title: Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection.
abstract: Past genome-wide association studies (GWAS) involving individuals with AIDS have mainly identified associations in the HLA region. Using the latest software, we imputed 7 million single-nucleotide polymorphisms (SNPs)/indels of the 1000 Genomes Project from the GWAS-determined genotypes of individuals in the Genomics of Resistance to Immunodeficiency Virus AIDS nonprogression cohort and compared them with those of control cohorts. The strongest signals were in MICA, the gene encoding major histocompatibility class I polypeptide-related sequence A (P = 3.31 × 10(-12)), with a particular exonic deletion (P = 1.59 × 10(-8)) in full linkage disequilibrium with the reference HCP5 rs2395029 SNP. Haplotype analysis also revealed an additive effect between HLA-C, HLA-B, and MICA variants. These data suggest a role for MICA in progression and elite control of human immunodeficiency virus type 1 infection.
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Sigrid
authors.initials: S
authors.lastname: Le Clerc
authors.affiliation: Département de Génétique et Développement, Faculté de Médecine, Université de Genève, Geneva, Switzerland.
authors.forename: Olivier
authors.initials: O
authors.lastname: Delaneau
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Cédric
authors.initials: C
authors.lastname: Coulonges
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Spadoni
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Taoufik
authors.initials: T
authors.lastname: Labib
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Vincent
authors.initials: V
authors.lastname: Laville
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Damien
authors.initials: D
authors.lastname: Ulveling
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Josselin
authors.initials: J
authors.lastname: Noirel
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Montes
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: François
authors.initials: F
authors.lastname: Schächter
authors.affiliation: Hôpital Robert Debré AP-HP UMR 1149 INSERM-Université, Paris, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Caillat-Zucman
authors.affiliation: Chaire de Bioinformatique, EA4627, Conservatoire National des Arts et Métiers.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Zagury
mesh_terms: D000328:Adult; D015331:Cohort Studies; D060467:Disease Resistance; D005260:Female; D056726:Genetic Association Studies; D015658:HIV Infections / Q000276:immunology* / Q000821:virology; D015497:HIV-1 / Q000276:immunology*; D006239:Haplotypes; D015395:Histocompatibility Antigens Class I / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D008285:Major Histocompatibility Complex / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D055815:Young Adult
chemical_list: C080521:HCP5 long noncoding RNA, human; D015395:Histocompatibility Antigens Class I; C099187:MHC class I-related chain A; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated
keywords: AIDS; GWAS; HIV-1; MICA; SNP; elite control; imputation; indel; non progression