Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome

Human Molecular Genetics

Volumn 13, Issue 15, 2004, Pages 1623-1632

  Tsunoda, Tatsuhiko ^a   Lathrop, G Mark ^b   Sekine, Akihiro ^a   Yamada, Ryo ^a   Takahashi, Atsushi ^a   Ohnishi, Yozo ^a   Tanaka, Toshihiro ^a   Nakamura, Yusuke ^a,c  

^a RIKEN   (Japan)

^b CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CHROMOSOME 6P; COHORT ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; EXON; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC SELECTION; GENOME; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN CELL; HUMAN GENETICS; JAPAN; MAJOR HISTOCOMPATIBILITY COMPLEX; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOMES, HUMAN, PAIR 6; GENE FREQUENCY; GENOME, HUMAN; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 4344671923     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddh177     Document Type: Article

References (45)

1. Boehnke, M. (2000) A look at linkage disequilibrium. Nat. Genet., 25, 246-247.
2. McCarthy, J.J. and Hilfiker, R. (2000) The use of single-nucleotide polymorphism maps in pharmacogenomics. Nat. Biotechnol., 18, 505-508.
3. Goldstein, D.B. (2001) Islands of linkage disequilibrium. Nat. Genet., 29, 109-111.
4. Cardon, L.R. and Bell, J.I. (2001) Association study designs for complex diseases. Nat. Rev. Genet., 2, 91-99.
5. Ozaki, K., Ohnishi, Y., Iida, A., Sekine, A., Yamada, R., Tsunoda, T., Sato, H., Hori, M., Nakamura, Y. and Tanaka, T. (2002) Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat. Genet., 32, 650-654.
6. Takei, T., Iida, A., Nitta, K., Tanaka, T., Ohnishi, Y., Yamada, R., Maeda, S., Tsunoda, T., Takeoka, S., Ito, K. et al. (2002) Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy. Am. J. Hum. Genet., 70, 781-786.
7. Suzuki, A., Yamada, R., Chang, X., Tokuhiro, S., Sawada, T., Suzuki, M., Nagasaki, M., Nakayama-Hamada, M., Kawaida, R., Ono, M. et al. (2003) Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat. Genet., 34, 395-402.
8. Tokuhiro, S., Yamada, R., Chang, X., Suzuki, A., Kochi, Y., Sawada, T., Suzuki, M., Nagasaki, M., Ohtsuki, M., Ono, M. et al. (2003) An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis. Nat. Genet., 35, 341-348.
9. Taillon-Miller, P., Bauer-Sardina, I., Saccone, N.L., Putzel, J., Laitinen, T., Cao, A., Kere, J., Pilia, G., Rice, J.P. and Kwok, P.Y. (2000) Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat. Genet., 25, 324-328.
10. Abecasis, G.R., Noguchi, E., Heinzmann, A., Traherne, J.A., Bhattacharyya, S., Leaves, N.I., Anderson, G.G., Zhang, Y., Lench, N.J., Carey, A. et al. (2001) Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet., 68, 191-197.
11. 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, 229-232.
12. Reich, D.E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R. et al. (2001) Linkage disequilibrium in the human genome. Nature, 411, 199-204.
13. Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S. et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418, 544-548.
14. 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.
15. Phillips, M.S., Lawrence, R., Sachidanandam, R., Morris, A.P., Balding, D.J., Donaldson, M.A., Studebaker, J.F., Ankener, W.M., Alfisi, S.V., Kuo, F. S. et al. (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet., 33, 382-387.
16. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet., 22, 231-238.
17. Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R. and Chakravarti, A. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet., 22, 239-247.
18. Haga, H., Yamada, R., Ohnishi, Y., Nakamura, Y. and Tanaka, T. (2002) Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190 562 genetic variations in the human genome. J. Hum. Genet., 47, 605-610.
19. Hughes, A.L., Packer, B., Welch, R., Bergen, A.W., Chanock, S.J. and Yeager, M. (2003) Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl Acad. Sci. USA, 100, 15754-15757.
20. Jeffreys, A.J., Kauppi, L. and Neumann, R. (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet., 29, 217-222.
21. Pritchard, J.K. and Przeworski, M. (2001) Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet., 69, 1-14.
22. The International HapMap Consortium (2003) The International HapMap Project. Nature, 426, 789-796.
23. Ohnishi, Y., Tanaka, T., Ozaki, K., Yamada, R., Suzuki, H. and Nakamura, Y. (2001) A high-throughput SNP typing system for genome-wide association studies. J. Hum. Genet., 46, 471-477.
24. Yamada, R., Kawakami, H., Yamaguchi, M., Tatsu, E., Sekine, A., Yamamoto, K., Nakamura, Y. and Tsunoda, T. (2001) Analysis of population structure of Japanese population using genotype data of genome wide hundreds of SNPs. 51th Annual meeting, The American Society of Human Genetics. San Diego, CA, 69 supplement, Nr. 1413.
25. Kimura, M. and Ota, T. (1974) On some principles governing molecular evolution. Proc. Natl Acad. Sci. USA, 71, 2848-2852.
26. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G. et al. (2002) A high-resolution recombination map of the human genome. Nat. Genet., 31, 241-247.
27. Zhang, J., Rowe, W.L., Clark, A.G. and Buetow, K.H. (2003) Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am. J. Hum. Genet., 73, 1073-1081.
28. Mungall, A.J., Palmer, S.A., Sims, S.K., Edwards, C.A., Ashurst, J.L., Wilming, L., Jones, M.C., Horton, R., Hunt, S.E., Scott, C.E. et al. (2003) The DNA sequence and analysis of human chromosome 6. Nature, 425, 805-811.
29. Begovich, A.B., McClure, G.R., Suraj, V.C., Helmuth, R.C., Fildes, N., Bugawan, T.L., Erlich, H.A. and Klitz, W. (1992) Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. J. Immunol., 148, 249-258.
30. Bugawan, T.L., Klitz, W., Blair, A. and Erlich, H.A. (2000) High-resolution HLA class I typing in the CEPH families: analysis of linkage disequilibrium among HLA loci. Tissue Antigens, 56, 392-404.
31. Klitz, W., Stephens, J.C., Grote, M. and Carrington, M. (1995) Discordant patterns of linkage disequilibrium of the peptide-transporter loci within the HLA class II region. Am. J. Hum. Genet., 57, 1436-1444.
32. Kochi, Y., Yamada, R., Kobayashi, K., Takahashi, A., Suzuki, A., Sekine, A., Mabuchi, A., Akiyama, F., Tsunoda, T., Nakamura, Y. et al. (2004) Analysis of single-nucleotide polymorphisms in Japanese rheumatoid arthritis patients shows additional susceptibility markers besides the classic shared epitope susceptibility sequences. Arthritis Rheum., 50, 63-71.
33. Walsh, E.C., Mather, K.A., Schaffner, S.F., Farwell, L., Daly, M.J., Patterson, N., Cullen, M., Carrington, M., Bugawan, T.L., Erlich, H. et al. (2003) An integrated haplotype map of the human major histocompatibility complex. Am. J. Hum. Genet., 73, 580-590.
34. Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y. and Ikemura, T. (2001) Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol. Evol., 53, 290-298.
35. Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith, J.D., Eberle, M.A., Kruglyak, L. and Nickerson, D.A. (2004) Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am. J. Hum. Genet., 74, 610-622.
36. Jorde, L.B., Bamshad, M. and Rogers, A.R. (1998) Using mitochondrial and nuclear DNA markers to reconstruct human evolution. Bioessays, 20, 126-136.
37. Ingman, M., Kaessmann, H., Paabo, S. and Gyllensten, U. (2000) Mitochondrial genome variation and the origin of modern humans. Nature, 408, 708-713.
38. Underhill, P.A., Shen, P., Lin, A.A., Jin, L., Passarino, G., Yang, W.H., Kauffman, E., Bonne-Tamir, B., Bertranpetit, J., Francalacci, P. et al. (2000) Y chromosome sequence variation and the history of human populations. Nat. Genet., 26, 358-361.
39. Ewing, B. and Green, P. (2000) Analysis of expressed sequence tags indicates 35 000 human genes. Nat. Genet., 25, 232-234.
40. Roest Crollius, H., Jaillon, O., Bernot, A., Dasilva, C., Bouneau, L., Fischer, C., Fizames, C., Wincker, P., Brottier, P., Quetier, F. et al. (2000) Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat. Genet., 25, 235-238.
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., McDonald, G.J. et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
42. Toomajian, C., Ajioka, R.S., Jorde, L.B., Kushner, J.P. and Kreitman, M. (2003) A method for detecting recent selection in the human genome from allele age estimates. Genetics, 165, 287-297.
43. Lewontin, R.C. (1988) On measures of gametic disequilibrium. Genetics, 120, 849-852.
44. Hartl, D.L. and Clark, A.G. (1997) Principles of population genetics. 3rd edn. Sinauer Associates, Sunderland, MA.
45. Abecasis, G.R., Cherny, S.S., Cookson, W.O. and Cardon, L.R. (2002) Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet., 30, 97-101.