D720 Nucleic Acids Research, 2007, Vol. 35, Database issue 2. Kent,W.J., Baertsch,R., Hinrichs,A., Miller,W. and Haussler,D. (2003) Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA, 100, 11484–11489. 3. Barrett,J.C., Fry,B., Maller,J. and Daly,M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265. 4. The International HapMap Consortium. (2005) A haplotype map of the human genome. Nature, 437, 1299–1320. 5. Marchini,J., Cutler,D., Patterson,N., Stephens,M., Eskin,E., Halperin,E., Lin,S., Qin,Z., Munro,H., Abecasis,G. et al. (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am. J. Hum. Genet., 78, 437–450. 6. Stephens,M., Smith,N.J. and Donnelly,P. (2001) A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet., 68, 978–989. 7. Stephens,M. and Donnelly,P. (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet., 73, 1162–1169. 8. Tajima,F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595. 9. Akey,J.M., Eberle,M.A., Rieder,M.J., Carlson,C.S., Shriver,M.D., Nickerson,D.A. and Kruglyak,L. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol., 2, e286. 10. Stajich,J.E. and Hahn,M.W. (2005) Disentangling the effects of demography and selection in human history. Mol. Biol. Evol., 22, 63–73. 11. Hinds,D.A., Stuve,L.L., Nilsen,G.B., Halperin,E., Eskin,E., Ballinger,D.G., Frazer,K.A. and Cox,D.R. (2005) Whole-genome patterns of common DNA variation in three human populations. Science, 307, 1072–1079. 12. Jeffreys,A.J., Kauppi,L. and Neumann,R. (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genet., 29, 217–222. 13. McVean,G.A., Myers,S.R., Hunt,S., Deloukas,P., Bentley,D.R. and Donnelly,P. (2004) The fine-scale structure of recombination rate variation in the human genome. Science, 304, 581–584. 14. Crawford,D.C., Bhangale,T., Li,N., Hellenthal,G., Rieder,M.J., Nickerson,D.A. and Stephens,M. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genet., 36, 700–706. 15. 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, 29, 229–232. 16. Gabriel,S.B., Schaffner,S.F., Nguyen,H., Moore,J.M., Roy,J., Blumenstiel,B., Higgins,J., DeFelice,M., Lochner,A., Faggart,M. et al. (2002) The structure of haplotype blocks in the human genome. Science, 296, 2225–2229. 17. Thorisson,G.A., Smith,A.V., Krishnan,L. and Stein,L.D. (2005) The International HapMap Project Web site. Genome Res., 15, 1591–1593. 18. Feuk,L., Carson,A.R. and Scherer,S.W. (2006) Structural variation in the human genome. Nature Rev. Genet., 7, 85–97. 19. Botstein,D. and Risch,N. (2003) Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nature Genet., 33, 228–237. 20. Sebat,J., Lakshmi,B., Troge,J., Alexander,J., Young,J., Lundin,P., Ma˚ne´r,S., Massa,H., Walker,M., Chi,M. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525–528. 21. Albertson,D.G. and Pinkel,D. (2003) Genomic microarrays in human genetic disease and cancer. Hum. Mol. Genet., 12, R145–R152. 22. Iafrate,A.J., Feuk,L., Rivera,M.N., Listewnik,M.L., Donahoe,P.K., Qi,Y., Scherer,S.W. and Lee,C. (2004) Detection of large-scale variation in the human genome. Nature Genet., 36, 949–951. 23. Sharp,A.J., Locke,D.P., McGrath,S.D., Cheng,Z., Bailey,J.A., Vallente,R.U., Pertz,L.M., Clark,R.A., Schwartz,S., Segraves,R. et al. (2005) Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet., 77, 78–88. 24. Tuzun,E, Sharp,A.J., Bailey,J.A., Kaul,R., Morrison,V.A., Pertz,L.M., Haugen,E., Hayden,H., Albertson,D., Pinkel,D. et al. (2005) Fine-scale structural variation of the human genome. Nature Genet., 37, 727–732. 25. McCarroll,S., Hadnott,T., Perry,G., Sabeti,P., Zody,M., Barrett,J., Dallaire,S., Gabriel,S., Lee,C., Daly,M. et al. (2006) Common deletion polymorphisms in the human genome. Nature Genet., 38, 86–92. 26. Conrad,D., Andrews,T., Carter,N., Hurles,M. and Pritchard,J. (2006) A high-resolution survey of deletion polymorphism in the human genome. Nature Genet., 38, 75–81. 27. Hinds,D., Kloek,A., Jen,M., Chen,X. and Frazer,K. (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nature Genet., 38, 82–85. 28. Hinrichs,A.S., Karolchik,D., Baertsch,R., Barber,G.P., Bejerano,G., Clawson,H., Diekhans,M., Furey,T.S., Harte,R.A., Hsu,F. et al. (2006) The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res., 34, D590–D598. 29. Hudson,R.R., Kreitman,M. and Aguade,M.A. (1987) Test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153–159. 30. Fay,J.C., Wyckoff,G.J. and Wu,C.I. (2001) Positive and negative selection on the human genome. Genetics, 158, 1227–1234. 31. SeattleSNPs. NHLBI Program for Genomic Applications, SeattleSNPs, Seattle, WA, July, 2006. 32. NIEHS SNPs. NIEHS Environmental Genome Project, University of Washington, Seattle, WA, July, 2006. 33. Drake,J.A., Bird,C., Nemesh,J., Thomas,D.J., Newton-Cheh,C., Reymond,A., Excoffier,L., Attar,H., Antonarakis,S.E., Dermitzakis,E.T. et al. (2006) Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nature Genet., 38, 223–227. 34. Bailey,J., Yavor,A., Massa,H., Trask,B. and Eichler,E. (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res., 11, 1005–1017. 35. The International Human Genome Sequencing Consortium. (2003) Initial sequencing and analysis of the human genome. Nature, 409, 860–921. 36. Smit,A.F.A. and Green,P. RepeatMasker. 37. Jurka,J. (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet., 16, 418–420. 38. Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573–580. 39. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996–1006. 40. Karolchik,D., Kent,W.J., Baertsch,R., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51–54. 41. Kuhn,B., Karolchik,D., Zweig,A.S., Trumbower,H., Thomas,D.J., Thakkapallayil,A., Sugnet,C.W., Stanke,M., Smith,K.E., Siepel,A. et al. (2007) The UCSC Genome Browser Database: Update 2007. Nucleic Acids Res., (in this issue). 42. Karolchik,D., Hinrichs,A.S., Furey,T.S., Roskin,K.M., Sugnet,C.W., Haussler,D. and Kent,W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493–D496.