A whole-genome association study of major determinants for host control of HIV-1.
paper
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- Authors
- Fellay, Jacques; Shianna, Kevin V; Ge, Dongliang; Colombo, Sara; Ledergerber, Bruno; Weale, Mike; Zhang, Kunlin; Gumbs, Curtis; Castagna, Antonella; Cossarizza, Andrea; Cozzi-Lepri, Alessandro; De Luca, Andrea; Easterbrook, Philippa; Francioli, Patrick; Mallal, Simon; Martinez-Picado, Javier; Miro, JosΓ© M; Obel, Niels; Smith, Jason P; Wyniger, Josiane; Descombes, Patrick; Antonarakis, Stylianos E; Letvin, Norman L; McMichael, Andrew J; Haynes, Barton F; Telenti, Amalio; Goldstein, David B
- Year
- 2007
- Journal
- Science (New York, N.Y.)
- PMID
- 17641165
- DOI
- 10.1126/science.1143767
- PMCID
- PMC1991296
Understanding why some people establish and maintain effective control of HIV-1 and others do not is a priority in the effort to develop new treatments for HIV/AIDS. Using a whole-genome association strategy, we identified polymorphisms that explain nearly 15% of the variation among individuals in viral load during the asymptomatic set-point period of infection. One of these is found within an endogenous retroviral element and is associated with major histocompatibility allele human leukocyte antigen (HLA)-B*5701, whereas a second is located near the HLA-C gene. An additional analysis of the time to HIV disease progression implicated two genes, one of which encodes an RNA polymerase I subunit. These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents.
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| Pharmacogenomics strategies to optimize treatments for multiple sclerosis: Insights from clinical research. | Grossman I et al. | β | 2017 | β |
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| Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression. | Kiguoya MW et al. | β | 2017 | β |
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| Utility of Systematic Isolation of immune cell subsets from HIV-infected individuals for miRNA profiling. | BargallΓ³ ME et al. | β | 2017 | β |
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| Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition. | Abdul-Jawad S et al. | β | 2016 | β |
| Isolation of full-length HLA-C*18:02 allele in an individual from Sub-Saharan Africa. | Shepherd BL et al. | β | 2016 | β |
| Killer-cell Immunoglobulin-like Receptor (KIR) gene profiles modify HIV disease course, not HIV acquisition in South African women. | Naranbhai V et al. | β | 2016 | β |
| Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. | Gross AM et al. | β | 2016 | β |
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| Identification of HLA-C restricted, HIV-1-specific CTL epitopes by peptide induced upregulation of HLA-C expression. | Stoll A et al. | β | 2015 | β |
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| Immunological biomarkers predict HIV-1 viral rebound after treatment interruption. | Hurst J et al. | β | 2015 | β |
| Impact of APOBEC Mutations on CD8+ T Cell Recognition of HIV Epitopes Varies Depending on the Restricting HLA. | Squires KD et al. | β | 2015 | β |
| Interferon-induced transmembrane protein-3 rs12252-C is associated with rapid progression of acute HIV-1 infection in Chinese MSM cohort. | Zhang Y et al. | β | 2015 | β |
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| Paediatric HIV infection in the 'omics era: defining transcriptional signatures of viral control and vaccine responses. | Cotugno N et al. | β | 2015 | β |
| Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. | McLaren PJ et al. | β | 2015 | β |
| Progress and promise in understanding the genetic basis of common diseases. | Price AL et al. | β | 2015 | β |
| Protective Effect of HLA-B*5701 and HLA-C -35 Genetic Variants in HIV-Positive Caucasians from Northern Poland. | Leszczyszyn-Pynka M et al. | β | 2015 | β |
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| The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals. | Perkins MR et al. | β | 2015 | β |
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| A novel Acute Retroviral Syndrome Severity Score predicts the key surrogate markers for HIV-1 disease progression. | Braun DL et al. | β | 2014 | β |
| A single nucleotide polymorphism -35 kb T>C (rs9264942) is strongly associated with psoriasis vulgaris depending on HLA-Cw(β)06. | Majorczyk E et al. | β | 2014 | β |
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| Comparative analysis of the capacity of elite suppressor CD4+ and CD8+ T cells to inhibit HIV-1 replication in monocyte-derived macrophages. | Walker-Sperling VE et al. | β | 2014 | β |
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| Distinct assembly profiles of HLA-B molecules. | Rizvi SM et al. | β | 2014 | β |
| Divergent antibody subclass and specificity profiles but not protective HLA-B alleles are associated with variable antibody effector function among HIV-1 controllers. | Lai JI et al. | β | 2014 | β |
| DNA evidence for strong genetic stability and increasing heritability of intelligence from age 7 to 12. | Trzaskowski M et al. | β | 2014 | β |
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| Evidence for an epistatic effect between TP53 R72P and MDM2 T309G SNPs in HIV infection: a cross-sectional study in women from South Brazil. | Hartwig FP et al. | β | 2014 | β |
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| Gene expression levels are a target of recent natural selection in the human genome. | Kudaravalli S et al. | β | 2009 | β |
| Genetic correlates of protection against HIV infection: the ally within. | Piacentini L et al. | β | 2009 | β |
| Genetic determinants of HIV-1 infection and progression to AIDS: immune response genes. | Kaur G et al. | β | 2009 | β |
| Genetic determinants of HIV-1 infection and progression to AIDS: susceptibility to HIV infection. | Kaur G et al. | β | 2009 | β |
| Genetics and the general physician: insights, applications and future challenges. | Knight JC | β | 2009 | β |
| Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing. | Allen AS et al. | β | 2009 | β |
| Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. | Scott LJ et al. | β | 2009 | β |
| Genome-wide association studies are coming for human infectious diseases. | Davila S et al. | β | 2009 | β |
| Genome-wide association study for empirically derived metabolic phenotypes in the Framingham Heart Study offspring cohort. | Wilcox M et al. | β | 2009 | β |
| Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). | Limou S et al. | β | 2009 | β |
| High-throughput SNP genotyping: combining tag SNPs and molecular beacons. | Barreiro LB et al. | β | 2009 | β |
| HIV-1 host interactions: integration of large-scale datasets. | Telenti A | β | 2009 | β |
| HIV and SIV infection: the role of cellular restriction and immune responses in viral replication and pathogenesis. | Williams KC et al. | β | 2009 | β |
| HIV escape from natural killer cytotoxicity: nef inhibits NKp44L expression on CD4+ T cells. | Fausther-Bovendo H et al. | β | 2009 | β |
| HIV-host interactions: a map of viral perturbation of the host system. | Pinney JW et al. | β | 2009 | β |
| HIV pathogenesis: 25 years of progress and persistent challenges. | Levy JA | β | 2009 | β |
| HLA and infectious diseases. | Blackwell JM et al. | β | 2009 | β |
| HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. | Daly AK et al. | β | 2009 | β |
| HLA-B*5701 screening prior to abacavir prescription: clinical and laboratory aspects. | Nolan D | β | 2009 | β |
| HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. | Thomas R et al. | β | 2009 | β |
| HLA-Cw*04 allele associated with nevirapine-induced rash in HIV-infected Thai patients. | Likanonsakul S et al. | β | 2009 | β |
| Host and viral factors influencing the pathogenesis of HIV-associated neurocognitive disorders. | Jayadev S et al. | β | 2009 | β |
| Host cell factors in HIV replication: meta-analysis of genome-wide studies. | Bushman FD et al. | β | 2009 | β |
| Host genetic determinants of spontaneous hepatitis C clearance. | Rauch A et al. | β | 2009 | β |
| Host genetics and HIV-1 viral load set-point in African-Americans. | Shrestha S et al. | β | 2009 | β |
| Host genetics influences on HIV type-1 disease. | Fellay J | β | 2009 | β |
| Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. | Boon AC et al. | β | 2009 | β |
| Host HLA B*allele-associated multi-clade Gag T-cell recognition correlates with slow HIV-1 disease progression in antiretroviral therapy-naΓ―ve Ugandans. | Serwanga J et al. | β | 2009 | β |
| Host sequence motifs shared by HIV predict response to antiretroviral therapy. | Dampier W et al. | β | 2009 | β |
| Human genetics and resistance to parasitic infection. | Shaw MA et al. | β | 2009 | β |
| Human genetics of infectious diseases: between proof of principle and paradigm. | AlcaΓ―s A et al. | β | 2009 | β |
| Human immunodeficiency virus type 1-specific CD8+ T-cell responses during primary infection are major determinants of the viral set point and loss of CD4+ T cells. | Streeck H et al. | β | 2009 | β |
| Immunogenetics of drug-induced skin blistering disorders. Part II: synthesis. | Bowman C et al. | β | 2009 | β |
| Impact of select immunologic and virologic biomarkers on CD4 cell count decrease in patients with chronic HIV-1 subtype C infection: results from Sinikithemba Cohort, Durban, South Africa. | Brumme Z et al. | β | 2009 | β |
| Implications of Nef: host cell interactions in viral persistence and progression to AIDS. | Arhel NJ et al. | β | 2009 | β |
| Increasing clinical virulence in two decades of the Italian HIV epidemic. | MΓΌller V et al. | β | 2009 | β |
| Infection with "escaped" virus variants impairs control of simian immunodeficiency virus SIVmac239 replication in Mamu-B*08-positive macaques. | Valentine LE et al. | β | 2009 | β |
| Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102: a bioinformatic approach to the prediction of new epitopes. | Walshe VA et al. | β | 2009 | β |
| Integrative genomics and drug development. | Lum PY et al. | β | 2009 | β |
| Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment. | Prosperi MC et al. | β | 2009 | β |
| Is systems biology the key to preventing the next pandemic? | Tisoncik JR et al. | β | 2009 | β |
| Joint analysis of tightly linked SNPs in screening step of genome-wide association studies leads to increased power. | Becker T et al. | β | 2009 | β |
| Maternal transmission of human immunodeficiency virus escape mutations subverts HLA-B57 immunodominance but facilitates viral control in the haploidentical infant. | Schneidewind A et al. | β | 2009 | β |
| NK cells in HIV-1 infection: evidence for their role in the control of HIV-1 infection. | Alter G et al. | β | 2009 | β |
| Novel approach to recognition of predicted HIV-1 Gag B3501-restricted CD8 T-cell epitopes by HLA-B3501(+) patients: confirmation by quantitative ELISpot analyses and characterisation using multimers. | Westrop SJ et al. | β | 2009 | β |
| Novel HIV-1 clade B candidate vaccines designed for HLA-B*5101(+) patients protected mice against chimaeric ecotropic HIV-1 challenge. | Roshorm Y et al. | β | 2009 | β |
| Parasite-host interaction in malaria: genetic clues and copy number variation. | Faik I et al. | β | 2009 | β |
| Personalizing antiretroviral therapy: is it a reality? | Phillips EJ et al. | β | 2009 | β |
| Prevalence and comparative characteristics of long-term nonprogressors and HIV controller patients in the French Hospital Database on HIV. | Grabar S et al. | β | 2009 | β |
| Proceedings of the first annual congress of the European association for haemophilia and allied disorders. | Gatt A et al. | β | 2009 | β |
| Proliferation, but not interleukin 2 production, of Gag-specific CD8+ T cells is associated with low HIV viremia and high CD4 counts in HIV-1-infected Chinese individuals. | Li H et al. | β | 2009 | β |
| Reciprocal recognition of an HLA-Cw4-restricted HIV-1 gp120 epitope by CD8+ T cells and NK cells. | Thananchai H et al. | β | 2009 | β |
| Role of natural killer cells in a cohort of elite suppressors: low frequency of the protective KIR3DS1 allele and limited inhibition of human immunodeficiency virus type 1 replication in vitro. | O'Connell KA et al. | β | 2009 | β |
| Seeking new pathways for HIV vaccine discovery. | Flores J | β | 2009 | β |
| Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. | Kenny EE et al. | β | 2009 | β |
| Systems-based candidate genes for human response to influenza infection. | Zhang L et al. | β | 2009 | β |
| T-cell vaccine strategies for human immunodeficiency virus, the virus with a thousand faces. | Korber BT et al. | β | 2009 | β |
| The combined effect of SNP-marker and phenotype attributes in genome-wide association studies. | Chan EK et al. | β | 2009 | β |
| The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression. | Walley NM et al. | β | 2009 | β |
| The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. | Goonetilleke N et al. | β | 2009 | β |
| The HapMap and genome-wide association studies in diagnosis and therapy. | Manolio TA et al. | β | 2009 | β |
| The HLA-B/-C haplotype block contains major determinants for host control of HIV. | Trachtenberg E et al. | β | 2009 | β |
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| The neurobiology of individual differences in complex behavioral traits. | Hariri AR | β | 2009 | β |
| The role of host genetics in the susceptibility for HIV-associated neurocognitive disorders. | Levine AJ et al. | β | 2009 | β |
| The search for protection against HIV infection. | Detels R | β | 2009 | β |
| Viral genetic determinants of nonprogressive HIV type 1 subtype C infection in antiretroviral drug-naive children. | Tzitzivacos DB et al. | β | 2009 | β |
| X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women. | Siddiqui RA et al. | β | 2009 | β |
| 25 years of HIV research on virology, virus restriction, immunopathogenesis, genes and vaccines. | Scherer E et al. | β | 2008 | β |
| Admixture as the basis for genetic mapping. | Buerkle CA et al. | β | 2008 | β |
| A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. | Liu Y et al. | β | 2008 | β |
| A HapMap harvest of insights into the genetics of common disease. | Manolio TA et al. | β | 2008 | β |
| Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. | Matthews PC et al. | β | 2008 | β |
| Comparison of population-based association study methods correcting for population stratification. | Zhang F et al. | β | 2008 | β |
| Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. | Dalmasso C et al. | β | 2008 | β |
| Doctor, why is my herpes so bad? The search continues. | Koelle DM et al. | β | 2008 | β |
| Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. | Kiwanuka N et al. | β | 2008 | β |
| Elite suppression of HIV-1 replication. | Blankson JN et al. | β | 2008 | β |
| From human genetics and genomics to pharmacogenetics and pharmacogenomics: past lessons, future directions. | Nebert DW et al. | β | 2008 | β |
| Genetic approaches to addiction: genes and alcohol. | Ducci F et al. | β | 2008 | β |
| Genetic determinants of phenotypic diversity in humans. | Rahim NG et al. | β | 2008 | β |
| Genetic factors that confer sensitivity to HAART in HIV-infected subjects: implication of a benefit of an earlier initiation of HAART. | Nakajima T et al. | β | 2008 | β |
| Genome-wide association studies for complex traits: consensus, uncertainty and challenges. | McCarthy MI et al. | β | 2008 | β |
| Genomics and biology come together to fight HIV. | Goldstein DB | β | 2008 | β |
| Getting personal about treating HIV. | Neaton JD et al. | β | 2008 | β |
| 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. | Catano G et al. | β | 2008 | β |
| HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. | Martinez-Picado J et al. | β | 2008 | β |
| HIV and chemokine binding to red blood cells--DARC matters. | Walton RT et al. | β | 2008 | β |
| HIV immunopathogenesis and strategies for intervention. | Cadogan M et al. | β | 2008 | β |
| HLA-C increases HIV-1 infectivity and is associated with gp120. | Matucci A et al. | β | 2008 | β |
| HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. | Rousseau CM et al. | β | 2008 | β |
| HLA class I-restricted T-cell responses may contribute to the control of human immunodeficiency virus infection, but such responses are not always necessary for long-term virus control. | Emu B et al. | β | 2008 | β |
| Host factors associated with outcome from primary human immunodeficiency virus-1 infection. | Telenti A et al. | β | 2008 | β |
| Host genetic determinants of HIV pathogenesis: an immunologic perspective. | Hunt PW et al. | β | 2008 | β |
| Host genetic factors and antiviral immune responses to hepatitis C virus. | Thio CL | β | 2008 | β |
| Host genetic factors that control immune responses to retrovirus infections. | Miyazawa M et al. | β | 2008 | β |
| Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. | Tang J et al. | β | 2008 | β |
| Human MHC architecture and evolution: implications for disease association studies. | Traherne JA | β | 2008 | β |
| Identification of host proteins required for HIV infection through a functional genomic screen. | Brass AL et al. | β | 2008 | β |
| Identifying host targets for drug development with knowledge from genome-wide studies: lessons from HIV-AIDS. | Winkler CA | β | 2008 | β |
| Impact of MHC class I diversity on immune control of immunodeficiency virus replication. | Goulder PJ et al. | β | 2008 | β |
| Initial spontaneous clearance and re-infection with a distinct hepatitis C virus genotype leading to chronic hepatitis C in an HIV+ intravenous drug user. | Vispo E et al. | β | 2008 | β |
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| KIR-HLA intercourse in HIV disease. | Carrington M et al. | β | 2008 | β |
| KIRigami: the case for studying NK cell receptors in SIV+ macaques. | Bimber B et al. | β | 2008 | β |
| Major trends in the imaging sciences: 2007 Eugene P. Pendergrass New Horizons Lecture. | Zerhouni EA | β | 2008 | β |
| Mapping the genetic architecture of gene expression in human liver. | Schadt EE et al. | β | 2008 | β |
| Microarray-based DNA profiling to study genomic aberrations. | Waddell N | β | 2008 | β |
| Microarray technology and applications in the arena of genome-wide association. | Grant SF et al. | β | 2008 | β |
| Mitochondrial DNA haplogroups and highly active antiretroviral therapy-related lipodystrophy. | Nasi M et al. | β | 2008 | β |
| Natural host genetic resistance to lentiviral CNS disease: a neuroprotective MHC class I allele in SIV-infected macaques. | Mankowski JL et al. | β | 2008 | β |
| Pharmacogenetics and the potential for the individualization of antiretroviral therapy. | Phillips EJ et al. | β | 2008 | β |
| Pharmacogenetics of anti-HIV drugs. | Telenti A et al. | β | 2008 | β |
| Pharmacogenetics of antiretroviral agents. | Owen A et al. | β | 2008 | β |
| Preparation for antiretroviral interruption by boosting the immune system. | Yves L | β | 2008 | β |
| Reflecting on a quarter century of HIV research. | Armitage AE et al. | β | 2008 | β |
| Revealing the architecture of gene regulation: the promise of eQTL studies. | Gilad Y et al. | β | 2008 | β |
| Role of CCL3L1-CCR5 genotypes in the epidemic spread of HIV-1 and evaluation of vaccine efficacy. | Kulkarni H et al. | β | 2008 | β |
| Special anniversary review: twenty-five years of human immunodeficiency virus research: successes and challenges. | Weiss RA | β | 2008 | β |
| STEP trial and HIV-1 vaccines inducing T-cell responses. | Hanke T | β | 2008 | β |
| T-cell responses in primary HIV-1 infection. | Streeck H et al. | β | 2008 | β |
| The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir. | Colombo S et al. | β | 2008 | β |
| The role of protective HCP5 and HLA-C associated polymorphisms in the control of HIV-1 replication in a subset of elite suppressors. | Han Y et al. | β | 2008 | β |
| The spread, treatment, and prevention of HIV-1: evolution of a global pandemic. | Cohen MS et al. | β | 2008 | β |
| The success of the genome-wide association approach: a brief story of a long struggle. | Seng KC et al. | β | 2008 | β |
| Tissue-specific genetic control of splicing: implications for the study of complex traits. | Heinzen EL et al. | β | 2008 | β |
| Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. | Chopera DR et al. | β | 2008 | β |
| Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor. | Bailey JR et al. | β | 2008 | β |
| WGAViewer: software for genomic annotation of whole genome association studies. | Ge D et al. | β | 2008 | β |
| Why is HIV a pathogen? | Forsman A et al. | β | 2008 | β |
| CCL3L1 and CCR5 influence cell-mediated immunity and affect HIV-AIDS pathogenesis via viral entry-independent mechanisms. | Dolan MJ et al. | β | 2007 | β |
| Correlates of immune protection and the development of a human immunodeficiency virus vaccine. | Letvin NL | β | 2007 | β |
| From influenza to HIV--and back? | McMichael AJ | β | 2007 | β |
| Human genetics: the hidden text of genome-wide associations. | Gibson G et al. | β | 2007 | β |
| Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. | Deeks SG et al. | β | 2007 | β |
| Systems biology and the host response to viral infection. | Tan SL et al. | β | 2007 | β |
| T cell responses to human endogenous retroviruses in HIV-1 infection. | Garrison KE et al. | β | 2007 | β |