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Djataou P, Djuidje Ngounoue M, Nkenfou-Tchinda CN, Ngoufack MN, Elong E, Tiga A, Muluh C, Kadji Kameni J, Djaouda M, Ndjolo A, Nkenfou CN. Low prevalence of HIV in the northern Cameroon: contribution of some AIDS restriction genes and potential implications for gene therapy. Front Genet 2024; 15:1447971. [PMID: 39346778 PMCID: PMC11427317 DOI: 10.3389/fgene.2024.1447971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/22/2024] [Indexed: 10/01/2024] Open
Abstract
Background HIV infection and its progression to AIDS depend on several factors including host genetic factors. The immunological mechanisms of host resistance to HIV infection greatly influence the prevalence of HIV in a given region. Worldwide, Cameroon not exempted, the frequency of AIDS-associated genes varies and may influence this prevalence. The North and Far North Regions of Cameroon have had the lowest HIV prevalence in the country for many years despite risky behaviors associated with their customs and habits. In this work, we seek to explore the contribution of host genes to the HIV low prevalence in these regions. Methodology Five genes variants previously described as HIV AIDS related were studied. These genes are: CCR5Δ32, CCR5promoter59029G, CCR2-64I, SDF1-3'A and Trim5α(R136Q). A total of 384 consented participants were included in this study. The HIV serological status was confirmed using national algorithm. Genomic DNA was extracted from the buffy coats and used for genotyping. The results obtained were compiled in Excel 2016, Epi Info 7.1 and snpStats software and Chi two tests allowed us to compare the frequencies of the AIDS related alleles in the North with those in other Regions of Cameroon and to measure the impact of these ARGs on protection against HIV. Results The frequency of protective alleles CCR5Δ32, CCR5promoter59029G, CCR2-64I, SDF1-3'A and Trim5α(R136Q) was the allelic frequencies should be expressed as percentages i.e. 0.52%; 37.56%; 36.46%; 25.19% and 69.33%. These allelic frequencies exhibited a significant difference when compared to those obtained in other regions of Cameroon (p < 0.01). Protective alleles were predominant in the Northern region compared to others and were associated with resistance to HIV [(p < 0.0001); OR = 2.02 CI, 95%]. Conclusion The higher frequency of HIV-protective alleles in the northern regions may be a contributing factor to the lower prevalence of HIV. Nevertheless, this should be reinforced by other preventive and surveillance methods to guarantee the sustained low prevalence. HIV can develop resistance through the process of mutation, but the host targets themselves are genetically stable. The study of these host genetic restriction factors is of great value in the design of a practical cure for HIV infection or an effective vaccine.
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Affiliation(s)
- Patrice Djataou
- Chantal BIYA International Reference Center (CBIRC), Yaounde, Cameroon
- Department of Biochemistry, Faculty of Science, University of Yaounde I, Yaounde, Cameroon
| | | | - Carine Nguefeu Nkenfou-Tchinda
- Department of Biochemistry, Faculty of Medicine and Pharmaceutical Sciences of Sangmelima, Ebolowa University, Sangmelima, Cameroon
| | | | - Elise Elong
- Chantal BIYA International Reference Center (CBIRC), Yaounde, Cameroon
| | - Aline Tiga
- Chantal BIYA International Reference Center (CBIRC), Yaounde, Cameroon
| | | | | | - Moussa Djaouda
- Department of Life and Earth Sciences, University of Maroua, Maroua, Cameroon
| | - Alexis Ndjolo
- Chantal BIYA International Reference Center (CBIRC), Yaounde, Cameroon
| | - Celine Nguefeu Nkenfou
- Chantal BIYA International Reference Center (CBIRC), Yaounde, Cameroon
- Department of Biological Sciences, Higher Teachers Training College, Yaounde, Cameroon
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Korayem OH, Ahmed AE, Meabed MH, Magdy DM, Abdelghany WM. Genetic clues to COVID-19 severity: exploring the stromal cell-derived factor-1/CXCL12 rs2839693 polymorphism in adult Egyptians. BMC Infect Dis 2023; 23:702. [PMID: 37858116 PMCID: PMC10588266 DOI: 10.1186/s12879-023-08691-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND A novel corona virus called SARS-CoV-2 was identified at the end of December 2019, and the illness induced by it was designated as coronavirus disease 2019 (COVID-19). Severity of the disease could vary significantly since most of the infected individuals experience mild to moderate respiratory symptoms and recover without specialized care. Genetic polymorphisms have implications in influencing the varying degrees of COVID-19 severity. This study aims to assess the potential association between the CXCL12 rs2839693 polymorphism and the severity of COVID-19 in Assiut University Quarantine Hospital during the period from May 2022 to August 2022. METHODS The present study is a cross-sectional study and is applied to 300 COVID-19 patients confirmed by RT-PCR admitted to Assiut University Quarantine Hospital from May 2022 to August 2022. Based on the clinical symptoms, the recruited participants had been divided into two groups. Group I involved mild or moderate cases; Group II involved severe or critical conditions. The rs2839693 polymorphism was detected by real time PCR using TaqMan assay probe. RESULTS The frequency of the T allele and the TT genotype was significantly higher in the severe or critical group compared with the mild or moderate group (p value < 0.001). C-reactive protein (CRP) and D-dimers are significantly elevated in the combined variants (CT + TT) and the TT compared with the CC (P value 0.006 and 0.017 respectively) and the CC,CT genotypes (p value 0.019 and 0.002 respectively). The combined variants (CT + TT) of CXCL12 were found to be independent predictors to severe or critical COVID-19 risk with P value = < 0.001, OR = 3.034& 95% CI = 1.805-5.098. CONCLUSION Our findings revealed that CXCL12 rs2839693 had a role in the development and seriousness of COVID-19. Patients with the TT genotype or the T allele at increased risk developed severe or critical rather than mild or moderate disease.
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Affiliation(s)
- Osama H Korayem
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Amr E Ahmed
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt.
| | - Mohamed H Meabed
- Department of Pediatrics,Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Doaa M Magdy
- Department of Chest Disease and Tuberculosis, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Wafaa M Abdelghany
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
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Endogenous Peptide Inhibitors of HIV Entry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:65-85. [DOI: 10.1007/978-981-16-8702-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gomez D, Power C, Fujiwara E. Neurocognitive Impairment and Associated Genetic Aspects in HIV Infection. Curr Top Behav Neurosci 2018; 50:41-76. [PMID: 30523615 DOI: 10.1007/7854_2018_69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
HIV enters the central nervous system (CNS) early after infection. HIV-associated neurocognitive disorders (HAND) remain a serious complication of HIV infection despite available antiretroviral therapy (ART). Neurocognitive deficits observed in HAND are heterogeneous, suggesting a variability in individuals' susceptibility or resiliency to the detrimental CNS effects of HIV infection. This chapter reviews primary host genomic changes (immune-related genes, genes implicated in cognitive changes in primary neurodegenerative diseases), epigenetic mechanisms, and genetic interactions with ART implicated in HIV progression or HAND/neurocognitive complications of HIV. Limitations of the current findings include diversity of the HAND phenotype and limited replication of findings across cohorts. Strategies to improve the precision of future (epi)genetic studies of neurocognitive consequences of HIV infection are offered.
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Affiliation(s)
- Daniela Gomez
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Christopher Power
- Departments of Psychiatry and Medicine, University of Alberta, Edmonton, AB, Canada
| | - Esther Fujiwara
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada.
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5
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Ding J, Zhao J, Zhou J, Li X, Wu Y, Ge M, Cen S. Association of gene polymorphism of SDF1(CXCR12) with susceptibility to HIV-1 infection and AIDS disease progression: A meta-analysis. PLoS One 2018; 13:e0191930. [PMID: 29420545 PMCID: PMC5805253 DOI: 10.1371/journal.pone.0191930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/15/2018] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES Genetic polymorphism of viral receptors is relevant to risks of HIV-1 infection, while it is still under debated whether the polymorphism of SDF1, a unique ligand for HIV-1 coreceptor CXCR4, is associated with HIV susceptibility and AIDS disease progression. Therefore, we provided an updated quantitative assessment by meta-analysis from 16 case-control and 7 cohort studies. METHODS Articles reporting the relationship between SDF1 polymorphism and HIV susceptibility or AIDS progression were retrieved from PubMed, Embase and Ovid electronic databases up to Apr 2017. Data were pooled by odds ratios (ORs) for HIV-1 infection with 95% confidence intervals (CIs) and summary relative hazards (RHs) for AIDS progression with 95% CIs using 1987 Center for Disease Control (CDC) case definition of AIDS (CDC87) and 1993 Center for Disease Control (CDC) case definition of AIDS (CDC93) and death as endpoints. RESULTS As a result, 16 studies regarding susceptibility to HIV-1 infection with 2803 HIV-infected patients and 3697 healthy individuals and 7 studies regarding disease progression with 4239 subjects were included in the meta-analysis. For risks of infection, no evidences indicated SDF1 polymorphism was associated with the risk of HIV-1 infection in all genetic models (recessive model: OR = 0.94, 95% Cl: 0.75-1.17; homozygous model: OR = 0.89, 95% Cl: 0.70-1.15; heterozygous model: OR = 1.06, 95% Cl: 0.83-1.35; allele model: OR = 0.95, 95% Cl: 0.79-1.13), Furthermore, we failed to find an delayed AIDS progression except in some specific cohorts including MACS cohorts (RH = 0.38, 95% Cl: 0.17-0.59 for time to AIDS; RH = 0.27, 95% Cl: 0.07-0.46 for time to death at the study entry). CONCLUSIONS Overall, no significant association was found between SDF1 polymorphism and HIV susceptibility. A protective effect of SDF1 on AIDS progression and death was seen especially in two studies based on the same cohorts. In conclusion, SDF1 polymorphism exerts a moderate protective effect against AIDS disease deterioration in some specific populations.
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Affiliation(s)
- Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
| | - Yanbin Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
| | - Mei Ge
- School of Pharmacy, Shanghai Jiaotong University, Shanghai, PR China
- * E-mail: (SC); (MG)
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical School, Beijing, PR China
- * E-mail: (SC); (MG)
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Khalid S, Hanif R. Association of rs1801157 single nucleotide polymorphism of CXCL12 gene in breast cancer in Pakistan and in-silico expression analysis of CXCL12-CXCR4 associated biological regulatory network. PeerJ 2017; 5:e3822. [PMID: 28929029 PMCID: PMC5602684 DOI: 10.7717/peerj.3822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
Background C-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and tumorigenesis. The single nucleotide polymorphism (SNP) rs1801157 of CXCL12 gene has been found to be associated with higher risk of BC. Methods Our study focuses on the genotypic and allelic distribution of SNP (rs1801157; G/A) in Pakistani population as well as its association with the clinico-pathological features. The association between rs1801157 genotypes (G/A) and BC risks was assessed by a multivariate logistic regression (MLR) analysis. Genotyping was performed in both healthy individuals and patients of BC using PCR-restriction fragment length polymorphism (PCR-RFLP) method. Furthermore, in-silico approaches were adapted to investigate the association of CXCL12 and its receptor CXCR4 with genes/proteins involved in BC signalling. Results Significant differences in allelic and genotypic distribution between BC patients and healthy individuals of genotype (G/G) and (A/G) (p < 0.05) were observed. The frequency of the allele G in the BC group (77%) was significantly higher as compared to control group (61%) (p = 0.01). The association of genotype GG with clinico-pathological features including age, stages of cancer and organ (lung, liver, bones and brain) metastasis (p > 0.05) was assessed. In a MLR analysis, a number of variables including age, weight of an individual, affected lymph nodes, hormonal status (estrogen and progesterone receptor), alcohol consumption and family history associated with the GG genotype (GG:AA, odds ratio (OR) = 1.30, 95% CI [1.06–1.60]) were found to be independent risk factors for BC. Our in-vitro results suggest that genotype GG is possibly increasing the risk of BC in Pakistani cohorts. in-silico analysis finds that CXCL12–CXCR4 is associated with an increased expression of PDZK1, PI3k and Akt which lead the breast tumor towards metastasis. Conclusion Multiple targets such as CXCL12, CXCR4, PDZK1, PI3k and Akt can be inhibited in combined strategies to treat BC metastasis.
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Affiliation(s)
- Samra Khalid
- Atta-ur-Rahman School of Applied Biosciences (ASAB)/Assistant Professor/Healthcare Biotechnology, National University of Science and Technology, Islamabad, Pakistan
| | - Rumeza Hanif
- Atta-ur-Rahman School of Applied Biosciences (ASAB)/Assistant Professor/Healthcare Biotechnology, National University of Science and Technology, Islamabad, Pakistan
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Pineda-Tenor D, Jiménez-Sousa MA, Rallón N, Berenguer J, Soriano V, Aldámiz-Echevarria T, García-Álvarez M, Diez C, Fernández-Rodríguez A, Benito JM, Resino S. Short Communication: CXCL12 rs1029153 Polymorphism Is Associated with the Sustained Virological Response in HIV/Hepatitis C Virus-Coinfected Patients on Hepatitis C Virus Therapy. AIDS Res Hum Retroviruses 2016; 32:226-31. [PMID: 26499461 DOI: 10.1089/aid.2015.0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The immune response against HIV and hepatitis C virus (HCV) infection partly depends on chemokine-mediated recruitment of specific T cells. CXCL12 polymorphisms have been associated with AIDS progression and survival, but there are no data related to HCV infection. The aim of this study was to determine whether CXCL12 polymorphisms are related so as to achieve sustained virological response (SVR) after HCV therapy with pegylated-interferon-alpha/ribavirin (pegIFN-α/ribavirin) in HIV/HCV-coinfected patients. We carried out a retrospective study in 319 naive patients who started HCV treatment. The CXCL12 (rs266093, rs1029153, and rs1801157) and IL28B (rs12980275) polymorphisms were genotyped by using the GoldenGate assay. Genetic data were analyzed under an additive inheritance model. The overall rates of the SVR were 54.9% (175/319) and 41.5% (90/217) in GT1/4 patients and 83.2% (84/101) in GT2/3 patients. Patients with a favorable CXCL12 rs1029153 T allele had higher SVR rates than patients with the rs1029153 CC genotype (44% CC, 49% CT, and 61.3% TT; p = 0.025). No significant results for the rs266093 and rs1801157 polymorphisms were found. Patients harboring the favorable rs1029153 T allele had significantly increased odds of achieving SVR [adjusted odds ratio (aOR) = 1.55; 95% confidence interval (95% CI) = 1.01; 2.40; p = 0.047]. Moreover, no significant association was found when the study population was stratified by HCV genotype (data not shown), possibly due to the low number of patients in each group. In conclusion, in this study we found that the favorable CXCL12 rs1029153 T allele seems to be related so as to achieve an SVR in HIV/HCV-coinfected patients on pegIFN-α/ribavirin therapy.
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Affiliation(s)
- Daniel Pineda-Tenor
- Servicio de Laboratorio Clínico, Hospital Universitario de Fuenlabrada, Madrid, Spain
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María A. Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Norma Rallón
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Berenguer
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IIS-GM), Madrid, Spain
| | - Vicente Soriano
- Servicio de Enfermedades Infecciosas, Hospital Carlos III, Madrid. Spain
- Servicio de Medicina Interna, Hospital Universitario La Paz, Madrid. Spain
| | - Teresa Aldámiz-Echevarria
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IIS-GM), Madrid, Spain
| | - Mónica García-Álvarez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Diez
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Jose Miguel Benito
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid, Madrid, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PIW, Zagury JF, Fellay J. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog 2013; 9:e1003515. [PMID: 23935489 PMCID: PMC3723635 DOI: 10.1371/journal.ppat.1003515] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS, although in generally small samples. Under the auspices of the International Collaboration for the Genomics of HIV, we have combined the genome-wide single nucleotide polymorphism (SNP) data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets (a list of all collaborators appears in Note S1 in Text S1). After imputation using the 1,000 Genomes Project reference panel, we tested approximately 8 million common DNA variants (SNPs and indels) for association with HIV-1 acquisition in 6,334 infected patients and 7,247 population samples of European ancestry. Initial association testing identified the SNP rs4418214, the C allele of which is known to tag the HLA-B*57:01 and B*27:05 alleles, as genome-wide significant (p = 3.6×10−11). However, restricting analysis to individuals with a known date of seroconversion suggested that this association was due to the frailty bias in studies of lethal diseases. Further analyses including testing recessive genetic models, testing for bulk effects of non-genome-wide significant variants, stratifying by sexual or parenteral transmission risk and testing previously reported associations showed no evidence for genetic influence on HIV-1 acquisition (with the exception of CCR5Δ32 homozygosity). Thus, these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size. Comparing the frequency differences between common DNA variants in disease-affected cases and in unaffected controls has been successful in uncovering the genetic component of multiple diseases. This approach is most effective when large samples of cases and controls are available. Here we combine information from multiple studies of HIV infected patients, including more than 6,300 HIV+ individuals, with data from 7,200 general population samples of European ancestry to test nearly 8 million common DNA variants for an impact on HIV acquisition. With this large sample we did not observe any single common genetic variant that significantly associated with HIV acquisition. We further tested 22 variants previously identified by smaller studies as influencing HIV acquisition. With the exception of a deletion polymorphism in the CCR5 gene (CCR5Δ32) we found no convincing evidence to support these previous associations. Taken together these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.
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Affiliation(s)
- Paul J. McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cédric Coulonges
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Stephan Ripke
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Andrea Cossarizza
- Department of Surgery, Medicine, Dentistry and Morphological Sciences University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Olivier Delaneau
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Institute of Clinical infectious Diseases, Università Cattolica del Sacro Cuore, Roma, Italy
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Olivier Lambotte
- INSERM U1012, Bicêtre, France
- University Paris-Sud, Bicêtre, France
- AP-HP, Department of Internal Medicine and Infectious Diseases, Bicêtre Hospital, Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Institute for Immunology & Infectious Diseases, Murdoch University and Pathwest, Perth, Australia
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laurence Meyer
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- Inserm, CESP U1018, University Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud; AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, France
| | - José M. Miro
- Infectious Diseases Service. Hospital Clinic – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Niels Obel
- Department of Infectious Diseases, The National University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Division of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francis A. Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University, School of Medicine & San Raffaele Scientific Institute, Milan, Italy
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Pierre Rucart
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Manj S. Sandhu
- Genetic Epidemiology Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Non-Communicable Disease Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Patrick R. Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ioannis Theodorou
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- INSERM UMRS 945, Paris, France
| | - Fredrik Vannberg
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Center for Cancer Research, NCI, SAIC-Frederick, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - David B. Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Paul I. W. de Bakker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Genetics Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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9
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Selvaraj P, Alagarasu K, Singh B. Stromal cell-derived factor-1 (SDF-1/CXCL12) gene polymorphisms in pulmonary tuberculosis patients of south India. Int J Immunogenet 2011; 39:26-31. [DOI: 10.1111/j.1744-313x.2011.01059.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population. AIDS 2011; 25:513-8. [PMID: 21160409 DOI: 10.1097/qad.0b013e328343817b] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To date, CCR5 variants remain the only human genetic factors to be confirmed to impact HIV-1 acquisition. However, protective CCR5 variants are largely absent in African populations, in which sporadic resistance to HIV-1 infection is still unexplained. We investigated whether common genetic variants associate with HIV-1 susceptibility in Africans. METHODS We performed a genome-wide association study (GWAS) in a population of 1532 individuals from Malawi, a country with high prevalence of HIV-1 infection. Using single-nucleotide polymorphisms (SNPs) present on the genome-wide chip, we also investigated previously reported associations with HIV-1 susceptibility or acquisition. Recruitment was coordinated by the Center for HIV/AIDS Vaccine Immunology at two sexually transmitted infection clinics. HIV status was determined by HIV rapid tests and nucleic acid testing. RESULTS After quality control, the population consisted of 848 high-risk seronegative and 531 HIV-1 seropositive individuals. Logistic regression testing in an additive genetic model was performed for SNPs that passed quality control. No single SNP yielded a significant P value after correction for multiple testing. The study was sufficiently powered to detect markers with genotype relative risk 2.0 or more and minor allele frequencies 12% or more. CONCLUSION This is the first GWAS of host determinants of HIV-1 susceptibility, performed in an African population. The absence of any significant association can have many possible explanations: rarer genetic variants or common variants with weaker effect could be responsible for the resistance phenotype; alternatively, resistance to HIV-1 infection might be due to nongenetic parameters or to complex interactions between genes, immunity and environment.
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11
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Wang B, Suo P, Chen B, Wei Z, Yang L, Zhou S, Wang J, Cao Y, Ma X. Haplotype analysis of chemokine CXCL12 polymorphisms and susceptibility to premature ovarian failure in Chinese women. Hum Reprod 2011; 26:950-4. [DOI: 10.1093/humrep/der001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Farouk S, Rader DJ, Reilly MP, Mehta NN. CXCL12: a new player in coronary disease identified through human genetics. Trends Cardiovasc Med 2010; 20:204-9. [PMID: 22137643 PMCID: PMC3235407 DOI: 10.1016/j.tcm.2011.08.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) of more than 100,000 people have revealed novel loci associated with coronary artery disease and myocardial infarction that present exciting opportunities to discover novel disease pathways. One such recently identified locus is on chromosome 10q11, near the gene for the chemokine CXCL12, which has been implicated in cardiovascular disease in both mouse and human studies. These GWAS demonstrate that CXCL12 may emerge as a potential therapeutic target for atherosclerosis and thrombosis.
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Affiliation(s)
| | - Daniel J. Rader
- Cardiovascular Institute, Philadelphia, PA
- Institute of Diabetes, Obesity and Metabolism, Philadelphia, PA
- Institute for Translational Medicine and Therapeutics, Philadelphia, PA
| | - Muredach P. Reilly
- Cardiovascular Institute, Philadelphia, PA
- Institute of Diabetes, Obesity and Metabolism, Philadelphia, PA
- Institute for Translational Medicine and Therapeutics, Philadelphia, PA
| | - Nehal N. Mehta
- Cardiovascular Institute, Philadelphia, PA
- Institute of Diabetes, Obesity and Metabolism, Philadelphia, PA
- Institute for Translational Medicine and Therapeutics, Philadelphia, PA
- Center for Clinical Epidemiology and Biostatistics, Philadelphia, PA
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13
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Grimaldi R, Acosta A, Machado T, Bomfim T, Galvão-Castro B. Distribution of SDF1-3’A polymorphisms in three different ethnic groups from Brazil. Braz J Infect Dis 2010. [DOI: 10.1016/s1413-8670(10)70039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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14
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Maley SN, Schwartz SM, Johnson LG, Malkki M, Du Q, Daling JR, Li SS, Zhao LP, Petersdorf EW, Madeleine MM. Genetic variation in CXCL12 and risk of cervical carcinoma: a population-based case-control study. Int J Immunogenet 2009; 36:367-75. [PMID: 19788587 DOI: 10.1111/j.1744-313x.2009.00877.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
CXCL12 provides a chemotactic signal-directing leucocyte migration and regulates metastatic behaviour of tumour cells. We conducted a population-based case-control study to test the hypothesis that common genetic variation in CXCL12 individual single nucleotide polymorphism (SNP) alleles and haplotypes] is associated with the risk of cervical carcinoma. Cases (n = 917) were residents of western Washington State diagnosed with invasive squamous cell cervical carcinoma (SCC), invasive adenocarcinoma or adenosquamous carcinoma, or adenocarcinoma in situ of the cervix. Control participants (n = 849) were identified from the source population by random digit telephone dialling and frequency matched to cases on county and age. Nine CXCL12 tagSNPs chosen from the SeattleSNPs database were genotyped. The minor allele of intronic SNP rs266085 was inversely associated with cervical cancer under a recessive genetic effects model (OR = 0.74, 95% CI: 0.56-0.98). Among the ten common haplotypes inferred from the nine tagSNPs, one haplotype defined by minor alleles at 5'-flanking SNP rs17885289 and rs266085, and common alleles at the other seven SNPs occurred among 7.8% of cases and 10.6% of controls (dominant model OR = 0.72, 95% CI: 0.56-0.93; recessive model OR = 0.35, 95% CI: 0.12-0.97; and log-additive model OR = 0.72, 95% CI: 0.57-0.90). A stepwise procedure identified rs17885289, rs266085 and 3'-untranslated region (UTR) SNP rs266093 as the most parsimonious subset of SNPs necessary to define the haplotype inversely associated with cervical cancer risk in our study. A 3'-UTR SNP, rs1801157, previously found to be related to HIV pathogenesis, was not associated with cervical cancer risk. Further population-based studies are warranted to confirm these associations between genetic variation in CXCL12 and cervical cancer risk.
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Affiliation(s)
- S N Maley
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
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15
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Chang SC, Lin PC, Yang SH, Wang HS, Li AFY, Lin JK. SDF-1α G801A Polymorphism Predicts Lymph Node Metastasis in Stage T3 Colorectal Cancer. Ann Surg Oncol 2009; 16:2323-30. [DOI: 10.1245/s10434-009-0501-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 04/13/2009] [Accepted: 04/13/2009] [Indexed: 11/18/2022]
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16
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Koizumi Y, Kageyama S, Fujiyama Y, Miyashita M, Lwembe R, Ogino K, Shioda T, Ichimura H. RANTES -28G delays and DC-SIGN - 139C enhances AIDS progression in HIV type 1-infected Japanese hemophiliacs. AIDS Res Hum Retroviruses 2007; 23:713-9. [PMID: 17530998 DOI: 10.1089/aid.2006.0225] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The relationships between host immune factors and HIV-1 disease progression are still in dispute. Unlike CCR5Delta32, which has been found to delay disease progression of HIV-1, there still remain several factors whose effect on the clinical course is unconfirmed. To clarify the relationships, we selected seven single-nucleotide polymorphisms (SNPs) out of the previously reported factors, namely, RANTES promoter -28G/-403A, RANTES In1.1C, SDF-1 3'A, IL-4 promoter -589T, and DC-SIGN promoter -139C/-336C, and examined these in Japanese HIV-1-infected hemophiliacs (n = 102). The genotypes were examined by the direct sequencing method, and the distributions of genotype and allelic frequencies were compared between two groups, slow progressors (n = 54) who did not develop AIDS more than 10 years after intravenous infection and others (progressors) (n = 48). The allelic frequency of RANTES -28G was significantly higher in slow progressors (0.185) than in the progressor group (0.074) [p = 0.023, OR = 0.35, 95% CI (0.142, 0.880)]. DC-SIGN promoter -139C, and appeared in progressors with significantly higher allelic frequency (0.333) than slow progressors [0.204, p = 0.040, OR = 1.95, 95% CI (1.039, 3.677)]. With RANTES -403A, RANTES In1.1C, SDF-1 3' A, IL-4 -589T, and DC-SIGN -336C, no significant difference was observed in allelic frequencies between the two groups. These results suggest that RANTES -28G was associated with delayed AIDS progression, while DC-SIGN -139C was associated with accelerated AIDS progression in HIV-1-infected Japanese hemophiliacs.
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Affiliation(s)
- Yusuke Koizumi
- Department of Viral Infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
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Modi WS, Lautenberger J, An P, Scott K, Goedert JJ, Kirk GD, Buchbinder S, Phair J, Donfield S, O'Brien SJ, Winkler C. Genetic variation in the CCL18-CCL3-CCL4 chemokine gene cluster influences HIV Type 1 transmission and AIDS disease progression. Am J Hum Genet 2006; 79:120-8. [PMID: 16773571 PMCID: PMC1474130 DOI: 10.1086/505331] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 04/24/2006] [Indexed: 12/20/2022] Open
Abstract
CCL3 (MIP-1 alpha), CCL4 (MIP-1 beta), and CCL18 (DC-CK1/PARC/AMAC-1) are potent chemoattractants produced by macrophages, natural killer cells, fibroblasts, mast cells, CD4(+) T cells, and CD8(+) T cells. CCL3 and CCL4 are natural ligands for the primary human immunodeficiency virus type 1 (HIV-1) coreceptor CCR5 and are also known to activate and enhance the cytotoxicity of natural killer cells. Genomic DNAs from >3,000 participants enrolled in five United States-based natural-history cohorts with acquired immunodeficiency syndrome (AIDS) were genotyped for 21 single-nucleotide polymorphisms (SNPs) in a 47-kb interval on chromosome 17q12 containing the genes CCL3, CCL4, and CCL18. All 21 SNPs were polymorphic in African Americans (AAs), whereas 7 of the 21 had minor-allele frequencies <0.01 in European Americans (EAs). Substantial linkage disequilibrium was observed in a 37-kb interval containing 17 SNPs where many pairwise D' values exceeded 0.70 in both racial groups, but particularly in EAs. Four and three haplotype blocks were observed in AAs and EAs, respectively. Blocks were strongly correlated with each other, and common haplotype diversity within blocks was limited. Two significant associations are reported that replicate an earlier study. First, among AA members of the AIDS Link to the Intravenous Experience cohort of injection drug users, frequencies of three correlated SNPs covering 2,231 bp in CCL3 were significantly elevated among highly exposed, persistently HIV-1-uninfected individuals compared with HIV-1-infected seroconvertors (P = .02-.03). Second, seven highly correlated SNPs spanning 36 kb and containing all three genes were significantly associated with more-rapid disease progression among EAs enrolled in the Multicenter AIDS Cohort Study cohort (P = .01-.02). These results reiterate the importance of chemokine gene variation in HIV-1/AIDS pathogenesis and emphasize that localized linkage disequilibrium makes the identification of causal mutations difficult.
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Affiliation(s)
- William S Modi
- SAIC-Frederick, Inc., Basic Research Program, Frederick, MD 21702-1201, USA
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