Haploscope: A tool for the graphical display of haplotype: Structure in populations

Genetic Epidemiology

Volumn 36, Issue 1, 2012, Pages 17-21

  San Lucas, F Anthony ^a,b   Rosenberg, Noah A ^c   Scheet, Paul ^a,b  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Clustering; Haplotypes; Linkage disequilibrium; Software; Visualization

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; GENE; GENE FREQUENCY; GENETIC VARIABILITY; HAPLOSCOPY; HAPLOTYPE; HUMAN GENOME; LCT GENE; OPTICAL INSTRUMENTATION; POPULATION GENETICS;

ALGORITHMS; GENE FREQUENCY; GENETICS, POPULATION; HAPLOTYPES; HUMANS; LACTASE; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84859100108     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20640     Document Type: Article

References (18)

1. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
2. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74:1111-1120.
3. Browning BL, Browning SR. 2007a. Efficient multilocus association testing for whole genome association studies using localized haplotype clustering. Genet Epidemiol 31:365-375.
4. Browning SR, Browning BL. 2007b. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097.
5. Browning SR, Weir BS. 2010. Population structure with localized haplotype clusters. Genetics 185:1337-1344.
6. Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK. 2006. Aworldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 38:1251-1260.
7. Davidovich O, Kimmel G, Shamir R. 2007. GEVALT: an integrated software tool for genotype analysis. BMC Bioinform 8:36.
8. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Sanchez JS, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. 2008. Genotype, haplotype and copynumber variation in worldwide human populations. Nature 451:998-1003.
9. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100-1104
10. Marchini J, Howie B, Myers S, McVean G, Donnelly P. 2007. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39:906-913.
11. Rabiner LR. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77:257-286.
12. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
13. Scheet P, Stephens M. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78:629-644.
14. Servin B, Stephens M. 2007. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3:e114.
15. Teo YY, Small KS. 2009. A novel method for haplotype clustering and visualization. Genet Epidemiol 34:34-41
16. Visual Haplotypes: Displaying Estimated Haplotype Data [http://gvs.gs.washington.edu/GVS/].
17. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol 4:e72.
18. Zhang J, Rowe WL, Struewing JP, Buetow KH. 2002. HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. Nucleic Acids Res 30: 5213-5221.