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. 2014 Dec 15;210(12):1946-50.
doi: 10.1093/infdis/jiu342. Epub 2014 Jun 16.

Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection

Sigrid Le Clerc  1 , Olivier Delaneau  2 , Cédric Coulonges  1 , Jean-Louis Spadoni  1 , Taoufik Labib  1 , Vincent Laville  1 , Damien Ulveling  1 , Josselin Noirel  1 , Matthieu Montes  1 , François Schächter  1 , Sophie Caillat-Zucman  3 , Jean-François Zagury  1
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Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection

Sigrid Le Clerc et al. J Infect Dis. .

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.

Keywords: AIDS; GWAS; HIV-1; MICA; SNP; elite control; imputation; indel; non progression.

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