Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS

Journal of Acquired Immune Deficiency Syndromes

Volumn 56, Issue 3, 2011, Pages 279-284

  Clerc, Sigrid Le ^a,b,c   Coulonges, Cédric ^a,c   Delaneau, Olivier ^a   Manen, Danielle Van ^d   Herbeck, Joshua T ^e   Limou, Sophie ^a,b,c,f   An, Ping ^g   Martinson, Jeremy J ^h   Spadoni, Jean Louis ^a   Therwath, Amu ⁱ   Veldink, Jan H ^j   Van Den Berg, Leonard H ^j   Taing, Lieng ^a   Labib, Taoufik ^a   Mellak, Safa ^a   Montes, Matthieu ^a   Delfraissy, Jean François ^c   Schächter, François ^a   Winkler, Cheryl ^g   Froguel, Philippe ^k,l   Mullins, James I ^e   Schuitemaker, Hanneke ^d   Zagury, Jean François ^a,b,c   more..

^a Bioinformatique et Chimie Moléculaire   (France)

^b INSERM U955   (France)

^c French National Agency for Research on AIDS and Viral Hepatitis   (France)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

^e UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^f DIF   (France)

^g SAIC FREDERICK INC   (United States)

^h UNIVERSITY OF PITTSBURGH   (United States)

ⁱ UNIVERSITÉ PARIS DESCARTES   (France)

^j UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^k INSTITUT PASTEUR DE LILLE   (France)

^l HAMMERSMITH HOSPITAL   (United Kingdom)

more..

Author keywords

AIDS; disease progression; genome wide association study; HIV 1; RICH2; SNP

Indexed keywords

CHEMOKINE RECEPTOR CXCR6; NOTCH4 RECEPTOR;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADULT; ARTICLE; CHROMOSOME 17; CHROMOSOME 6; CONTROLLED STUDY; DISEASE COURSE; EUROPE; FEMALE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC RISK; HLA SYSTEM; HUMAN; MAJOR CLINICAL STUDY; MALE; PHENOTYPE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

ACQUIRED IMMUNODEFICIENCY SYNDROME; ADULT; ALLELES; DISEASE PROGRESSION; EUROPE; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GTPASE-ACTIVATING PROTEINS; HIV LONG-TERM SURVIVORS; HUMANS; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED STATES;

EID: 79951811670     PISSN: 15254135     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAI.0b013e318204982b     Document Type: Article

References (31)

1. Dubois PC, Trynka G, Franke L, et al. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet. 2010;42: 295-302.
2. O'Donovan MC, Craddock N, Norton N, et al. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet. 2008;40:1053-1055.
3. Zeggini E, Scott LJ, Saxena R, et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008;40:638-645. (Pubitemid 351601209)
4. Fellay J, Shianna KV, Ge D, et al. A whole-genome association study of major determinants for host control of HIV-1. Science. 2007;317: 944-947. (Pubitemid 47301321)
5. Fellay J, Ge D, Shianna KV, et al. Common genetic variation and the control of HIV-1 in humans. PLoS Genet. 2009;5:e1000791.
6. Limou S, Le Clerc S, Coulonges C, et al. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). J Infect Dis. 2009; 199:419-426.
7. Le Clerc S, Limou S, Coulonges C, et al. Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). J Infect Dis. 2009;200:1194-1201.
8. Herbeck JT, Gottlieb GS, Winkler CA, et al. Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. J Infect Dis. 2010;201:618-626.
9. Dalmasso C, Carpentier W, Meyer L, et al. 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. 2008;3:e3907.
10. Pelak K, Goldstein DB, Walley NM, et al. Host determinants of HIV-1 control in African Americans. J Infect Dis. 2010;201:1141-1149.
11. van Manen D, Kootstra NA, Boeser-Nunnink B, et al. Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. AIDS. 2009;23:19-28.
12. Limou S, Coulonges C, Herbeck JT, et al. Multi-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in AIDS long-term non-progression. J Infect Dis. 2010;202:908-915.
13. Kottgen A, Pattaro C, Boger CA, et al. New loci associated with kidney function and chronic kidney disease. Nat Genet. 2010;42: 376-384.
14. Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet. 2007;80:727-739. (Pubitemid 46564409)
15. Gorlov IP, Gorlova OY, Sunyaev SR, et al. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet. 2008;82:100-112. (Pubitemid 351726083)
16. Bodmer W, Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet. 2008;40:695-701. (Pubitemid 351748875)
17. Flores-Villanueva PO, Hendel H, Caillat-Zucman S, et al. Associations of MHC ancestral haplotypes with resistance/susceptibility to AIDS disease development. J Immunol. 2003;170:1925-1929. (Pubitemid 36197411)
18. Hendel H, Caillat-Zucman S, Lebuanec H, et al. New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. J Immunol. 1999;162:6942-6946. (Pubitemid 29309424)
19. Rappaport J, Cho YY, Hendel H, et al. 32 bp CCR-5 gene deletion and resistance to fast progression in HIV-1 infected heterozygotes. Lancet. 1997;349:922-923. (Pubitemid 27139825)
20. Winkler CA, Hendel H, Carrington M, et al. Dominant effects of CCR2-CCR5 haplotypes in HIV-1 disease progression. J Acquir Immune Defic Syndr. 2004;37:1534-1538. (Pubitemid 39602345)
21. Kaslow RA, Ostrow DG, Detels R, et al. The Multicenter AIDS Cohort Study: rationale, organization, and selected characteristics of the participants. Am J Epidemiol. 1987;126:310-318. (Pubitemid 17102758)
22. Balkau B. An epidemiologic survey from a network of French Health Examination Centres, (D.E.S.I.R.): epidemiologic data on the insulin resistance syndrome [in French]. Rev Epidemiol Sante Publique. 1996;44:373-375.
23. van Es MA, Veldink JH, Saris CG, et al. Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis. Nat Genet. 2009;41:1083-1087.
24. Price AL, Patterson NJ, Plenge RM, et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904-909. (Pubitemid 44141658)
25. Marchini J, Howie B, Myers S, et al. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906-913. (Pubitemid 47014502)
26. Ge D, Zhang K,Need AC, et al.WGAViewer: software for genomic annotation of whole genome association studies. Genome Res. 2008;18:640-643. (Pubitemid 351482788)
27. Dixon AL, Liang L, Moffatt MF, et al. A genome-wide association study of global gene expression. Nat Genet. 2007;39:1202-1207. (Pubitemid 47482680)
28. Yuan HY, Chiou JJ, Tseng WH, et al. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006;34(Web Server issue):W635-W641.
29. Rebhan M, Chalifa-Caspi V, Prilusky J, et al. GeneCards: integrating information about genes, proteins and diseases. Trends Genet. 1997; 13:163. (Pubitemid 127739947)
30. Rollason R, Korolchuk V, Hamilton C, et al. A CD317/tetherin-RICH2 complex plays a critical role in the organization of the subapical actin cytoskeleton in polarized epithelial cells. J Cell Biol. 2009;184:721-736.
31. Tokarev A, Skasko M, Fitzpatrick K, et al. Antiviral activity of the interferon-induced cellular protein BST-2/tetherin. AIDS Res Hum Retroviruses. 2009;25:1197-1210.