A map of human genome variation from population-scale sequencing, Nature, vol.467, pp.1061-73, 2010. ,
SNPs for a universal individual identification panel, Human Genetics, vol.2, issue.3, pp.315-339, 2010. ,
DOI : 10.1007/s00439-009-0771-1
The Structure of Haplotype Blocks in the Human Genome, Science, vol.296, issue.5576, pp.2225-2234, 2002. ,
DOI : 10.1126/science.1069424
Highresolution haplotype structure in the human genome Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression, Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), pp.229-261, 1997. ,
Mapping the whole human genome by fingerprinting yeast artificial chromosomes, Cell, vol.70, issue.6, pp.1059-68, 1992. ,
DOI : 10.1016/0092-8674(92)90254-A
Continuum of overlapping clones spanning the entire human chromosome 21q, Nature, vol.359, issue.6394, pp.380-387, 1992. ,
DOI : 10.1038/359380a0
A second-generation linkage map of the human genome, Nature, vol.359, issue.6398, pp.794-801, 1992. ,
DOI : 10.1038/359794a0
A first-generation physical map of the human genome, Nature, vol.366, issue.6456, pp.1484-1492, 1993. ,
DOI : 10.1038/366698a0
The Sequence of the Human Genome, Science, vol.291, issue.5507, pp.1304-51, 2001. ,
DOI : 10.1126/science.1058040
URL : https://hal.archives-ouvertes.fr/hal-00465088
Integrating common and rare genetic variation in diverse human populations, Nature, vol.35, issue.7311, pp.52-60, 2010. ,
DOI : 10.1038/nature09298
Multilocus LD measure and tagging SNP selection with generalized mutual information, Genetic Epidemiology, vol.73, issue.4, pp.353-64, 2005. ,
DOI : 10.1002/gepi.20092
Genome-wide association studies for complex traits: consensus, uncertainty and challenges, Nature Reviews Genetics, vol.3, issue.5, pp.356-69, 2008. ,
DOI : 10.1038/nrg2344
Efficiency and power in genetic association studies, Nature Genetics, vol.21, issue.11, pp.1217-1240, 2005. ,
DOI : 10.1038/ng1488
Tag SNP selection for association studies, Genetic Epidemiology, vol.14, issue.4, pp.365-74, 2004. ,
DOI : 10.1002/gepi.20028
Complement Factor H Polymorphism in Age-Related Macular Degeneration, Science, vol.308, issue.5720, pp.385-394, 2005. ,
DOI : 10.1126/science.1109557
Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations, Nature Genetics, vol.276, issue.2, pp.157-166, 2009. ,
DOI : 10.1016/S0006-291X(02)00379-0
Segregation of HLA/TNF region is linked to leprosy clinical spectrum in families displaying mixed leprosy subtypes, Genes and Immunity, vol.4, issue.1, pp.67-73, 2003. ,
DOI : 10.1038/sj.gene.6363911
A comprehensive review of genetic association studies, Genetics in Medicine, vol.50, issue.2, pp.45-61, 2002. ,
DOI : 10.1097/00125817-200203000-00002
Genome-wide association studies for common diseases and complex traits, Nature Reviews Genetics, vol.158, issue.2, pp.95-108, 2005. ,
DOI : 10.1086/339258
A tutorial on statistical methods for population association studies, Nature Reviews Genetics, vol.5, issue.10, pp.781-91, 2006. ,
DOI : 10.1038/nrg1155
The Future of Genetic Studies of Complex Human Diseases, Science, vol.273, issue.5281, pp.1516-1523, 1996. ,
DOI : 10.1126/science.273.5281.1516
Gene set analysis of SNP data: benefits, challenges, and future directions, European Journal of Human Genetics, vol.11, issue.8, pp.837-880, 2011. ,
DOI : 10.1093/nar/gkq324
A gene-centric approach to genome-wide association studies, Nature Reviews Genetics, vol.8, issue.11 ,
DOI : 10.1086/502803
A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS, BMC Genomics, vol.36, issue.Suppl, p.504, 2011. ,
DOI : 10.1093/nar/gkm995
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies, Nucleic Acids Research, vol.37, issue.Web Server, pp.600-605, 2009. ,
DOI : 10.1093/nar/gkp290
Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies, Bioinformatics, vol.26, issue.19, pp.2474-2480, 2010. ,
DOI : 10.1093/bioinformatics/btq452
A genome-wide association study of global gene expression, Nature Genetics, vol.32, issue.10, pp.1202-1209, 2007. ,
DOI : 10.1038/ng2109
Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen, Science, vol.319, issue.5865, pp.921-927, 2008. ,
DOI : 10.1126/science.1152725
Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication, Cell, vol.135, issue.1, pp.49-60, 2008. ,
DOI : 10.1016/j.cell.2008.07.032
Genome-Scale RNAi Screen for Host Factors Required for HIV Replication, Cell Host & Microbe, vol.4, issue.5, pp.495-504, 2008. ,
DOI : 10.1016/j.chom.2008.10.004
Analysing biological pathways in genome-wide association studies, Nature Reviews Genetics, vol.81, issue.12, pp.843-54, 2010. ,
DOI : 10.1038/nrg2884
Genome-wide association studies: quality control and population-based measures, Genetic Epidemiology, vol.50, issue.S1, pp.45-50, 2009. ,
DOI : 10.1002/gepi.20472
Statistical Methods for Research Workers, 1932. ,
A Note on Exact Tests of Hardy-Weinberg Equilibrium, The American Journal of Human Genetics, vol.76, issue.5, pp.887-93, 2005. ,
DOI : 10.1086/429864
Genetic dissection of complex traits, Science, vol.265, issue.5181, pp.2037-2085, 1994. ,
DOI : 10.1126/science.8091226
Genomic Control for Association Studies, Biometrics, vol.280, issue.4, pp.997-1004, 1999. ,
DOI : 10.1111/j.0006-341X.1999.00997.x
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies, Genetics, vol.164, pp.1567-87, 2003. ,
Haplotype inference by maximum parsimony, Bioinformatics, vol.19, issue.14, pp.1773-80, 2003. ,
DOI : 10.1093/bioinformatics/btg239
THE INCOMPLETE PERFECT PHYLOGENY HAPLOTYPE PROBLEM, Journal of Bioinformatics and Computational Biology, vol.03, issue.02, pp.359-84, 2005. ,
DOI : 10.1142/S0219720005001090
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population, Mol. Biol. Evol, vol.12, pp.921-928, 1995. ,
Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data, The American Journal of Human Genetics, vol.67, issue.4, pp.947-59, 2000. ,
DOI : 10.1086/303069
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals, The American Journal of Human Genetics, vol.78, issue.3, pp.437-50, 2006. ,
DOI : 10.1086/500808
A New Statistical Method for Haplotype Reconstruction from Population Data, The American Journal of Human Genetics, vol.68, issue.4, pp.978-89, 2001. ,
DOI : 10.1086/319501
ISHAPE: new rapid and accurate software for haplotyping, BMC Bioinformatics, vol.8, issue.1, p.205, 2007. ,
DOI : 10.1186/1471-2105-8-205
Shape-IT: new rapid and accurate algorithm for haplotype inference, BMC Bioinformatics, vol.9, issue.1, p.540, 2008. ,
DOI : 10.1186/1471-2105-9-540
Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset, BMC Genetics, vol.5, issue.1, p.22, 2004. ,
DOI : 10.1186/1471-2156-5-22
Haplotype phasing: existing methods and new developments, Nature Reviews Genetics, vol.447, issue.10, pp.703-717, 2011. ,
DOI : 10.1038/nrg3054
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217888
The role of haplotypes in candidate gene studies, Genetic Epidemiology, vol.73, issue.4, pp.321-354, 2004. ,
DOI : 10.1002/gepi.20025
The importance of phase information for human genomics, Nature Reviews Genetics, vol.84, issue.3, pp.215-238, 2011. ,
DOI : 10.1038/nrg2950
Haplotypic analysis of tag SNPs of the interleukin-18 gene in relation to cardiovascular disease events: the MORGAM Project, European Journal of Human Genetics, vol.12, issue.12, pp.1512-1532, 2008. ,
DOI : 10.1111/j.1467-9469.2006.00481.x
Interacting haplotypes at the NPAS3 locus alter risk of schizophrenia and bipolar disorder, Molecular Psychiatry, vol.141, issue.9, pp.874-84, 2009. ,
DOI : 10.1038/sj.mp.4002012
Dominant Effects of CCR2-CCR5 Haplotypes in HIV-1 Disease Progression, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.37, issue.4, pp.1534-1542, 2004. ,
DOI : 10.1097/01.qai.0000127353.01578.63
Associations of MHC Ancestral Haplotypes with Resistance/Susceptibility to AIDS Disease Development, The Journal of Immunology, vol.170, issue.4, pp.1925-1934, 2003. ,
DOI : 10.4049/jimmunol.170.4.1925
Haplotype analysis in VEGF gene and increased risk of Alzheimer's disease ,
Meta-Analysis in Genome-Wide Association Datasets: Strategies and Application in Parkinson Disease, PLoS ONE, vol.162, issue.2, p.196, 2007. ,
DOI : 10.1371/journal.pone.0000196.t003
Meta-Analysis of Genome-Wide Association Studies, Cold Spring Harbor Protocols, vol.2010, issue.6, p.81, 2010. ,
DOI : 10.1101/pdb.top81
Practical Issues in Imputation-Based Association Mapping, PLoS Genetics, vol.37, issue.16, 2008. ,
DOI : 10.1371/journal.pgen.1000279.s003
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes, Genetic Epidemiology, vol.80, issue.8, pp.816-850, 2010. ,
DOI : 10.1002/gepi.20533
A new multipoint method for genome-wide association studies by imputation of genotypes, Nature Genetics, vol.164, issue.7, pp.906-919, 2007. ,
DOI : 10.1038/nrg1916
Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits, PLoS Genetics, vol.37, issue.7, p.114, 2007. ,
DOI : 10.1371/journal.pgen.0030114.sd002
Missing data imputation and haplotype phase inference for genome-wide association studies, Human Genetics, vol.316, issue.5, pp.439-50, 2008. ,
DOI : 10.1007/s00439-008-0568-7
Genotype Imputation, Annual Review of Genomics and Human Genetics, vol.10, issue.1, pp.387-406, 2009. ,
DOI : 10.1146/annurev.genom.9.081307.164242
Analyses and Comparison of Imputation-Based Association Methods, PLoS ONE, vol.309, issue.5, p.10827, 2010. ,
DOI : 10.1371/journal.pone.0010827.t004
Genotype imputation for genome-wide association studies, Nature Reviews Genetics, vol.42, issue.7, pp.499-511, 2010. ,
DOI : 10.1038/nrg2796
Genotype Imputation with Thousands of Genomes, G3: Genes|Genomes|Genetics, vol.1, issue.6, pp.457-470, 2011. ,
DOI : 10.1534/g3.111.001198
Pneumocystis Pneumonia???Los Angeles, American Journal of Public Health, vol.96, issue.6, pp.980-981, 1981. ,
DOI : 10.2105/AJPH.96.6.980
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470612
Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS), Science, vol.220, issue.4599, pp.868-71, 1983. ,
DOI : 10.1126/science.6189183
Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS, Science, vol.224, issue.4648, pp.500-503, 1984. ,
DOI : 10.1126/science.6200936
Isolation of a new human retrovirus from West African patients with AIDS, Science, vol.233, issue.4761, pp.343-349, 1986. ,
DOI : 10.1126/science.2425430
Reduced rate of disease development after HIV-2 infection as compared to HIV-1, Science, vol.265, issue.5178, pp.1587-90, 1994. ,
DOI : 10.1126/science.7915856
Prospective Comparison of Mother-to-Child Transmission of HIV-1 and HIV-2 in Abidjan, Ivory Coast, JAMA: The Journal of the American Medical Association, vol.272, issue.6, pp.462-468, 1994. ,
DOI : 10.1001/jama.1994.03520060062033
HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy, Science, vol.267, issue.5197, pp.483-492, 1995. ,
DOI : 10.1126/science.7824947
Oncogenes in Retroviruses and Cells: Biochemistry and Molecular Genetics, Adv. Cancer Res, vol.47, pp.99-188, 1986. ,
DOI : 10.1016/S0065-230X(08)60199-2
Effects of Retroviruses on Host Genome Function, Annual Review of Genetics, vol.42, issue.1, pp.709-741, 2008. ,
DOI : 10.1146/annurev.genet.42.110807.091501
Mechanism of transduction by retroviruses, Science, vol.255, issue.5046, pp.841-846, 1992. ,
DOI : 10.1126/science.1371365
HIV-1 and the host cell: an intimate association, Trends in Microbiology, vol.12, issue.4, pp.170-177, 2004. ,
DOI : 10.1016/j.tim.2004.02.001
Regulation of Human Immunodeficiency Virus Replication, Annual Review of Microbiology, vol.45, issue.1, pp.219-50, 1991. ,
DOI : 10.1146/annurev.mi.45.100191.001251
HIV pathogenesis: 25 years of progress and persistent challenges, AIDS, vol.23, issue.2, pp.147-60, 2009. ,
DOI : 10.1097/QAD.0b013e3283217f9f
In vitro infection of human primary adipose cells with HIV-1, AIDS, vol.17, issue.17, pp.2537-2546, 2003. ,
DOI : 10.1097/00002030-200311210-00019
URL : https://hal.archives-ouvertes.fr/hal-00315040
Human adipose cells express CD4, CXCR4, and CCR5 [corrected] receptors: a new target cell type for the immunodeficiency virus-1?, FASEB J, vol.16, pp.1254-1260, 2002. ,
AIDS as a Zoonosis: Scientific and Public Health Implications, Science, vol.287, issue.5453, pp.607-621, 2000. ,
DOI : 10.1126/science.287.5453.607
Availability of AZT for treatment of AIDS, N. Engl. J. Med, pp.316-1158, 1987. ,
Les antagonistes du r??cepteur CCR5 : une nouvelle classe d???antir??troviraux, Th??rapie, vol.64, issue.1, pp.9-16, 2009. ,
DOI : 10.2515/therapie/2009006
Prevalence and comparative characteristics of long-term nonprogressors and HIV controller patients in the French Hospital Database on HIV, AIDS, vol.23, issue.9, pp.1163-1172, 2009. ,
DOI : 10.1097/QAD.0b013e32832b44c8
Who are the elite controllers?, GMHC Treat Issues, vol.19, p.12, 2005. ,
Elite HIV controllers: myth or reality?, AIDS Rev, vol.9, pp.195-207, 2007. ,
Genetic and Immunologic Heterogeneity among Persons Who Control HIV Infection in the Absence of Therapy, The Journal of Infectious Diseases, vol.197, issue.4, pp.563-71, 2008. ,
DOI : 10.1086/526786
Resistance to HIV-1 infection: lessons learned from studies of highly exposed persistently seronegative (HEPS) individuals, AIDS Rev, vol.5, pp.87-103, 2003. ,
Polymorphisms in the CCR5 Coding and Noncoding Regions among HIV Type 1-Exposed, Persistently Seronegative Female Sex-Workers from Thailand, AIDS Research and Human Retroviruses, vol.19, issue.8, pp.661-666, 2003. ,
DOI : 10.1089/088922203322280883
Distinctive Effects of CCR5, CCR2, and SDF1 Genetic Polymorphisms in AIDS Progression, Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, vol.19, issue.4 ,
DOI : 10.1097/00042560-199812010-00009
Effects of CCR5-?? 32, CCR2-64I, and SDF-1 3???A Alleles on HIV-1 Disease Progression: An International Meta-Analysis of Individual-Patient Data, Annals of Internal Medicine, vol.135, issue.9, pp.782-95, 2001. ,
DOI : 10.7326/0003-4819-135-9-200111060-00008
Evidence for the cure of HIV infection by CCR5??32/??32 stem cell transplantation, Blood, vol.117, issue.10, pp.2791-2800, 2011. ,
DOI : 10.1182/blood-2010-09-309591
Ex vivo gene therapy for HIV-1 treatment, Human Molecular Genetics, vol.20, issue.R1, pp.100-107, 2011. ,
DOI : 10.1093/hmg/ddr160
Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene, Nature, vol.382, issue.6593, pp.722-727, 1996. ,
DOI : 10.1038/382722a0
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 Science, vol.273, pp.1856-62, 1996. ,
32 bp CCR-5 gene deletion and resistance to fast progression in HIV-1 infected heterozygotes, The Lancet, vol.349, issue.9056, pp.922-925, 1997. ,
DOI : 10.1016/S0140-6736(05)62697-9
CCR5 promoter polymorphism and HIV-1 disease progression, The Lancet, vol.352, issue.9131, pp.866-70, 1998. ,
DOI : 10.1016/S0140-6736(98)04158-0
Genetic Acceleration of AIDS Progression by a Promoter Variant of CCR5, Science, vol.282, issue.5395, pp.1907-1918, 1998. ,
DOI : 10.1126/science.282.5395.1907
HLA and HIV-1: Heterozygote Advantage and B*35-Cw*04 Disadvantage, Science, vol.283, issue.5408, pp.1748-52, 1999. ,
DOI : 10.1126/science.283.5408.1748
Effect of a Single Amino Acid Change in MHC Class I Molecules on the Rate of Progression to AIDS, New England Journal of Medicine, vol.344, issue.22, pp.1668-75, 2001. ,
DOI : 10.1056/NEJM200105313442203
New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS, J. Immunol, vol.162, pp.6942-6948, 1999. ,
Genomic approach of AIDS pathogenesis: exhaustive genotyping of the TNFR1 gene in a French AIDS cohort, Biomedicine & Pharmacotherapy, vol.59, issue.8, pp.474-80, 2005. ,
DOI : 10.1016/j.biopha.2005.07.011
Exhaustive genotyping of??the??interferon alpha receptor 1 (IFNAR1) gene and??association of??an??IFNAR1 protein variant with AIDS progression or??susceptibility to??HIV-1 infection in??a??French AIDS cohort, Biomedicine & Pharmacotherapy, vol.60, issue.9, pp.569-77, 2006. ,
DOI : 10.1016/j.biopha.2006.08.002
Gene and Absence of Association with AIDS Progression in a French Cohort, The Journal of Infectious Diseases, vol.191, issue.2, pp.159-63, 2005. ,
DOI : 10.1086/426826
Associations of the IL2R??, IL4R??, IL10R??, and IFN ?? R1 cytokine receptor genes with AIDS progression in a French AIDS cohort, Immunogenetics, vol.2, issue.2-3, pp.89-98, 2006. ,
DOI : 10.1007/s00251-005-0072-3
Exhaustive Genotyping of the Interleukin???1 Family Genes and Associations with AIDS Progression in a French Cohort, The Journal of Infectious Diseases, vol.194, issue.11, pp.1492-504, 2006. ,
DOI : 10.1086/508545
Exploration of associations between phospholipase A2 gene family polymorphisms and AIDS progression using the SNPlex??? method, Biomedicine & Pharmacotherapy, vol.62, issue.1, pp.31-40, 2008. ,
DOI : 10.1016/j.biopha.2007.11.001
URL : https://hal.archives-ouvertes.fr/hal-00315368
Host genes associated with HIV/AIDS: advances in gene discovery, Trends in Genetics, vol.26, issue.3, pp.119-150, 2010. ,
DOI : 10.1016/j.tig.2010.01.002
Contribution of cohort studies in understanding HIV pathogenesis: introduction of the GRIV cohort and preliminary results, Biomedicine & Pharmacotherapy, vol.50, issue.10, pp.480-487, 1996. ,
DOI : 10.1016/S0753-3322(97)89278-5
Statistical power of association using the extreme discordant phenotype design, Pharmacogenetics and Genomics, vol.16, issue.6, pp.401-414, 2006. ,
DOI : 10.1097/01.fpc.0000204995.99429.0f
A Whole-Genome Association Study of Major Determinants for Host Control of HIV-1, Science, vol.317, issue.5840, pp.944-951, 2007. ,
DOI : 10.1126/science.1143767
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, vol.46, issue.12, p.3907, 2008. ,
DOI : 10.1371/journal.pone.0003907.s002
The gene encoding TBC1D1 with homology to the tre-2/USP6 oncogene, BUB2, and cdc16 maps to mouse chromosome 5 and human chromosome 4, Cytogenetic and Genome Research, vol.89, issue.3-4, pp.272-277, 2000. ,
DOI : 10.1159/000015632
Mammalian SP/KLF transcription factors: Bring in the family, Genomics, vol.85, issue.5, pp.551-557, 2005. ,
DOI : 10.1016/j.ygeno.2005.01.005
Repression of interferon-gamma expression in T cells by Prospero-related homeobox protein. Cell Res, pp.911-931, 2008. ,
Host Determinants of HIV???1 Control in African Americans, The Journal of Infectious Diseases, vol.201, issue.8, pp.1141-1150, 2010. ,
DOI : 10.1086/651382
Host genetics and HIV-1 viral load set-point in African???Americans, AIDS, vol.23, issue.6, pp.673-680, 2009. ,
DOI : 10.1097/QAD.0b013e328325d414
Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages, PLoS ONE, vol.18, issue.2, p.17190, 2011. ,
DOI : 10.1371/journal.pone.0017190.s010
URL : https://hal.archives-ouvertes.fr/inserm-00580542
Background and rationale behind the SU.VI.MAX Study, a prevention trial using nutritional doses of a combination of antioxidant vitamins and minerals to reduce cardiovascular diseases and cancers. SUpplementation en VItamines et Minéraux AntioXydants Stud, Int J Vitam Nutr Res, vol.68, pp.3-20, 1998. ,
[An epidemiologic survey from a network of French Health Examination Centres): epidemiologic data on the insulin resistance syndrome]. Rev Epidemiol Sante Publique, pp.373-378, 1996. ,
Genome-Wide Association Scan in HIV-1-Infected Individuals Identifying Variants Influencing Disease Course, PLoS ONE, vol.11, issue.RR-17, p.22208, 2011. ,
DOI : 10.1371/journal.pone.0022208.t002
Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection, AIDS, vol.23, issue.1, pp.19-28, 2009. ,
DOI : 10.1097/QAD.0b013e32831db247
The effects of human population structure on large genetic association studies, Nature Genetics, vol.21, issue.5, pp.512-519, 2004. ,
DOI : 10.1038/nrg1229
MySQL -Guide officiel, 1782. ,
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, The American Journal of Human Genetics, vol.81, issue.3, pp.559-75, 2007. ,
DOI : 10.1086/519795
GenABEL: an R library for genome-wide association analysis, Bioinformatics, vol.23, issue.10, pp.1294-1300, 2007. ,
DOI : 10.1093/bioinformatics/btm108
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/10/1294
Haploview: analysis and visualization of LD and haplotype maps, Bioinformatics, vol.21, issue.2, pp.263-268, 2005. ,
DOI : 10.1093/bioinformatics/bth457
Principal components analysis corrects for stratification in genome-wide association studies, Nature Genetics, vol.15, issue.8, pp.904-913, 2006. ,
DOI : 10.1038/ng1653
TAGster: efficient selection of LD tag SNPs in single or multiple populations, Bioinformatics, vol.23, issue.23, pp.3254-3259, 2007. ,
DOI : 10.1093/bioinformatics/btm426
FastTagger: An efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium, BMC Bioinformatics, vol.11, issue.1, p.66, 2010. ,
DOI : 10.1186/1471-2105-11-66
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase, The American Journal of Human Genetics, vol.78, issue.4 ,
DOI : 10.1086/502802
INTERSNP: genome-wide interaction analysis guided by a priori information, Bioinformatics, vol.25, issue.24, pp.3275-81, 2009. ,
DOI : 10.1093/bioinformatics/btp596
Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits, PLoS Genetics, vol.102, issue.8, 2010. ,
DOI : 10.1371/journal.pgen.1001058.s024
ProbABEL package for genome-wide association analysis of imputed data, BMC Bioinformatics, vol.11, issue.1, p.134, 2010. ,
DOI : 10.1186/1471-2105-11-134
WHAP: haplotype-based association analysis, Bioinformatics, vol.23, issue.2, pp.255-261, 2007. ,
DOI : 10.1093/bioinformatics/btl580
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/2/255
BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies, The American Journal of Human Genetics, vol.87, issue.3, pp.325-365, 2010. ,
DOI : 10.1016/j.ajhg.2010.07.021
Screening Low-Frequency SNPS From Genome-Wide Association Study Reveals a New Risk Allele for Progression to AIDS, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.56, issue.3, 2010. ,
DOI : 10.1097/QAI.0b013e318204982b
Multiple???Cohort Genetic Association Study Reveals CXCR6 as a New Chemokine Receptor Involved in Long???Term Nonprogression to AIDS, The Journal of Infectious Diseases, vol.202, issue.6, pp.908-923, 2010. ,
DOI : 10.1086/655782
Common Genetic Variation and the Control of HIV-1 in Humans, PLoS Genetics, vol.18, issue.12, p.1000791, 2009. ,
DOI : 10.1371/journal.pgen.1000791.s016
Efficient Genomewide Selection of PCA-Correlated tSNPs for Genotype Imputation, Annals of Human Genetics, vol.21, issue.5, pp.707-729, 2011. ,
DOI : 10.1111/j.1469-1809.2011.00673.x
Population Structure and Eigenanalysis, PLoS Genetics, vol.15, issue.12, p.190, 2006. ,
DOI : 1088-9051(2005)015[1576:CACSOH]2.0.CO;2
URL : http://doi.org/10.1371/journal.pgen.0020190
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies, PLoS Genetics, vol.84, issue.6, p.1000529, 2009. ,
DOI : 10.1371/journal.pgen.1000529.s004
The use of imputed values in the meta-analysis of genome-wide association studies, Genetic Epidemiology, vol.10, issue.7, pp.597-605, 2011. ,
DOI : 10.1002/gepi.20608
Genomics and Biology Come Together to Fight HIV, PLoS Biology, vol.359, issue.3, p.76, 2008. ,
DOI : 0140-6736(2002)359[1121:GVIHRA]2.0.CO;2
URL : http://doi.org/10.1371/journal.pbio.0060076
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation, Science, vol.330, pp.1551-1558, 2010. ,
Methodological challenges of genome-wide association analysis in Africa, Nature Reviews Genetics, vol.1, issue.2, pp.149-60, 2010. ,
DOI : 10.1038/nrg2731
Kif26b, a kinesin family gene, regulates adhesion of the embryonic kidney mesenchyme, Proceedings of the National Academy of Sciences, vol.107, issue.20 ,
DOI : 10.1073/pnas.0913748107
Cleavage of human and mouse cytoskeletal and sarcomeric proteins by human immunodeficiency virus type 1 ,
Actin, desmin, myosin, and tropomyosin, Am. J. Pathol, vol.142, pp.221-251, 1993. ,
Practical aspects of imputation-driven meta-analysis of genome-wide association studies, Human Molecular Genetics, vol.17, issue.R2 ,
DOI : 10.1093/hmg/ddn288
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes, Nature Genetics, vol.447, issue.5, pp.638-683, 2008. ,
DOI : 10.1038/ng1457
Finding the missing heritability of complex diseases, Nature, vol.41, issue.7265, pp.747-53, 2009. ,
DOI : 10.1038/nature08494
Interpretation of Association Signals and Identification of Causal Variants from Genome-wide Association Studies, The American Journal of Human Genetics, vol.86, issue.5, pp.730-772, 2010. ,
DOI : 10.1016/j.ajhg.2010.04.003
Genetic influence of CXCR6 chemokine receptor alleles on PCP-mediated AIDS progression among African Americans, Genes and Immunity, vol.4, issue.4, pp.245-50, 2003. ,
DOI : 10.1038/sj.gene.6363950
Expression cloning of new receptors used by simian and human immunodeficiency viruses, Nature, vol.388, pp.296-300, 1997. ,
CXCR6 expression defines type 1-polarized T-cell subsets with extralymphoid tissue homing potential, J. Clin. Invest, vol.107, pp.595-601, 2001. ,
Critical Role for the Chemokine Receptor CXCR6 in Homeostasis and Activation of CD1d-Restricted NKT Cells, The Journal of Immunology, vol.181, issue.1, pp.81-91, 2008. ,
DOI : 10.4049/jimmunol.181.1.81
Genome-wide algorithm for detecting CNV associations with diseases, BMC Bioinformatics, vol.12, issue.1, p.331, 2011. ,
DOI : 10.1038/nature08035
???94 Insertion/Deletion ATTG Polymorphism Contributes to Risk of Systemic Lupus Erythematosus, DNA and Cell Biology, vol.31, issue.4, 2011. ,
DOI : 10.1089/dna.2011.1389
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, vol.105, issue.8, p.3636, 2008. ,
DOI : 10.1371/journal.pone.0003636.s005
The HLA-B/-C haplotype block contains major determinants for host control of HIV, Genes and Immunity, vol.10, issue.8, pp.673-680, 2009. ,
DOI : 10.1007/s00251-007-0222-x
Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases, PLoS ONE, vol.4, issue.11, p.8068, 2009. ,
DOI : 10.1371/journal.pone.0008068.s010
The SNP ratio test: pathway analysis of genome-wide association datasets, Bioinformatics, vol.25, issue.20, pp.2762-2765, 2009. ,
DOI : 10.1093/bioinformatics/btp448
Meta-analysis and imputation identifies a 109???kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations, Genes and Immunity, vol.156, issue.5, pp.470-477, 2009. ,
DOI : 10.1038/ng2088
Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies, Lancet, vol.377, pp.641-650, 2011. ,
The pursuit of genome-wide association studies: where are we now?, Journal of Human Genetics, vol.461, issue.4, pp.195-206, 2010. ,
DOI : 10.1038/jhg.2010.19
Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application, The American Journal of Human Genetics, vol.86, issue.1, pp.6-22, 2010. ,
DOI : 10.1016/j.ajhg.2009.11.017
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information, BMC Bioinformatics, vol.12, issue.1, p.299, 2011. ,
DOI : 10.1093/nar/28.1.45
Genome-wide Significant Associations for Variants With Minor Allele Frequency of 5% or Less--An Overview: A HuGE Review, American Journal of Epidemiology, vol.172, issue.8, pp.869-89, 2010. ,
DOI : 10.1093/aje/kwq234
What will whole genome searches for susceptibility genes for common complex disease offer to clinical practice?, Journal of Internal Medicine, vol.8, issue.1, pp.16-27, 2008. ,
DOI : 10.1111/j.1365-2796.2007.01895.x
Statistical analysis strategies for association studies involving rare variants, Nature Reviews Genetics, vol.101, issue.11, pp.773-85, 2010. ,
DOI : 10.1038/nrg2867
Exome Sequencing Identifies ZNF644 Mutations in High Myopia, PLoS Genetics, vol.10, issue.6, 2011. ,
DOI : 10.1371/journal.pgen.1002084.s002
A rare variant in MYH6 is associated with high risk of sick sinus syndrome, Nature Genetics, vol.460, issue.4, pp.316-336, 2011. ,
DOI : 10.1371/journal.pgen.1000099
Who's afraid of epistasis?, Nature Genetics, vol.7, issue.4, pp.371-374, 1996. ,
DOI : 10.1016/S0168-9525(00)89155-6
Detecting gene???gene interactions that underlie human diseases, Nature Reviews Genetics, vol.8, issue.6, pp.392-404, 2009. ,
DOI : 10.1038/nrg2579
Epistasis ??? the essential role of gene interactions in the structure and evolution of genetic systems, Nature Reviews Genetics, vol.1, issue.11, pp.855-67, 2008. ,
DOI : 10.1038/nrg2452
Significance Levels in Genome-Wide Interaction Analysis (GWIA), Annals of Human Genetics, vol.447, issue.1, pp.29-35, 2011. ,
DOI : 10.1111/j.1469-1809.2010.00610.x
CNV discovery using SNP genotyping arrays, Cytogenetic and Genome Research, vol.123, issue.1-4, pp.307-319, 2008. ,
DOI : 10.1159/000184722
Methods and strategies for analyzing copy number variation using DNA microarrays, Nature Genetics, vol.5, issue.7s, pp.16-21, 2007. ,
DOI : 10.1038/ng2028
Epigenome-wide association studies for common human diseases, Nature Reviews Genetics, vol.14, issue.8, pp.529-570, 2011. ,
DOI : 10.1038/nrg3000
Implication of next-generation sequencing on association studies, BMC Genomics, vol.40, issue.12, p.322, 2011. ,
DOI : 10.1038/ng.180
Field guide to next-generation DNA sequencers, Molecular Ecology Resources, vol.463, issue.Suppl. 1, pp.759-69, 2011. ,
DOI : 10.1111/j.1755-0998.2011.03024.x
Performance comparison of exome DNA sequencing technologies, Nature Biotechnology, vol.29, issue.10, pp.908-922, 2011. ,
DOI : 10.1101/gr.112326.110
Exome sequencing: a transformative technology, The Lancet Neurology, vol.10, issue.10, pp.942-948, 2011. ,
DOI : 10.1016/S1474-4422(11)70196-X
Whole-exome sequencing: a powerful technique for identifying novel genes of complex disorders, Clinical Genetics, vol.27, issue.3, pp.132-135, 2011. ,
DOI : 10.1111/j.1399-0004.2010.01585.x
Exome sequencing and its application, Hereditas (Beijing), vol.33, issue.8, pp.847-56, 2011. ,
DOI : 10.3724/SP.J.1005.2011.00847
dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions, Human Mutation, vol.38, issue.8, pp.894-903, 2011. ,
DOI : 10.1002/humu.21517
Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome, PLoS ONE, vol.5, issue.10, p.13630, 2010. ,
DOI : 10.1371/journal.pone.0013630.t002
Revisiting Mendelian disorders through exome sequencing, Human Genetics, vol.19, issue.4, pp.351-70, 2011. ,
DOI : 10.1007/s00439-011-0964-2
Exome sequencing identifies the cause of a mendelian disorder, Nature Genetics, vol.137, issue.1, pp.30-35, 2010. ,
DOI : 10.1101/gr.078212.108
Exome sequencing makes medical genomics a reality, Nature Genetics, vol.42, issue.1, pp.13-17, 2010. ,
DOI : 10.1038/ng817
Human genetic variation and its contribution to complex traits, Nature Reviews Genetics, vol.40, issue.4, pp.241-51, 2009. ,
DOI : 10.1038/nrg2554
Low-coverage sequencing: Implications for design of complex trait association studies, Genome Research, vol.21, issue.6, pp.940-51, 2011. ,
DOI : 10.1101/gr.117259.110
The Power of the Extreme in Elucidating Obesity, New England Journal of Medicine, vol.359, issue.9, pp.891-894, 2008. ,
DOI : 10.1056/NEJMp0805396
Common and rare variants in multifactorial susceptibility to common diseases, Nature Genetics, vol.602, issue.6, pp.695-701, 2008. ,
DOI : 10.1186/bcr1826
Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies, The American Journal of Human Genetics, vol.80, issue.4, pp.727-766, 2007. ,
DOI : 10.1086/513473
Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms, The American Journal of Human Genetics, vol.82, issue.1, pp.100-112, 2008. ,
DOI : 10.1016/j.ajhg.2007.09.006
The regulation of direct-to-consumer genetic tests, Human Molecular Genetics, vol.17, issue.R2, pp.180-183, 2008. ,
DOI : 10.1093/hmg/ddn253
Ethical and Social Issues in Pharmacogenomics Testing, Current Pharmaceutical Design, vol.16, issue.2, pp.245-52, 2010. ,
DOI : 10.2174/138161210790112700
Genome-wide association studies in pharmacogenomics, Nature Reviews Genetics, vol.14, issue.4, pp.241-247, 2010. ,
DOI : 10.1038/nrg2751
Genomic approach of AIDS pathogenesis: exhaustive genotyping of the TNFR1 gene in a French AIDS cohort, Biomedicine & Pharmacotherapy, vol.59, issue.8, pp.474-80, 2005. ,
DOI : 10.1016/j.biopha.2005.07.011
Gene and Absence of Association with AIDS Progression in a French Cohort, The Journal of Infectious Diseases, vol.191, issue.2, pp.159-63, 2005. ,
DOI : 10.1086/426826
Computation of haplotypes on SNPs subsets: advantage of the "global method ,
URL : https://hal.archives-ouvertes.fr/inserm-00112875
Exhaustive genotyping of??the??interferon alpha receptor 1 (IFNAR1) gene and??association of??an??IFNAR1 protein variant with AIDS progression or??susceptibility to??HIV-1 infection in??a??French AIDS cohort, Biomedicine & Pharmacotherapy, vol.60, issue.9, pp.569-77, 2006. ,
DOI : 10.1016/j.biopha.2006.08.002
Exhaustive Genotyping of the Interleukin???1 Family Genes and Associations with AIDS Progression in a French Cohort, The Journal of Infectious Diseases, vol.194, issue.11, pp.1492-504, 2006. ,
DOI : 10.1086/508545
Associations of the IL2R??, IL4R??, IL10R??, and IFN ?? R1 cytokine receptor genes with AIDS progression in a French AIDS cohort, Immunogenetics, vol.2, issue.2-3, pp.89-98, 2006. ,
DOI : 10.1007/s00251-005-0072-3
Shape-IT: new rapid and accurate algorithm for haplotype inference, BMC Bioinformatics, vol.9, issue.1, p.540, 2008. ,
DOI : 10.1186/1471-2105-9-540
Exploration of associations between phospholipase A2 gene family polymorphisms and AIDS progression using the SNPlex??? method, Biomedicine & Pharmacotherapy, vol.62, issue.1 ,
DOI : 10.1016/j.biopha.2007.11.001
URL : https://hal.archives-ouvertes.fr/hal-00315368
Genes (ANRS Genomewide Association Study 02), The Journal of Infectious Diseases, vol.199, issue.3, pp.419-445, 2009. ,
DOI : 10.1086/596067
Screening Low-Frequency SNPS From Genome-Wide Association Study Reveals a New Risk Allele for Progression to AIDS, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.56, issue.3 ,
DOI : 10.1097/QAI.0b013e318204982b
Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS, J. Infect. Dis, vol.202, pp.908-923, 2010. ,
Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages, PLoS ONE, vol.18, issue.2, p.17190, 2011. ,
DOI : 10.1371/journal.pone.0017190.s010
URL : https://hal.archives-ouvertes.fr/inserm-00580542