The Genom of Homo sapiens.pdf

62 BENTLEYACKNOWLEDGMENTSThe author especially thanks Ines Barroso, Lon Cardon,Panos Deloukas, Peter Donnelly, Christine Rees, and othersfor discussion and assistance. The author gratefully acknowledgesthe support of the Wellcome Trust.REFERENCESAbecasis G.R., Noguchi E., Heinzmann A., Traherne J.A., BhattacharyyaS., Leaves N.I., Anderson G.G., Zhang Y., LenchN.J., Carey A., Cardon L.R., Moffatt M.F., and CooksonW.O. 2001. Extent and distribution of linkage disequilibriumin three genomic regions. Am. J. Hum. Genet. 68: 191.Altshuler D., Hirschhorn J.N., Klannemark M., Lindgren C.M.,Vohl M.C., Nemesh J., Lane C.R., Schaffner S.F., Bolk S.,Brewer C., Tuomi T., Gaudet D., Hudson T.J., Daly M.,Groop L., and Lander E.S. 2000. The common PPARgammaPro12Ala polymorphism is associated with decreased risk oftype 2 diabetes. Nat. Genet. 26: 76.Barbujani G., Magagni A., Minch E., and Cavalli-Sforza L.L.1997. An apportionment of human DNA diversity. Proc. Natl.Acad. Sci. 94: 4516.Bell G. I. and Polonsky K.S. 2001. Diabetes mellitus and geneticallyprogrammed defects in beta-cell function. Nature 414:788.Bell G.I., Horita S., and Karam J.H. 1984. A polymorphic locusnear the human insulin gene is associated with insulin-dependentdiabetes mellitus. Diabetes 33: 176.Bentley A.K., Rees D.J., Rizza C., and Brownlee G.G. 1986. Defectivepropeptide processing of blood clotting factor IXcaused by mutation of arginine to glutamine at position -4.Cell 45: 343.Bentley D.R. 2004. Genome vision. Nature (in press).Bertina R.M., Koeleman B.P., Koster T., Rosendaal F.R., DirvenR.J., de Ronde H., van der Velden P.A., and Reitsma P.H.1994. Mutation in blood coagulation factor V associated withresistance to activated protein C. Nature 369: 64.Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N.,Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., Nemesh J.,Ziaugra L., Friedland L., Rolfe A., Warrington J., LipshutzR., Daley G.Q., and Lander E.S. 1999. Characterization ofsingle-nucleotide polymorphisms in coding regions of humangenes. Nat. Genet. 22: 231.Cavalli-Sforza L.L. and Feldman M.W. 2003. The application ofmolecular genetic approaches to the study of human evolution.Nat. Genet. (suppl.) 33: 266.Clark A.G., Weiss K.M., Nickerson D.A., Taylor S.L.,Buchanan A., Stengard J., Salomaa V., Vartiainen E., PerolaM., Boerwinkle E., and Sing C.F. 1998. Haplotype structureand population genetic inferences from nucleotide-sequencevariation in human lipoprotein lipase. Am. J. Hum. Genet. 63:595.Collins F.S. 1992. Positional cloning: Let’s not call it reverseanymore. Nat. Genet. 1: 3.Collins F.S., Guyer M.S., and Charkravarti A. 1997. Variationson a theme: Cataloging human DNA sequence variation. Science278: 1580.Daly M.J., Rioux J.D., Schaffner S.F., Hudson T.J., and LanderE.S. 2001. High-resolution haplotype structure in the humangenome. Nat. Genet. 29: 229.Davies H., Bignell G.R., Cox C., Stephens P., Edkins S., CleggS., Teague J., Woffendin H., Garnett M.J., Bottomley W.,Davis N., Dicks E., Ewing R., Floyd Y., Gray K., Hall S.,Hawes R., Hughes J., Kosmidou V., Menzies A., Mould C.,Parker A., Stevens C., Watt S., and Hooper S., et al. 2002.Mutations of the BRAF gene in human cancer. Nature 417:949.Dawson E., Abecasis G.R., Bumpstead S., Chen Y., Hunt S.,Beare D.M., Pabial J., Dibling T., Tinsley E., Kirby S., CarterD., Papaspyridonos M., Livingstone S., Ganske R., LohmussaarE., Zernant J., Tonisson N., Remm M., Magi R., PuurandT., Vilo J., Kurg A., Rice K., Deloukas P., and Mott R., et al.2002. A first-generation linkage disequilibrium map of humanchromosome 22. Nature 418: 544.Dean M., Carrington M., Winkler C., Huttley G.A., Smith M.W.,Allikmets R., Goedert J.J., Buchbinder S.P., Vittinghoff E.,Gomperts E., Donfield S., Vlahov D., Kaslow R., Saah A.,Rinaldo C., Detels R., and O’Brien S.J. 1996. Genetic restrictionof HIV-1 infection and progression to AIDS by a deletionallele of the CKR5 structural gene. Hemophilia Growth andDevelopment Study, Multicenter AIDS Cohort Study, MulticenterHemophilia Cohort Study, San Francisco City Cohort,ALIVE Study. Science 273: 1856.Drake J.W., Charlesworth B., Charlesworth D., and Crow J.F.1998. Rates of spontaneous mutation. Genetics 148: 1667.Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J.,Blumenstiel B., Higgins J., DeFelice M., Lochner A., FaggartM., Liu-Cordero S.N., Rotimi C., Adeyemo A., Cooper R.,Ward R., Lander E.S., Daly M.J., and Altshuler D. 2002. Thestructure of haplotype blocks in the human genome. Science296: 2225.Giannelli F., Anagnostopoulos T., and Green P.M. 1999. Mutationrates in humans. II. Sporadic mutation-specific rates andrate of detrimental human mutations inferred fromhemophilia B. Am. J. Hum. Genet. 65: 1580.Green P.M., Saad S., Lewis C.M., and Giannelli F. 1999. Mutationrates in humans. I. Overall and sex-specific rates obtainedfrom a population study of hemophilia B. Am. J. Hum. Genet.65: 1572.Halushka M.K., Fan J.B., Bentley K., Hsie L., Shen N., WederA., Cooper R., Lipshutz R., and Chakravarti A. 1999. Patternsof single-nucleotide polymorphisms in candidate genes forblood-pressure homeostasis. Nat. Genet. 22: 239.Hill W.G. and Robertson A. 1968. Linkage disequilibrium in finitepopulations. Theor. Appl. Genet. 38: 226.Hugot J.P., Chamaillard M., Zouali H., Lesage S., Cezard J.P.,Belaiche J., Almer S., Tysk C., O’Morain C.A., Gassull M.,Binder V., Finkel Y., Cortot A., Modigliani R., Laurent-PuigP., Gower-Rousseau C., Macry J., Colombel J.F., SahbatouM., and Thomas G. 2001. Association of NOD2 leucine-richrepeat variants with susceptibility to Crohn’s disease. Nature411: 599.International HapMap Consortium. 2003. The InternationalHapMap Project. Nature 426: 789.Jeffreys A.J., Kauppi L., and Neumann R. 2001. Intensely punctatemeiotic recombination in the class II region of the majorhistocompatibility complex. Nat. Genet. 29: 217.Jobling M.A., Hurles M.E., and Tyler-Smith C. 2004. Humanevolutionary genetics. Garland Science, New York.Johnson G.C., Esposito L., Barratt B.J., Smith A.N., Heward J.,Di Genova G., Ueda H., Cordell H.J., Eaves I.A., DudbridgeF., Twells R.C., Payne F., Hughes W., Nutland S., Stevens H.,Carr P., Tuomilehto-Wolf E., Tuomilehto J., Gough S.C.,Clayton D.G., and Todd J.A. 2001. Haplotype tagging for theidentification of common disease genes. Nat. Genet. 29: 233.Ke X., Hunt S., Tapper W., Lawrence R., Stavrides G., Ghori J.,Whittaker P., Collins A., Morris A.P., Bentley D., CardonL.R., and Deloukas P. 2004. The impact of SNP density onfine-scale patterns of linkage disequilibrium. Hum. Mol.Genet. 13: 577.Kruglyak L. and Nickerson D.A. 2001. Variation is the spice oflife. Nat. Genet. 27: 234.Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C.,Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W.,Funke R., Gage D., Harris K., Heaford A., Howland J., KannL., Lehoczky J., LeVine R., McEwan P., McKernan K.,Meldrim J., Mesirov J.P., Miranda C., Morris W., and NaylorJ., et al. (International Human Genome Sequencing Consortium).2001. Initial sequencing and analysis of the humangenome. Nature 409: 860.Lewontin R.C. 1964. The interaction of selection and linkage. I.General considerations: Heterotic models. Genetics 49: 49.Li W.D., Reed D.R., Lee J.H., Xu W., Kilker R.L., Sodam B.R.,and Price R.A. 1999. Sequence variants in the 5´ flanking regionof the leptin gene are associated with obesity in women.Ann. Hum. Genet. 63: 227.