Structure of linkage disequilibrium in humans: Genome factors and population stratification

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 68, Issue , 2003, Pages 79-88

  Bertranpetit, J ^a   Calafell, F ^a   Comas, D ^a   Gonzalez Neira A ^a   Navarro, A ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; GENE LINKAGE DISEQUILIBRIUM; GENE LINKAGE GROUP; GENE LOCATION; GENE LOCUS; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; HAPLOTYPE; HUMAN; HUMAN GENOME; POPULATION GENETICS; PRIORITY JOURNAL; ARTICLE; GENETIC VARIATION;

EID: 3242737365     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2003.68.79     Document Type: Conference Paper

References (50)

1. Amheim N., Calabrese P., and Nordborg M. 2003. Hot and cold spots of recombination in the human genome: The reason we should find them and how this can be achieved. Am. J. Hum. Genet. 73: 5.
2. Bertranpetit J. and Calafell F. 2001. Genome versus population understanding in human population studies. In Genes, fossils and behaviour (ed. P. Donnelly and R.A. Foley), p. 49. IOS Press, Amsterdam, The Netherlands.
3. -. 2003. Genome views on human evolution. In Evolution: From molecules to ecosystems (ed. A. Moya and E. Font), p. 260. Oxford University Press, Oxford, United Kingdom.
4. Cann H.M., de Toma C., Cazes L., Legrand M.F., Morel V., Piouffre L., Bodmer J., Bodmer W.F., Bonne-Tamir B., Cambon-Thomsen A., Chen Z., Chu J., Carcassi C., Contu L., Du R., Excoffier L., Ferrara G.B., Friedlaender J.S., Groot H., Gurwitz D., Jenkins T., Herrera R.J., Huang X., Kidd J., and Kidd K.K., et al. 2002. A human genome diversity cell line panel. Science 296: 261.
5. 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. Nat. Genet. 29: 229.
6. Dawson E., Abecasis G.R., Bumpstead S., Chen Y., Hunt S., Beare D.M., Pabial J., Dibling T., Tinsley E., Kirby S., Carter D., Papaspyridonos M., Livingstone S., Ganske R., Lohmussaar E., Zemant J., Tonisson N., Remm M., Magi R., Puurand T., Vilo J., Kurg A., Rice K., Deloukas P., Mott R., Metspalu A., Bentley D.R., Cardon L.R., and Dunham I. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544.
7. DeMille M.M., Kidd J.R., Ruggeri V., Palmatier M.A., Goldman D., Odunsi A., Okonofua F., Grigorenko E., Schulz L.O., Bonne-Tamir B., Lu R.B., Parnas J., Pakstis A.J., and Kidd K.K. 2002. Population variation in linkage disequilibrium across the COMT gene considering promoter region and coding region variation. Hum. Genet. 111: 521.
8. Ding Y.C., Chi H.C., Grady D.L., Morishima A., Kidd J.R., Kidd K.K., Flodman P., Spence M.A., Schuck S., Swanson J.M., Zhang Y.P., and Moyzis R.K. 2002. Evidence of positive selection acting at the human dopamine receptor D4 gene locus. Proc. Natl. Acad. Sci. 99: 309.
9. Fullerton S.M., Bartoszewicz A., Ybazeta G., Horikawa Y., Bell G.I., Kidd K.K., Cox N.J., Hudson R.R., and Di Rienzo A. 2002. Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus. Am. J. Hum. Genet. 70: 1096.
10. Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blumenstiel B., Higgins J., DeFelice M., Lochner A., Faggart M., Liu-Cordero S.N., Rotimi C., Adeyemo A., Cooper R., Ward R., Lander E.S., Daly M.J., and Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225.
11. Gelernter J., Cubells J.F., Kidd J.R., Pakstis A.J., and Kidd K.K. 1999. Population studies of polymorphisms of the serotonin transporter protein gene. Am. J. Med. Genet. 88: 61.
12. Hastbacka J., de la Chapelle A., Kaitila I., Sistonen P., Weaver A., and Lander E. 1992. Linkage disequilibrium mapping in isolated founder populations: Diastrophic dysplasia in Finland. Nat. Genet. 23: 204.
13. Hudson R. 1990. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7: 1.
14. -. 2001. Linkage disequilibrium and recombination. In Handbook of statistical genetics (ed. D. Balding et al.), p. 309. Wiley & Sons, New York.
15. Jeffreys A.J. and Neumann R. 2002. Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat. Genet. 31: 267.
16. Kaessmann H., Zollner S., Gustafsson A.C., Wiebe V., Laan M., Lundeberg J., Uhlen M., and Paabo S. 2002. Extensive linkage disequilibrium in small human populations in Eurasia. Am. J. Hum. Genet. 70: 673.
17. Kauppi L., Sajantila A., and Jefrreys A. 2003. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum. Mol. Genet. 121: 33.
18. Kidd J.R., Pakstis A.J., Zhao H., Lu R.B., Okonofua F.E., Odunsi A., Grigorenko E., Tamir B.B., Friedlaender J., Schulz L.O., Parnas J., and Kidd K.K. 2000. Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus. PAH, in a global representation of populations. Am. J. Hum. Genet. 66: 1882.
19. Kidd K.K., Morar B., Castiglione C.M., Zhao H., Pakstis A.J., Speed W.C., Bonne-Tamir B., Lu R.B., Goldman D., Lee C., Nam Y.S., Grandy D.K., Jenkins T., and Kidd J.R. 1998. A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Hum. Genet. 103: 211.
20. Kong A., Gudbjartsson D.F., Sainz J., Jonsdottir G.M., Gudjonsson S.A., Richardsson B., Sigurdardottir S., Barnard J., Hallbeck B., Masson G., Shlien A., Palsson S.T., Frigge M.L., Thorgeirsson T.E., Gulcher J.R., and Stefansson K. 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31: 241.
21. Kruglyak L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139.
22. Laan M. and Pääbo S. 1997. Demographic history and linkage disequilibrium in human populations. Nat. Genet. 17: 435.
23. Martinez-Arias R., Calafell F., Mateu E., Comas D., Andres A., and Bertranpetit J. 2001. Sequence variability of a human pseudogene. Gen. Res. 11: 1071.
24. Mateu E., Perez-Lezaun A., Martinez-Arias R., Andres A., Valles M., Bertranpetit J., and Calafell F. 2002. PKLR-GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldwide populations. Hum. Genet. 110: 532.
25. Mateu E., Calafell F., Lao O., Bonne-Tamir B., Kidd J.R., Pakstis A., Kidd K.K., and Bertranpetit J. 2001. Worldwide genetic analysis of the CFTR region. Am. J. Hum. Genet. 68: 103.
26. Meng Z., Zaykin D.V., Xu C.F., Wagner M., and Ehm M.G. 2003. Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am. J. Hum. Genet. 73: 115.
27. Navarro A. and Barton N.H. 2002. The effect of multilocus balancing selection on neutral variability. Genetics 161: 849.
28. Navarro A., Betran E., Zapata C., and Ruiz A. 1996. Dynamics of gametic disequilibria between loci linked to chromosome inversions: The recombination redistributing effect of inversions. Genet. Res. 67: 67.
29. Nordborg M. and Tavare S. 2002. Linkage disequilibrium: What history has to tell us. Trends Genet. 18: 83.
30. Osier M.V., Pakstis A.J., Soodyall H., Comas D., Goldman D., Odunsi A., Okonofua F., Parnas J., Schulz L.O., Bertranpetit J., Bonne-Tamir B., Lu R.B., Kidd J.R., and Kidd K.K. 2002. A global perspective on genetic variation at the ADH genes reveals unusual patterns of linkage disequilibrium and diversity. Am. J. Hum. Genet. 71: 84.
31. Patil N., Berno A.J., Hinds D.A., Barrett W.A., Doshi J.M., Hacker C.R., Kautzer C.R., Lee D.H., Marjoribanks C., Mc-Donough D.P., Nguyen B.T., Norris M.C., Sheehan J.B., Shen N., Stem D., Stokowski R.P., Thomas D.J., Trulson M.O., Vyas K.R., Frazer K.A., Fodor S.P., and Cox D.R. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719.
32. Pérez-Lezaun A., Calafell F., Mateu E., Comas D., Ruiz-Pacheco R., and Bertranpetit J. 1997. Microsatellite variation and the differentiation of modern humans. Hum. Genet. 99: 1.
33. Pritchard J.K. 2001. Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69: 124.
34. Pritchard J. and Przeworski M. 2001. Linkage disequilibrium in humans: Models and data. Am. J. Hum. Genet. 69: 1.
35. Przeworski M. and Wall J.D. 2001. Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77: 143.
36. Przeworski M., Hudson R.R., and Di Rienzo A. 2000. Adjusting the focus on human variation. Trends Genet. 16: 296.
37. Reich D.E., and Lander E.S. 2001. On the allelic spectrum of human disease. Trends Genet. 17: 502.
38. Reich D.E., Schaffner S.F., Daly M.J., McVean G., Mullikin J.C., Higgins J.M., Richter D.J., Lander E.S., and Altshuler D. 2002. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32: 135.
39. Reich D.E., Cargill M., Bolk S., Ireland J., Sabeti P.C., Richter D.J., Lavery T., Kouyoumjian R., Farhadian S.F., Ward R., and Lander E.S. 2001. Linkage disequilibrium in the human genome. Nature 411: 199.
40. Romualdi C., Balding D., Nasidze I.S., Risch G., Robichaux M., Sherry S.T., Stoneking M., Batzer M.A., and Barbujani G. 2002. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res. 12: 602.
41. Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., Mc-Donald G.J., Ackerman H.C., Campbell S.J., Altshuler D., Cooper R., Kwiatkowski D., Ward R., and Lander E.S. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832.
42. Stumpf M.P. 2002. Haplotype diversity and the block structure of linkage disequilibrium. Trends Genet. 18: 226.
43. Tishkoff S.A., Dietzsch E., Speed W., Pakstis A.J., Kidd J.R., Cheung K., Bonne-Tamir B., Santachiara-Benerecetti A.S., Moral P., and Krings M. 1996. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380.
44. Tishkoff S.A., Goldman A., Calafell F., Speed W.C., Deinard A.S., Bonne-Tamir B., Kidd J.R., Pakstis A.J., Jenkins T., and Kidd K.K. 1998. A global haplotype analysis of the myotonic dystrophy locus: Implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am. J Hum. Genet. 62: 1389.
45. Tishkoff S.A., Pakstis A.J., Stoneking M., Kidd J.R., Destro-Bisol G., Sanjantila A., Lu R.B., Deinard A.S., Sirugo G., Jenkins T., Kidd K.K., and Clark A.G. 2000. Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: Implications for modem human origins. Am. J. Hum. Genet. 67: 901.
46. Tishkoff S.A., Varkonyi R., Cahinhinan N., Abbes S., Argyropoulos G., Destro-Bisol G., Drousiotou A., Dangerfield B., Lefranc G., Loiselet J., Piro A., Stoneking M., Tagarelli A., Tagarelli G., Touma E.H., Williams S.M., and Clark A.G. 2001. Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293: 455.
47. Wall J.D. and Pritchard J.K. 2003a. Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73: 502.
48. -. 2003b. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4: 587.
49. Zhang K., Calabrese P., Nordborg M., and Sun F. 2002. Haplotype block structure and its applications to association studies: Power and study designs. Am. J. Hum. Genet. 71: 1386.
50. Zhang K., Akey J.M., Wang N., Xiong M., Chakraborty R., and Jin L. 2003. Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: An act of genetic drift. Hum. Genet. 113: 51.