190 J. A. Traherne haplotype map for disease association studies in the extended human MHC. Nature Genetics, 38, 1166. Bansal, V., Bashir, A. & Bafna, V. (2007) Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Research, 17, 219. Barcellos, L.F., Sawcer, S., Ramsay, P.P., Baranzini, S.E., Thomson, G., Briggs, F. et al. (2006) Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis. Human Molecular Genetics, 15, 2813. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z. et al. (2007) High-resolution proﬁling of histone methylations in the human genome. Cell, 129, 823. Bernstein, B.E., Meissner, A. & Lander, E.S. (2007) The mammalian epigenome. Cell, 128, 669. Bjornsson, H.T., Fallin, M.D. & Feinberg, A.P. (2004) An integrated epigenetic and genetic approach to common human disease. Trends in Genetics, 20, 350. Boyle, L.H., Gillingham, A.K., Munro, S. & Trowsdale, J. (2006) Selective export of HLA-F by its cytoplasmic tail. Journal of Immunology, 176, 6464. Boyle, L.H., Traherne, J.A., Plotnek, G., Ward, R. & Trowsdale, J. (2007) Splice variation in the cytoplasmic domains of myelin oligodendrocyte glycoprotein affects its cellular localisation and transport. Journal of Neurochemistry, 102, 1853. Cabestre, F.A., Lefebvre, S., Moreau, P., Rouas-Friess, N., Dausset, J., Carosella, E.D. & Paul, P. (1999) HLA-G expression: immune privilege for tumour cells? Seminars in Cancer Biology, 9, 27. Chung, E.K., Yang, Y., Rennebohm, R.M., Lokki, M.L., Higgins, G.C., Jones, K.N., Zhou, B., Blanchong, C.A. & Yu, C.Y. (2002) Genetic sophistication of human complement components C4A and C4B and RP-C4-CYP21-TNX (RCCX) modules in the major histocompatibility complex. American Journal of Human Genetics, 71, 823. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. (2006) A high-resolution survey of deletion polymorphism in the human genome. Nature Genetics, 38, 75. Crews, D., Gore, A.C., Hsu, T.S., Dangleben, N.L., Spinetta, M., Schallert, T., Anway, M.D. & Skinner, M.K. (2007) Transgenerational epigenetic imprints on mate preference. Proceedings of the National Academy of Sciences USA, 104, 5942. De Tomaso, A.W., Nyholm, S.V., Palmeri, K.J., Ishizuka, K.J., Ludington, W.B., Mitchel, K. & Weissman, I.L. (2005) Isolation and characterization of a protochordate histocompatibility locus. Nature, 438, 454. Distante, S., Robson, K.J., Graham-Campbell, J., Arnaiz-Villena, A., Brissot, P. & Worwood, M. (2004) The origin and spread of the HFE-C282Y haemochromatosis mutation. Human Genetics, 115, 269. Dixon, A.L., Liang, L., Moffatt, M.F., Chen, W., Heath, S., Wong, K.C. et al. (2007) A genome-wide association study of global gene expression. Nature Genetics, 39, 1202. Eagle, R.A., Traherne, J.A., Ashiru, O., Wills, M.R. & Trowsdale, J. (2006) Regulation of NKG2D ligand gene expression. Human Immunology, 67, 159. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M. et al. (2006) DNA methylation proﬁling of human chromosomes 6, 20 and 22. Nature Genetics, 38, 1378. Feinberg, A.P. (2007) Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433. Fellay, J., Shianna, K.V., Ge, D., Colombo, S., Ledergerber, B., Weale, M. et al. (2007) A whole-genome association study of major determinants for host control of HIV-1. Science, 317, 944. Fellermann, K., Stange, D.E., Schaeffeler, E., Schmalzl, H., Wehkamp, J., Bevins, C.L. et al. (2006) A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. American Journal of Human Genetics, 79, 439. Flanagan, J.M., Popendikyte, V., Pozdniakovaite, N., Sobolev, M., Assadzadeh, A., Schumacher, A. et al. (2006) Intra- and interindividual epigenetic variation in human germ cells. American Journal of Human Genetics, 79, 67. Flores, M., Morales, L., Gonzaga-Jauregui, C., Dominguez-Vidana, R., Zepeda, C., Yanez, O. et al. (2007) Recurrent DNA inversion rearrangements in the human genome. Proceedings of the National Academy of Sciences USA, 104, 6099. Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851. Friaes, A., Rego, A.T., Aragues, J.M., Moura, L.F., Mirante, A., Mascarenhas, M.R. et al. (2006) CYP21A2 mutations in Portuguese patients with congenital adrenal hyperplasia: identiﬁcation of two novel mutations and characterization of four different partial gene conversions. Molecular Genetics Metabolism, 88, 58. Gherman, A., Chen, P.E., Teslovich, T.M., Stankiewicz, P., Withers, M., Kashuk, C.S., Chakravarti, A., Lupski, J.R., Cutler, D.J. & Katsanis, N. (2007) Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture. PLoS Genetics, 3, e119. Gonzalez, E., Kulkarni, H., Bolivar, H., Mangano, A., Sanchez, R., Catano, G. et al. (2005) The inﬂuence of CCL3L1 ene-containing segmental duplications on HIV-1/AIDS susceptibility. Science, 307, 1434. Greetham, D., Ellis, C.D., Mewar, D., Fearon, U., Nic An Ultaigh, S., Veale, D.J., Guesdon, F. & Wilson, A.G. (2007) Functional characterisation of NF-{kappa}B inhibitor-like protein 1 (NF{kappa}BIL1), a candidate susceptibility gene for rheumatoid arthritis. Human Molecular Genetics, 16, 3027. Gregersen, J.W., Kranc, K.R., Ke, X., Svendsen, P., Madsen, L.S., Thomsen, A.R., Cardon, L.R., Bell, J.I. & Fugger, L. (2006) Functional epistasis on a common MHC haplotype associated with multiple sclerosis. Nature, 443, 574. Guethlein, L.A., Older Aguilar, A.M., Abi-Rached, L. & Parham, P. (2007) Evolution of killer cell Ig-like receptor (KIR) genes: deﬁnition of an orangutan KIR haplotype reveals expansion of lineage III KIR associated with the emergence of MHC-C. Journal of Immunology, 179, 491. Horton, R., Gibson, R., Coggill, P., Miretti, M., Allcock, R.J., Almeida, J. et al. (2008) Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics, 60, 1. Horton, R., Wilming, L., Rand, V., Lovering, R.C., Bruford, E.A., Khodiyar, V.K. et al. (2004) Gene map of the extended human MHC. Nature Reviews. Genetics, 5, 889. Hull, J., Campino, S., Rowlands, K., Chan, M.S., Copley, R.R., Taylor, M.S. et al. (2007) Identiﬁcation of common genetic variation that modulates alternative splicing. PLoS Genetics, 3, e99. Jirtle, R.L. & Skinner, M.K. (2007) Environmental epigenomics and disease susceptibility. Nature Reviews. Genetics, 8, 253. Kapp, C. (1999) WHO warns of microbial threat. Lancet, 353, 2222. Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316, 1484. Khaja, R., Zhang, J., MacDonald, J.R., He, Y., Joseph-George, A.M., Wei, J. et al. (2006) Genome assembly comparison identiﬁes structural variants in the human genome. Nature Genetics, 38, 1413. Khakoo, S.I. & Carrington, M. (2006) KIR and disease: a model system or system of models? Immunological Reviews, 214, 186. Koeleman, B.P., Lie, B.A., Undlien, D.E., Dudbridge, F., Thorsby, E., de Vries, R.R., Cucca, F., Roep, B.O., Giphart, M.J. & Todd, J.A. (2004) Genotype effects and epistasis in type 1 diabetes and © 2008 The Author Journal compilation © 2008 Blackwell Publishing Ltd, International Journal of Immunogenetics 35, 179–192