Common genetic variation and the control of HIV-1 in humans

PLoS Genetics

Volumn 5, Issue 12, 2009, Pages

  Fellay, Jacques ^a   Ge, Dongliang ^a   Shianna, Kevin V ^a   Colombo, Sara ^b   Ledergerber, Bruno ^c   Cirulli, Elizabeth T ^a   Urban, Thomas J ^a   Zhang, Kunlin ^b,d   Gumbs, Curtis E ^a   Smith, Jason P ^a   Castagna, Antonella ^e   Cozzi Lepri, Alessandro ^f   De Luca, Andrea ^g   Easterbrook, Philippa ^h   Günthard, Huldrych F ^c   Mallal, Simon ⁱ   Mussini, Cristina ^j   Dalmau, Judith ^k   Martinez Picado, Javier ^k,l   Miro, José M ^m   Obel, Niels ⁿ   Wolinsky, Steven M ^o   Martinson, Jeremy J ^p   Detels, Roger ^q   Margolick, Joseph B ^r   Jacobson, Lisa P ^r   Descombes, Patrick ^s   Antonarakis, Stylianos E ^t   Beckmann, Jacques S ^u   O'Brien, Stephen J ^v   Letvin, Norman L ^w   McMichael, Andrew J ^x   Haynes, Barton F ^y   Carrington, Mary ^v,z   Feng, Sheng ^a   Telenti, Amalio ^b   Goldstein, David B ^a   more..

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^d INSTITUTE OF PSYCHOLOGY   (China)

^e VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

^f UNIVERSITY COLLEGE LONDON   (United Kingdom)

^g CATHOLIC UNIVERSITY   (Italy)

^h ST THOMAS HOSPITAL   (United Kingdom)

ⁱ MURDOCH UNIVERSITY   (Australia)

^j UNIVERSITY HOSPITAL OF TRIESTE   (Italy)

^k HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^l INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^m UNIVERSITY OF BARCELONA   (Spain)

ⁿ Rigshospitalet   (Denmark)

^o NORTHWESTERN UNIVERSITY   (United States)

^p UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^q UNIVERSITY OF CALIFORNIA   (United States)

^r JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^s UNIVERSITY OF GENEVA   (Switzerland)

^t UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^u LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^v NATIONAL CANCER INSTITUTE   (United States)

^w HARVARD MEDICAL SCHOOL   (United States)

^x JOHN RADCLIFFE HOSPITAL   (United Kingdom)

^y DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^z MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR; HLA ANTIGEN CLASS 1;

ADULT; ARTICLE; CHROMOSOME 3; CONTROLLED STUDY; DISEASE COURSE; DNA POLYMORPHISM; FEMALE; GENE CLUSTER; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC VARIABILITY; HEREDITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; REPORTER GENE; VIRUS LOAD; ALLELE; GENETICS; GENOTYPE; HUMAN IMMUNODEFICIENCY VIRUS 1; KAPLAN MEIER METHOD; PHENOTYPE; PHYSIOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

ADULT; ALLELES; DISEASE PROGRESSION; FEMALE; GENETIC VARIATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; KAPLAN-MEIERS ESTIMATE; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; VIRAL LOAD;

EID: 74249086566     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000791     Document Type: Article

References (40)

1. Telenti A, Bleiber G (2006) Host genetics of HIV-1 susceptibility. Future Virology 1: 55-70.
2. O'Brien SJ, Nelson GW (2004) Human genes that limit AIDS. Nat Genet 36: 565-574.
3. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, et al. (2007) A whole-genome association study of major determinants for host control of HIV-1. Science 317: 944-947.
4. Martin MP, Carrington M (2005) Immunogenetics of viral infections. Curr Opin Immunol 17: 510-516.
5. Carrington M, O'Brien SJ (2003) The influence of HLA genotype on AIDS. Annu Rev Med 54: 535-551.
6. Detels R, Liu Z, Hennessey K, Kan J, Visscher BR, et al. (1994) Resistance to HIV-1 infection. Multicenter AIDS Cohort Study. J Acquir Immune Defic Syndr 7: 1263-1269.
7. Catano G, Kulkarni H, He W, Marconi VC, Agan BK, et al. (2008) HIV-1 disease-influencing effects associated with ZNRD1, HCP5 and HLA-C alleles are attributable mainly to either HLA-A10 or HLA-B*57 alleles. PLoS ONE 3: e3636. doi:10.1371/journal.pone.0003636.
8. van Manen D, Kootstra NA, Boeser-Nunnink B, Handulle MA, van't Wout AB, et al. (2009) Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. AIDS 23: 19-28.
9. Trachtenberg E, Bhattacharya T, Ladner M, Phair J, Erlich H, et al. (2009) The HLA-B/-C haplotype block contains major determinants for host control of HIV. Genes Immun;Aug 20 [Epub ahead of print].
10. Limou S, Le Clerc S, Coulonges C, Carpentier W, Dina C, et al. (2009) Genomewide Association Study of an AIDS-Nonprogression Cohort Emphasizes the Role Played by HLA Genes (ANRS Genomewide Association Study 02). J Infect Dis 199: 419-426.
11. Dalmasso C, Carpentier W, Meyer L, Rouzioux C, Goujard C, et al. (2008) Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. PLoS ONE 3: e3907. doi:10.1371/journal.pone.0003907.
12. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
13. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. (2008) Genes mirror geography within Europe. Nature.
14. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
15. Colombo S, Rauch A, Rotger M, Fellay J, Martinez R, et al. (2008) The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir. J Infect Dis 198: 864-867.
16. 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. Nat Genet 38: 1166-1172.
17. Yuan H-Y, Chiou J-J, Tseng W-H, Liu C-H, Liu C-K, et al. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucl Acids Res 34: W635-641.
18. Telenti A, Goldstein DB (2006) Genomics meets HIV-1. Nat Rev Microbiol 4: 865-873.
19. Urban TJ, Weintrob AC, Fellay J, Colombo S, Shianna KV, et al. (2009) CCL3L1 and HIV/AIDS susceptibility. Nat Med 15: 1110-1112.
20. Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C, et al. (1996) Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382: 722-725.
21. Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, et al. (1996) Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273: 1856-1862.
22. Liu R, Paxton WA, Choe S, Ceradini D, Martin SR, et al. (1996) Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86: 367-377.
23. Martin MP, Dean M, Smith MW, Winkler C, Gerrard B, et al. (1998) Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science 282: 1907-1911.
24. Salkowitz JR, Bruse SE, Meyerson H, Valdez H, Mosier DE, et al. (2003) CCR5 promoter polymorphism determines macrophage CCR5 density and magnitude of HIV-1 propagation in vitro. Clin Immunol 108: 234-240.
25. Smith MW, Dean M, Carrington M, Winkler C, Huttley GA, et al. (1997) Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study. Science 277: 959-965.
26. Rizzardi GP, Morawetz RA, Vicenzi E, Ghezzi S, Poli G, et al. (1998) CCR2 polymorphism and HIV disease. Swiss HIV Cohort. Nat Med 4: 252-253.
27. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
28. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
29. Wang K, Li M, Bucan M (2007) Pathway-Based Approaches for Analysis of Genomewide Association Studies. Am J Hum Genet 81.
30. Han Y, Lai J, Barditch-Crovo P, Gallant JE, Williams TM, et al. (2008) The role of protective HCP5 and HLA-C associated polymorphisms in the control of HIV-1 replication in a subset of elite suppressors. AIDS 22: 541-544.
31. Shrestha S, Aissani B, Song W, Wilson CM, Kaslow RA, et al. (2009) Host genetics and HIV-1 viral load set-point in African-Americans. AIDS 23: 673-677.
32. Yoon W, Ma B, Fellay J, WH, SX, et al. (2009) A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro. AIDS In press.
33. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1: e78. doi:10.1371/journal.pgen.0010078.
34. Towers G (2007) The control of viral infection by tripartite motif proteins and cyclophilin A. Retrovirology 4: 40.
35. Schneidewind A, Brockman MA, Yang R, Adam RI, Li B, et al. (2007) Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J Virol 81: 12382-12393.
36. Gao X, Nelson GW, Karacki P, Martin MP, Phair J, et al. (2001) Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. N Engl J Med 344: 1668-1675.
37. Little J, Higgins JPT, Ioannidis JPA, Moher D, Gagnon F, et al. (2009) STrengthening the REporting of Genetic Association Studies (STREGA); An Extension of the STROBE Statement. PLoS Med 6: e22. doi:10.1371/journal.pmed. 1000022.
38. Attia J, Ioannidis JP, Thakkinstian A, McEvoy M, Scott RJ, et al. (2009) How to use an article about genetic association: B: Are the results of the study valid? JAMA 301: 191-197.
39. Brem RB, Storey JD, Whittle J, Kruglyak L (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701-703.
40. Ge D, Zhang K, Need AC, Martin O, Fellay J, et al. (2008) WGAViewer: software for genomic annotation of whole genome association studies. Genome Res 18: 640-643.