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Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from to

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The human major histocompatibility complex (MHC) is a gene-dense region highly enriched in immune response genes. MHC genetic variation is among the highest in the human genome and is associated with both tissue transplant compatibility and many genetic disorders. Long-range (1–3 Mb) MHC haplotypes of essentially identical DNA sequence at relatively high (≥0.5%) population frequency (“genetic fixity”), called conserved extended haplotypes (CEHs), comprise roughly half of all European population haplotypes. We sequenced an aggregate of 27 kb over 580 kb in the MHC class II region from HLA-DQA2 to DAXX in 158 European haplotypes to quantify the breakdown of this genetic fixity in the centromeric portion of the MHC and to determine the representative nature within that region of eight previously fully or nearly fully sequenced “common” European haplotypes. We identified the dominant sequences of 13 European CEHs and determined where the “common” sequences did (or did not) represent related CEHs. We found patterns of shared sequence identity among different CEHs surrounded by fixed (for each CEH) but differing sequence. Our direct observational results for population haplotypes explain the mutual occurrence of CEHs and short (5–200 kb) blocks of fixed sequence detected by the statistical measure of linkage disequilibrium.

Vyšlo v časopise: Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from to. PLoS Genet 10(10): e32767. doi:10.1371/journal.pgen.1004637
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004637

Souhrn

The human major histocompatibility complex (MHC) is a gene-dense region highly enriched in immune response genes. MHC genetic variation is among the highest in the human genome and is associated with both tissue transplant compatibility and many genetic disorders. Long-range (1–3 Mb) MHC haplotypes of essentially identical DNA sequence at relatively high (≥0.5%) population frequency (“genetic fixity”), called conserved extended haplotypes (CEHs), comprise roughly half of all European population haplotypes. We sequenced an aggregate of 27 kb over 580 kb in the MHC class II region from HLA-DQA2 to DAXX in 158 European haplotypes to quantify the breakdown of this genetic fixity in the centromeric portion of the MHC and to determine the representative nature within that region of eight previously fully or nearly fully sequenced “common” European haplotypes. We identified the dominant sequences of 13 European CEHs and determined where the “common” sequences did (or did not) represent related CEHs. We found patterns of shared sequence identity among different CEHs surrounded by fixed (for each CEH) but differing sequence. Our direct observational results for population haplotypes explain the mutual occurrence of CEHs and short (5–200 kb) blocks of fixed sequence detected by the statistical measure of linkage disequilibrium.

Zdroje

1. AwdehZL, RaumD, YunisEJ, AlperCA (1983) Extended HLA/complement allele haplotypes: evidence for T/t-like complex in man. Proc Natl Acad Sci USA 80 : 259–263.

2. RaumD, AwdehZ, YunisEJ, AlperCA, GabbayKH (1984) Extended major histocompatibility complex haplotypes in type I diabetes mellitus. J Clin Invest 74 : 449–454.

3. YunisEJ, LarsenCE, Fernandez-VinaM, AwdehZL, RomeroT, 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.

4. AlperCA, LarsenCE, DubeyDP, AwdehZL, FiciDA, et al. (2006) The haplotype structure of the human major histocompatibility complex. Hum Immunol 67 : 73–84.

5. Degli-EspostiMA, LeaverAL, ChristiansenFT, WittCS, AbrahamLJ, et al. (1992) Ancestral haplotypes: conserved population MHC haplotypes. Hum Immunol 34 : 242–252.

6. DawkinsR, LeelayuwatC, GaudieriS, TayG, HuiJ, et al. (1999) Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease. Immunol Rev 167 : 275–304.

7. AlperCA, RaumD, KarpS, AwdehZL, YunisEJ (1983) Serum complement ‘supergenes’ of the major histocompatibility complex in man (complotypes). Vox Sang 45 : 62–67.

8. Yunis EJ, Zuñiga J, Larsen CE, Fernández-Viña M, Granados J, et al. (2005) Single nucleotide polymorphism blocks and haplotypes: human MHC block diversity. In: Meyers RA, editor.Encyclopedia of molecular cell biology and molecular medicine. 2nd Edition.Volume 13. Weinheim: Wiley-VCH. pp.191–215.

9. AlyTA, EllerE, IdeA, GowanK, BabuSR, et al. (2006) Multi-SNP analysis of MHC region: remarkable conservation of HLA-A1-B8-DR3 haplotype. Diabetes 55 : 1265–1269.

10. SmithWP, VuQ, LiSS, HansenJA, ZhaoLP, et al. (2006) Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 87 : 561–571.

11. BilbaoJR, CalvoB, AransayAM, Martin-PagolaA, Perez de NanclaresG, et al. (2006) Conserved extended haplotypes discriminate HLA-DR3-homozygous Basque patients with type 1 diabetes mellitus and celiac disease. Genes Immun 7 : 550–554.

12. ZhangWJ, Degli-EspostiMA, CobainTJ, CameronPU, ChristiansenFT, et al. (1990) Differences in gene copy number carried by different MHC ancestral haplotypes. Quantitation after physical separation of haplotypes by pulsed field gel electrophoresis. J Exp Med 171 : 2101–2114.

13. JongeneelCV, BriantL, UdalovaIA, SevinA, NedospasovSA, et al. (1991) Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes. Proc Natl Acad Sci USA 88 : 9717–9721.

14. RomeroV, LarsenCE, Duke-CohanJS, FoxEA, RomeroT, et al. (2007) Genetic fixity in the human major histocompatibility complex and block size diversity in the class I region including HLA-E. BMC Genet 8 : 14.

15. YunisJJ, SalazarM, DelgadoMB, AlperCA, BingDH, et al. (1993) HLA-DQA1, DQB1 and DPB1 alleles on HLA-DQ2 -⁠ and DQ9-carrying extended haplotypes. Tissue Antigens 41 : 37–41.

16. PintoC, SmithAG, LarsenCE, Fernández-ViñaM, HusainZ, et al. (2004) HLA-Cw*0409N is associated with HLA-A*2301 and HLA-B*4403-carrying haplotypes. Hum Immunol 65 : 181–187.

17. AllcockRJN, AtrazhevAM, BeckS, de JongPJ, ElliottJF, et al. (2002) The MHC haplotyping project: A resource for HLA-linked association studies. Tissue Antigens 59 : 520–521.

18. StewartCA, HortonR, AllcockRJ, AshurstJL, AtrazhevAM, et al. (2004) Complete MHC haplotype sequencing for common disease gene mapping. Genome Res 14 : 1176–1187.

19. TraherneJA, HortonR, RobertsAN, MirettiMM, HurlesME, et al. (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2: e9.

20. HortonR, GibsonR, CoggillP, MirettiM, AllcockRJ, et al. (2008) Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project. Immunogenet 60 : 1–18.

21. SzilágyiÁ, BánlakiZ, PozsonyiÉ, YunisEJ, AwdehZL, et al. (2010) Frequent occurrence of conserved extended haplotypes (CEHs) in two Caucasian populations. Mol Immunol 47 : 1899–1904.

22. CullenM, PerfettoSP, KlitzW, NelsonG, CarringtonM (2002) High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am J Hum Genet 71 : 759–776.

23. JeffreysAJ, KauppiL, NeumannR (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29 : 217–222.

24. MirettiMM, WalshEC, KeX, DelgadoM, GriffithsM, 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.

25. BaschalEE, AlyTA, JasinskiJM, SteckAK, NobleJA, et al. (2009) Defining multiple common “completely” conserved major histocompatibility complex SNP haplotypes. Clin Immunol 132 : 203–214.

26. TruedssonL, AlperCA, AwdehZL, JohansenP, Sjöholm, etal (1993) Characterization of type I complement C2 deficiency MHC haplotypes. Strong conservation of the complotype/HLA-B-region and absence of disease association due to linked class II genes. J Immunol 151 : 5856–5863.

27. TewheyR, BansalV, TorkamaniA, TopolEJ, SchorkNJ (2011) The importance of phase information for human genomics. Nat Rev Genet 12 : 215–223.

28. GuoZ, HoodL, MalkkiM, PetersdorfEW (2006) Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci USA 103 : 6964–6969.

29. RoachJC, GlusmanG, SmitAFA, HuffCD, HubleyR, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328 : 636–639.

30. RoachJC, GlusmanG, HubleyR, MontsaroffSZ, HollowayAK, et al. (2011) Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet 89 : 382–397.

31. Yang SY, Milford E, Hämmerling U, Dupont B (1987) Description of the reference panel of B-lymphoblastoid cell lines for factors of the HLA system: The B-cell line panel designed for the tenth International Histocompatibility Workshop. In Dupont B, editor. Immunobiology of HLA, Volume 1. Histocompatibility testing. Berlin: Springer-Verlag. pp.11–19.

32. DorakMT, ShaoW, MachullaHKG, LobashevskyES, TangJ, et al. (2006) Conserved extended haplotypes of the major histocompatibility complex: further characterization. Genes Immun 7 : 450–467.

33. BrowningSR, BrowningBL (2011) Haplotype phasing: existing methods and new developments. Nat Rev Genet 12 : 703–714.

34. ZúñigaJ, YuN, BarqueraR, AloscoS, OhashiM, et al. (2013) HLA class I and class II conserved extended haplotypes and their fragments or blocks in Mexicans: implications for the study of genetic diversity in admixed populations. PLoS ONE 8: e74442.

35. Hopkins KA (2000) The basic lymphocyte microcytotoxicity tests: standard and AHG enhancement. In: Hahn AB, Land GA, Strothman RM, editors.ASHI laboratory manual.Volume 1. 4th edition.Lenexa KS: American Society for Histocompatibility and Immunogenetics. pp.1–7.

36. Marcus-Bagley D, Alper CA (1992) Methods for allotyping complement proteins. In: Rose NR, de Macario EC, Fahey JL, Friedman H, Penn GM, editors. Manual of clinical laboratory immunology. 4th edition. Washington DC: American Society for Microbiology. pp.124–141.

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