Evolutionary Analysis of Classical HLA Class I and II Genes Suggests That Recent Positive Selection Acted on DPB1*04:01 in Japanese Population

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Kawashima, Minae ^a   Ohashi, Jun ^b   Nishida, Nao ^a,c   Tokunaga, Katsushi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

^c NATIONAL CENTER FOR GLOBAL HEALTH AND MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

HLA A ANTIGEN; HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; HLA B ANTIGEN; HLA C ANTIGEN; HLA DPB1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN;

ALLELE; ARTICLE; COMPUTER SIMULATION; GENE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC CONSERVATION; GENETIC SELECTION; GENOTYPE; HAPLOTYPE; HLA CLASS 1 GENE; HLA CLASS 2 GENE; HLA DPB1 GENE; HOMOZYGOSITY; HUMAN; JAPAN; JAPANESE; KOREA; STOCHASTIC MODEL;

ASIAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENOTYPE; HAPLOTYPES; HISTOCOMPATIBILITY ANTIGENS CLASS I; HISTOCOMPATIBILITY ANTIGENS CLASS II; HLA-A ANTIGENS; HLA-B ANTIGENS; HLA-C ANTIGENS; HLA-DP BETA-CHAINS; HLA-DQ BETA-CHAINS; HUMANS; SELECTION, GENETIC;

EID: 84867077547     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046806     Document Type: Article

References (42)

1. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, et al. (1987) The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329: 512-518.
2. Campbell RD, Trowsdale J, (1993) Map of the human MHC. Immunology today 14: 349-352.
3. Takahata N, Nei M, (1990) Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124: 967-978.
4. Takahata N, (1990) A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism. Proc Natl Acad Sci U S A 87: 2419-2423.
5. Hughes AL, Nei M, (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
6. Hughes AL, Nei M, (1989) Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc Natl Acad Sci U S A 86: 958-962.
7. Klein J, (1987) Origin of major histocompatibility complex polymorphism: the trans-species hypothesis. Hum Immunol 19: 155-162.
8. Hedrick PW, Thomson G, (1983) Evidence for balancing selection at HLA. Genetics 104: 449-456.
9. Solberg OD, Mack SJ, Lancaster AK, Single RM, Tsai Y, et al. (2008) Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol 69: 443-464.
10. Aly TA, Eller E, Ide A, Gowan K, Babu SR, et al. (2006) Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 55: 1265-1269.
11. Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, et al. (2008) Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 60: 1-18.
12. Alper CA, Larsen CE, Dubey DP, Awdeh ZL, Fici DA, et al. (2006) The haplotype structure of the human major histocompatibility complex. Hum Immunol 67: 73-84.
13. Yunis EJ, Larsen CE, Fernandez-Vina M, Awdeh ZL, Romero T, et al. (2003) Inheritable variable sizes of DNA stretches in the human MHC: conserved extended haplotypes and their fragments or blocks. Tissue Antigens 62: 1-20.
14. Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, et al. (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2: e9.
15. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, et al. (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature genetics 38: 1166-1172.
16. Awdeh ZL, Raum D, Yunis EJ, Alper CA, (1983) Extended HLA/complement allele haplotypes: evidence for T/t-like complex in man. Proc Natl Acad Sci U S A 80: 259-263.
17. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
18. Ohashi J, Naka I, Patarapotikul J, Hananantachai H, Brittenham G, et al. (2004) Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. Am J Hum Genet 74: 1198-1208.
19. Ewens WJ, (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.
20. Excoffier L, Slatkin M, (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12: 921-927.
21. Lewontin RC, (1964) The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. Genetics 49: 49-67.
22. Mitsunaga S, Kuwata S, Tokunaga K, Uchikawa C, Takahashi K, et al. (1992) Family study on HLA-DPB1 polymorphism: linkage analysis with HLA-DR/DQ and two "new" alleles. Human immunology 34: 203-211.
23. Cullen M, Erlich H, Klitz W, Carrington M, (1995) Molecular mapping of a recombination hotspot located in the second intron of the human TAP2 locus. American journal of human genetics 56: 1350-1358.
24. Djilali-Saiah I, Benini V, Daniel S, Assan R, Bach JF, et al. (1996) Linkage disequilibrium between HLA class II (DR, DQ, DP) and antigen processing (LMP, TAP, DM) genes of the major histocompatibility complex. Tissue antigens 48: 87-92.
25. Stephens M, Scheet P, (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76: 449-462.
26. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
27. Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, et al. (2005) A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am J Hum Genet 76: 634-646.
28. Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR, (2011) Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res 39: D913-919.
29. Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, et al. (2009) Mapping human genetic diversity in Asia. Science 326: 1541-1545.
30. Gjesing AP, Andersen G, Burgdorf KS, Borch-Johnsen K, Jorgensen T, et al. (2007) Studies of the associations between functional beta2-adrenergic receptor variants and obesity, hypertension and type 2 diabetes in 7,808 white subjects. Diabetologia 50: 563-568.
31. Song EY, Park MH, Kang SJ, Park HJ, Kim BC, et al. (2002) HLA class II allele and haplotype frequencies in Koreans based on 107 families. Tissue Antigens 59: 475-486.
32. Ohashi J, Naka I, Tsuchiya N, (2011) The impact of natural selection on an ABCC11 SNP determining earwax type. Mol Biol Evol 28: 849-857.
33. Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, et al. (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293: 455-462.
34. Blackwell JM, Jamieson SE, Burgner D (2009) HLA and infectious diseases. Clin Microbiol Rev 22: 370-385, Table of Contents.
35. Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, et al. (2009) A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet 41: 591-595.
36. Voight BF, Kudaravalli S, Wen X, Pritchard JK, (2006) A map of recent positive selection in the human genome. PLoS Biol 4: e72.
37. Dunbar SA, (2006) Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363: 71-82.
38. Rousset F, (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8: 103-106.
39. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
40. Watterson GA, (1978) The homozygosity test of neutrality. Genetics 88: 405-417.
41. Martin M, Mann D, Carrington M, (1995) Recombination rates across the HLA complex: use of microsatellites as a rapid screen for recombinant chromosomes. Hum Mol Genet 4: 423-428.
42. Begovich AB, McClure GR, Suraj VC, Helmuth RC, Fildes N, et al. (1992) Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. J Immunol 148: 249-258.