Advantage of rare HLA supertype in HIV disease progression (original) (raw)
Trowsdale, J. & Campbell, R.D. Complexity in the major histocompatibility complex. Eur. J. Immunogenet.19, 45–55 (1992). ArticleCASPubMed Google Scholar
Bjorkman, P.J. & Parham, P. Structure, function, and diversity of class I major histocompatibility complex molecules. Annu. Rev. Biochem.59, 253–288 (1990). ArticleCASPubMed Google Scholar
Buus, S., Sette, A., Colon, S., Miles, C. & Grey, H.M. The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenetic peptides. Science235, 1353–1358 (1987). ArticleCASPubMed Google Scholar
Hill, A.V.S. et al. Common West African HLA antigens are associated with protection from severe malaria. Nature352, 595–600 (1991). ArticleCASPubMed Google Scholar
Little, A.M. & Parham, P. Polymorphism and evolution of HLA class I and II genes and molecules. Rev. Immunogenet.1, 105–123 (1999). CASPubMed Google Scholar
Hughes, A.L., Ota, T. & Nei, M. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol. Biol. Evol.7, 515–524 (1990). CASPubMed Google Scholar
Slatkin, M. & Muirhead, C.A. A method for estimating the intensity of overdominant selection from the distribution of allele frequencies. Genetics156, 2119–2126 (2000). CASPubMedPubMed Central Google Scholar
Hill, A.V.S. The immunogenetics of human infectious diseases. Ann. Rev. Immunol.16, 593–617 (1998). ArticleCAS Google Scholar
Propato, A. et al. Spreading of HIV-specific CD8+ T-cell repertoire in long-term nonprogressors and its role in the control of viral load and disease activity. Hum. Immunol.62, 561–576 (2001). ArticleCASPubMed Google Scholar
MacDonald, K.S. et al. Human leucocyte antigen supertypes and immune susceptibility to HIV-1, implications for vaccine design. Immunol. Lett.79, 151–157 (2001). ArticleCASPubMed Google Scholar
Bertoni, R. et al. Human histocompatibility leukocyte antigen-binding supermotifs predict broadly cross-reactive cytotoxic T lymphocyte responses in patients with acute hepatitis. J. Clin. Invest.100, 503–513 (1997). ArticleCASPubMedPubMed Central Google Scholar
Tomiyama, H., Yamada, N., Komatsu, H., Hirayama, K. & Takiguchi, M. A single CTL clone can recognize a naturally processed HIV-1 epitope presented by two different HLA class I molecules. Eur. J. Immunol.30, 2521–2530 (2000). ArticleCASPubMed Google Scholar
Altfeld, M.A. et al. Identification of novel HLA-A2-restricted human immunodeficiency virus type 1-specific cytotoxic T-lymphocyte epitopes predicted by the HLA-A2 supertype peptide-binding motif. J. Virol.75, 1301–1311 (2001). ArticleCASPubMedPubMed Central Google Scholar
Clarke, B. The ecological genetics of host-parasite relationships. in Genetic aspects of host-parasite relationships. (eds. Taylor, A.E.R. & Muller, R.M.) 87–103 (Blackwell Oxford, 1976). Google Scholar
Howard, J.C. MHC organization of the rat: evolutionary considerations. in Evolution and Vertebrate Immunity (eds. Kelsoe, G. & Schulze, D.H.) 397–411 (University of Texas Press,, Austin, 1987). Google Scholar
Trachtenberg, E.A. & Erlich, H.A. A review of the role of the human leukocyte antigen (HLA) system as a host immunogenetic factor influencing HIV transmission and course of infection with progression to AIDS. in HIV Molecular Immunology Database (eds. Korber, B. et al.) 1–60 (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM., 2001). Google Scholar
Carrington, M. et al. HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science283, 1748–1752 (1999). ArticleCASPubMed Google Scholar
Keet, I.P. et al. Consistent associations of HLA class I and II and transporter gene products with progression of human immunodeficiency virus type 1 infection in homosexual men. J. Infect. Dis.180, 299–309 (1999). ArticleCASPubMed Google Scholar
Marsh, S.G.E., Parham, P. & Barber, L.D. The HLA FactsBook398 (Academic Press, New York, 2002). Google Scholar
Sette, A. & Sidney, J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics50, 201–112 (1999). ArticleCASPubMed Google Scholar
Kaslow, R.A. et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat. Med.2, 405–411 (1996). ArticleCASPubMed Google Scholar
Hendel, H. et al. New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. J. Immunol.162, 6942–6946 (1999). CASPubMed Google Scholar
Begovich, A.B. et al. Polymorphism, recombination and linkage disequilibrium within the HLA class II region. J. Immunol.148, 249–258 (1992). CASPubMed Google Scholar
Goulder, P.J. et al. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature412, 334–338 (2001). ArticleCASPubMed Google Scholar
Rissanen, J. Stochastic Complexity in Statistical Inquiry. 171 (World Scientific (Singapore), 1989). Google Scholar
Rissanen, J. Hypothesis selection and testing by the MDL principle. Comput. J.42, 260–269 (1999). Article Google Scholar
Li, M. & Vitanyi, P. An Introduction to Kolmogorov Complexity and its Applications. 546 (Springer-Verlag (New York), 1993). Book Google Scholar
Nelson, G.W., Kaslow, R. & Mann, D.L. Frequency of HLA allele-specific peptide motifs in HIV-1 proteins correlates with the allele's association with relative rates of disease progression after HIV-1 infection. Proc. Natl. Acad. Sci. USA94, 9802–9807 (1997). ArticleCASPubMedPubMed Central Google Scholar
Anastos, K. et al. Association of race and gender with HIV-1 RNA levels and immunologic progression. J. Acquir. Immune Defic. Syndr.24, 218–226 (2000). ArticleCASPubMed Google Scholar
Phair, J. et al. Acquired immune deficiency syndrome occurring within 5 years of infection with human immune deficiency virus type-1: the Multicenter AIDS Cohort Study. J. Acquir. Immune Defic. Syndr.5, 490–496 (1992). ArticleCASPubMed Google Scholar
Saah, A.J. et al. Predictors of the risk of development of acquired immunodeficiency syndrome within 24 months among gay men seropositive for human immunodeficiency virus type 1: a report from the Multicenter AIDS Cohort Study. Am. J. Epidemiol.135, 1147–1155 (1992). ArticleCASPubMed Google Scholar
Allen, T.M. et al. _Tat_-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature407, 386–390 (2000). ArticleCASPubMed Google Scholar
van der Burg, S.H. et al. HIV-1 reverse transcriptase-specific CTL against conserved epitopes do not protect against progression to AIDS. J. Immunol.159, 3648–3654 (1997). CASPubMed Google Scholar
Moore, C.B. et al. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science296, 1439–1443 (2002). ArticleCASPubMed Google Scholar
Hill, A., Takiguchi, M. & McMichael, A. Different rates of HLA class I molecule assembly which are determined by amino acid sequence in the alpha 2 domain. Immunogenetics37, 95–101 (1993). ArticleCASPubMed Google Scholar
Williams, A., Peh, C.A. & Elliott, T. The cell biology of MHC class I antigen presentation. Tissue Antigens59, 3–17 (2002). ArticleCASPubMed Google Scholar
Boon, A.C. et al. The magnitude and specificity of influenza A virus-specific cytotoxic T-lymphocyte responses in humans is related to HLA-A and -B phenotype. J. Virol.76, 582–590 (2002). ArticleCASPubMedPubMed Central Google Scholar
Yusim, K. et al. Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J. Virol.76, 8757–8768 (2002). ArticleCASPubMedPubMed Central Google Scholar
de Groot, N.G. et al. Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc. Natl. Acad. Sci. USA99, 11748–11753 (2002). ArticleCASPubMedPubMed Central Google Scholar
Bugawan, T.L., Begovich, A.B. & Erlich, H.A. Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence specific oligonucleotide probes. Immunogenetics34, 413 (1991). ArticleCASPubMed Google Scholar
Bugawan, T.L. & Erlich, H.A. Rapid typing of HLA-DQB1 DNA polymorphism using nonradioactive oligonucleotide probes and amplified DNA. Immunogenetics33, 163–170 (1991). ArticleCASPubMed Google Scholar
Bugawan, T.L., Apple, R. & Erlich, H.A. A method for typing polymorphism at the HLA-A locus using PCR amplification and immobilized oligonucleotide probes. Tissue Antigens44, 137–147 (1994). ArticleCASPubMed Google Scholar
Scharf, S.J., Griffith, R.L. & Erlich, H.A. Rapid typing of DNA sequence polymorphism at the HLA-DRB1 locus using the polymerase chain reaction and nonradioactive oligonucleotide probes. Hum. Immunol.30, 190–201 (1991). ArticleCASPubMed Google Scholar
Erlich, H.A. & Trachtenberg E.A. PCR-based methods of HLA typing. in Molecular Epidemiology: A Practical Approach (eds. Carrington, M. & Hoelzel, A.R.) 181–207 (Oxford University Press, Oxford, 2001). Google Scholar
Cao, K. et al. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum. Immunol.62, 1009–1030 (2001). ArticleCASPubMed Google Scholar
Venables, W.N. & Ripley, B.D. Modern Applied Statistics with S-PLUS. 501 (Springer (New York), 1999). Book Google Scholar
Hope, A.C.A. A simplified Monte-Carlo significance test procedure. J. R. Stat. Soc. Ser. B, 582–598 (1968).