Jung, J.-J. Lee, H. J. Kim, and D. H. Kim Interaction between BCL2 and Interleukin-10 Gene Polymorphisms Alter Outcomes of Diffuse Large B-Cell Lymphoma following Rituximab Plus CHOP Chemotherapy Clin. Cancer Res., March 15, 2009; 15(6): 2107 - 2115. [Abstract] [Full Text] [PDF] |
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U. Nowak-Gottl, B. Frohlich, S. Thedieck, A. Huge, and M. Stoll Association of the protein Z ATG haplotype with symptomatic nonvascular stroke or thromboembolism in white children: a family-based cohort study Blood, March 5, 2009; 113(10): 2336 - 2341. [Abstract] [Full Text] [PDF] |
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M. T. Vuong, S. Lundberg, I. Gunnarsson, L. Wramner, M. Seddighzadeh, M. Hahn-Zoric, A. Fernstrom, L. A Hanson, L. T. Do, S. H. Jacobson, et al. Genetic variation in the transforming growth factor-{beta}1 gene is associated with susceptibility to IgA nephropathy Nephrol. Dial. Transplant., March 3, 2009; (2009) gfp079v1. [Abstract] [Full Text] [PDF] |
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E Sanchez, M. Gonzalez-Gay, J. Callejas-Rubio, N Ortego-Centeno, J. Sabio, J Jimenez-Alonso, L Mico, A Suarez, C Gutierrez, E de Ramon, et al. No evidence for genetic association of interferon regulatory factor 3 in systemic lupus erythematosus Lupus, March 1, 2009; 18(3): 230 - 234. [Abstract] [PDF] |
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E. T. Chang, B. M. Birmann, J. L. Kasperzyk, D. V. Conti, P. Kraft, R. F. Ambinder, T. Zheng, and N. E. Mueller Polymorphic Variation in NFKB1 and Other Aspirin-Related Genes and Risk of Hodgkin Lymphoma Cancer Epidemiol. Biomarkers Prev., March 1, 2009; 18(3): 976 - 986. [Abstract] [Full Text] [PDF] |
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