Complex divergence at a microsatellite marker C1-2-5 in the lineage of HLA-Cw/-B haplotype

Journal of Human Genetics

Volumn 54, Issue 4, 2009, Pages 224-229

  Shichi, Daisuke ^a   Ota, Masao ^b   Katsuyama, Yoshihiko ^c   Inoko, Hidetoshi ^d   Naruse, Taeko K ^a   Kimura, Akinori ^a  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^b SHINSHU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c SHINSHU UNIVERSITY HOSPITAL   (Japan)

^d TOKAI UNIVERSITY   (Japan)

Author keywords

C1 2 5; HLA; microsatellite; repeat motif

Indexed keywords

ARTICLE; GENE LOCUS; GENE STRUCTURE; GENETIC LINKAGE; GENETIC VARIABILITY; HAPLOTYPE; HLA SYSTEM; HUMAN; JAPANESE; MICROSATELLITE MARKER; MUTATIONAL ANALYSIS; STRUCTURE ANALYSIS;

ALLELES; ASIAN CONTINENTAL ANCESTRY GROUP; GENETIC LOCI; GENETIC VARIATION; HAPLOTYPES; HLA-B ANTIGENS; HLA-C ANTIGENS; HUMANS; JAPAN; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS; PHYLOGENY;

EID: 66349095186     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1038/jhg.2009.15     Document Type: Article

References (34)

1. Horton, R.,Wilming, L., Rand, V., Lovering, R.C., Bruford, E.A., Khodhiyar, V.K., et al. Gene map of the extended human MHC. Nat. Rev. Genet. 5, 889-899 (2004).
2. Cooke, G.S. &Hill, A.V. Genetics of susceptiblity to human infectious disease. Nat. Rev. Genet. 2, 967-977(2001).
3. Rudolph, M.G., Stanfield, R.L., Wilson, I.A., How TCRs bind MHCs, peptides, and coreceptors. Annu. Rev. Immunol. 24, 419-466 (2006).
4. Little, A.M., Parham, P., Polymorphism and evolution of HLA class I and II genes and molecules. Rev. Immunogenet. 1, 105-123 (1999).
5. Meyer, D., Single, R.M., Mack, S.J., Erlich, H.A., &Thomson, G., Signatures of demographic history and natural selection in the human major histocompatibility complex loci. Genetics. 173, 2121-2142(2006).
6. Miretti, M.M.,Walsh, E.C., Ke, X., Delgado, M., Griffiths, M., Hunt, S., et al. A high resolution linkage-disequilibrium map of the human major histocompatibility complex and first genration of tag single-nucleotide polymorphism. Am.J.Hum.Genet.76, 634-636 (2005).
7. Shichi, D., Kikkawa, E.F., Ota, M., Katsuyama, Y., Kimura, A., Matsumori, A., et al. The haplotype block, NFKBIL1-ATP6V1G2-BAT1-MICB-MICA, within the class III-class I boundary region of the human major histocompatibility complex may control susceptiblity to hepatitis C virus-associated dilated cardiomyopathy. Tissue Antigens 66, 200-208 (2005).
8. Shiina, T., Ota, M., Shimizu, S., Katsuyama, Y., Hashimoto, N., Takasu, M., et al. Rapid evolution of major histocompatability complex class I genes in primates generates new disease alleles in human via hitchhking diversity. Genetics 173, 1555-1570 (2006).
9. Ahmad, T., Neville, M., Marshall, S.E., Armuzzi, A., Mulcahy-Hawes, K., Crawshaw, J., et al. Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. Hum. Mol. Genet. 12, 647-656 (2003).
10. Horton, R., Gibson, R., Coggill, P., Mireti, M., Allcock, R.J., Almeida, J., et al. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.Immunogenetics 60, 1-8 (2008).
11. Nagy, M., Entz, P., Otremba, P., Schoenemann, C, Murphy, N. &Dapprich, J. Haplotype-specific extraction: a universal method to resolve ambiguous genotypes and detect new alleles-demonstrated on HLA-B. Tissue Antigens 69, 176-180 (2007). (Pubitemid 46174873)
12. Subirana J.A. Messeguer, X. Structural families of genomic microsatellites. Gene 408, 124-132 (2008).
13. Matsuzaka, Y, Makino, S., Nakajima, K., Tomizawa, M., Oka, A., Bahrain, S. etal. New polymorphic microsatellite markers in the human MHC class III region. Tissue Antigens 57, 397-404 (2001). (Pubitemid 32588546)
14. Matsuzaka, Y., Makino, S., Nakajima, K., Tomizawa, M., Oka, A., Kimura, M. etal. New polymorphic microsatellite markers in the human MHC class II region. Tissue Antigens 56, 492-500 (2000).
15. Foissac, A., Salhi, M. Cambon-Thomsen, A. Microsatellites in the HLA region: 1999 update. Tissue Antigens 55, 477-509 (2000).
16. Cullen, M., Malasky, M., Harding, A. &Carrington, M. High-density map of short tandem repeats across the human major histocompatibility complex. Immunogenetics 54, 900-910 (2003). (Pubitemid 36470085)
17. Malkki, M., Single, R., Carrington, M., Thomson, G. &Petersdorf, E. MHC micro-satellite diversity and linkage disequilibrium among common HLA-A, HLA-B, DRB1 haplotypes: implications for unrelated donor hematopoietic transplantation and disease association studies. Tissue Antigens 66, 114-124 (2005). (Pubitemid 41025933)
18. Mungall, A. J., Palmer, S. A., Sims, S. K., Edwards, C. A., Ashurst, J. L, Wilming, L. etal. The DNA sequence and analysis of human chromosome 6. Nature 425, 805-811 (2003).
19. Saito, S., Ota, S., Yamada, E., Inoko, H. &Ota, M. Allele frequencies and haplotypic associations defined by allelic DNA typing at HLA class I and class II loci in the Japanese population. Tissue Antigens 56, 522-529 (2000). (Pubitemid 32039363)
20. Stewart, C. A., Horton, R., Allcock, R. J., Ashurst, J. L, Atrazhev, A. M., Coggill, P. etal. Complete MHC haplotype sequencing for common disease gene mapping. Genome Res. 14, 1176-1187 (2004).
21. Lancaster, A. K., Single, R. M., Solberg, O. D., Nelson M.P. &Thomson, G. PyPop update-software pipeline for large-scale multilocus population genomics. Tissue Antigens 69(Suppl 1), 192-197 (2007).
22. Warnes G.R. The genetics package. R News 3, 9-13 (2003).
23. Schaid, D. J., Rowland, C. M., Tines, D. E., Jacobson R.M. & Poland G.A. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet. 70, 425-434 (2002). (Pubitemid 34112296)
24. Sabeti, P. C, Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner S.F. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837 (2002).
25. Hedrick P.W. Gametic disequilibrium measures: proceed with caution. Genetics 117, 331-341 (1987).
26. Cramer, H. Mathematical Methods of Statistics (Princeton University Press, Princeton, New Jersey, 1946).
27. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C, Zody, M. C, Baldwin, J. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
28. Tokunaga, K., Ishikawa, Y, Ogawa, A., Wang, H., Mitsunaga, S., Moriyama, S. et al. Sequence-based association analysis of HLA class I and II alleles in Japanese supports conservation of common haplotypes. Immunogenetics 46, 199-205 (1997). (Pubitemid 27292360)
29. Ellegren, H. Microsatellites: simple sequences with complex evolution. Wat Rev. Genet. 5, 435-445 (2004).
30. Lai, Y. Sun, F. The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol. Biol. Evol. 20, 2123-2131 (2003).
31. Boyer, J. C, Hawk, J. D., Stefanovic, L. Farber R.A. Sequence-dependent effect of interruptions on microsatellite mutation rate in mismatch repair-deficient human cells. Mutat. Res. 640, 89-96 (2008).
32. Macaubas, C, Jin, L, Hallmayer, J., Kimura, A. Mignot, E. The complex mutation pattern of a microsatellite. Genome Res. 7, 635-641 (1997).
33. Leslie, S., Donnelly, P. McVean, G. A Statistical method for predicting classical HLA alleles from SNP data. Am. J. Hum. Genet. 82, 48-56 (2008).
34. de Bakker, P. I., McVean, G., Sabeti, P. C, Miretti, M. M., Green, T, Marchini, J. etal. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. War. Genef. 38, 1166-1172 (2006).