Hapmap

Haplotype map을 만드는 프로젝트.

Haplotype: A set of associated SNP alleles in a region of a chromosome is called a haplotype.
The HapMap will identify which 200,000 to 1 million tag SNPs provide almost as much mapping information as the 10 million SNPs. This substantial cost reduction will make such studies feasible to do.


International Hapmap project
DNA beginner's guide

 

References

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Cardon LR, Abecasis GR. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet. 19(3):135-40. Review. 

Carlson, C. S. et al. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for wholegenome association studies in humans. Nature Genet. 33, 518–521.

Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E. (2003). Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet. 73(2):285-300. 

Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. and Lander, E. S. (2001). High-resolution haplotype structure in the human genome. Nature Genetics 29, 229–232.

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature. 418(6897):544-8.

Falush D, Stephens M, Pritchard JK (2003). Inference of population structure: Extensions to linked loci and correlated allele frequencies. Genetics.

Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. (2002). The structure of haplotype blocks in the human genome. 296, 2225-2229.

Kang HJ, Choi KO, Kim BD, Kim SS, Kim YJ. (2005). FESD: a Functional Element SNPs Database in human, Nucleic Acids Research, 33, D518-D522.

Dana C Crawford, Tushar Bhangale, Na Li, Garrett Hellenthal, Mark J Rieder, Deborah A Nickerson & Matthew Stephens. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics, Nat Genet. 36(7):700-706.

Lynn BJ, Stephen PW. (2004). Genetic variation, classification and 'race'. Nature Genetics. 36(11):s28-s33.

Lu X, Niu T, Liu JS. (2003). Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Res. 13(9):2112-7.

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT, Cardon LR. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet. 33(3):382-7.

Pritchard JK, Stephens M, Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155:945-959.

Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. (2001). Linkage disequilibrium in the human genome. Nature. 411(6834):199-204. 

Stumpf MP, Goldstein DB. (2003). Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr Biol. 13(1):1-8. 

Tapper WJ, Maniatis N, Morton NE, Collins A. (2003). A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet. 67(Pt 6):487-94. 

The International HapMap Consortium. (2003). The International HapMap Project. Nature. 426(6968):789-96. 

The International HapMap Consortium. (2005). A haplotype map of the human genome, Nature 437, 1299-1320.

The International SNPWorking Group. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.

Wheeler D.L., Church D.M., Edgar R., Federhen S., Helmberg W., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E, Suzek T.O., Tatusova T.A. and Wagner L. (2004) Database resources of the national center for biotechnology information: update. Nucleic Acids Res., 32, D35-D40.

Zhang K, Sun F, Waterman MS, Chen T. (2003). Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet. 73(1):63-73.