Distinct Genetic Loci Control Plasma HIV-RNA and Cellular HIV-DNA Levels in HIV-1 Infection: The ANRS Genome Wide Association 01 Study
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{"title"=>"Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: The ANRS Genome Wide Association 01 study", "type"=>"journal", "authors"=>[{"first_name"=>"Cyril", "last_name"=>"Dalmasso", "scopus_author_id"=>"6603358047"}, {"first_name"=>"Wassila", "last_name"=>"Carpentier", "scopus_author_id"=>"23767878700"}, {"first_name"=>"Laurence", "last_name"=>"Meyer", "scopus_author_id"=>"7203050208"}, {"first_name"=>"Christine", "last_name"=>"Rouzioux", "scopus_author_id"=>"35227863200"}, {"first_name"=>"Cécile", "last_name"=>"Goujard", "scopus_author_id"=>"34975059100"}, {"first_name"=>"Marie Laure", "last_name"=>"Chaix", "scopus_author_id"=>"34568404900"}, {"first_name"=>"Olivier", "last_name"=>"Lambotte", "scopus_author_id"=>"55123896400"}, {"first_name"=>"Véronique", "last_name"=>"Avettand-Fenoel", "scopus_author_id"=>"35313349500"}, {"first_name"=>"Sigrid", "last_name"=>"Le Clerc", "scopus_author_id"=>"25932158000"}, {"first_name"=>"Laure Denis", "last_name"=>"de Senneville", "scopus_author_id"=>"57197779948"}, {"first_name"=>"Christiane", "last_name"=>"Deveau", "scopus_author_id"=>"6603946227"}, {"first_name"=>"Faroudy", "last_name"=>"Boufassa", "scopus_author_id"=>"6701475038"}, {"first_name"=>"Patrice", "last_name"=>"Debré", "scopus_author_id"=>"7102483451"}, {"first_name"=>"Jean François", "last_name"=>"Delfraissy", "scopus_author_id"=>"35274714800"}, {"first_name"=>"Philippe", "last_name"=>"Broet", "scopus_author_id"=>"55909494300"}, {"first_name"=>"Ioannis", "last_name"=>"Theodorou", "scopus_author_id"=>"7004642137"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"19107206", "sgr"=>"58149203242", "doi"=>"10.1371/journal.pone.0003907", "scopus"=>"2-s2.0-58149203242", "pui"=>"354030199", "isbn"=>"1932-6203 (Electronic)", "issn"=>"19326203"}, "id"=>"99b35ca7-5a79-3f79-b9fc-c156dc0a63d5", "abstract"=>"Previous studies of the HIV-1 disease have shown that HLA and Chemokine receptor genetic variants influence disease progression and early viral load. We performed a Genome Wide Association study in a cohort of 605 HIV-1-infected seroconverters for detection of novel genetic factors that influence plasma HIV-RNA and cellular HIV-DNA levels. Most of the SNPs strongly associated with HIV-RNA levels were localised in the 6p21 major histocompatibility complex (MHC) region and were in the vicinity of class I and III genes. Moreover, protective alleles for four disease-associated SNPs in the MHC locus (rs2395029, rs13199524, rs12198173 and rs3093662) were strikingly over-represented among forty-five Long Term HIV controllers. Furthermore, we show that the HIV-DNA levels (reflecting the HIV reservoir) are associated with the same four SNPs, but also with two additional SNPs on chromosome 17 (rs6503919; intergenic region flanked by the DDX40 and YPEL2 genes) and chromosome 8 (rs2575735; within the Syndecan 2 gene). Our data provide evidence that the MHC controls both HIV replication and HIV reservoir. They also indicate that two additional genomic loci may influence the HIV reservoir.", "link"=>"http://www.mendeley.com/research/distinct-genetic-loci-control-plasma-hivrna-cellular-hivdna-levels-hiv1-infection-anrs-genome-wide-a", "reader_count"=>55, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>29, "Medicine and Dentistry"=>14, "Chemistry"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>14}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Turkey"=>1, "Hungary"=>1, "Belgium"=>1, "United States"=>1, "Italy"=>1, "France"=>1, "Australia"=>1, "Spain"=>1}, "group_count"=>3}

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  • {"files"=>["https://ndownloader.figshare.com/files/452374", "https://ndownloader.figshare.com/files/452380"], "description"=>"<div><p>Previous studies of the HIV-1 disease have shown that HLA and Chemokine receptor genetic variants influence disease progression and early viral load. We performed a Genome Wide Association study in a cohort of 605 HIV-1-infected seroconverters for detection of novel genetic factors that influence plasma HIV-RNA and cellular HIV-DNA levels. Most of the SNPs strongly associated with HIV-RNA levels were localised in the 6p21 major histocompatibility complex (MHC) region and were in the vicinity of class I and III genes. Moreover, protective alleles for four disease-associated SNPs in the MHC locus (rs2395029, rs13199524, rs12198173 and rs3093662) were strikingly over-represented among forty-five Long Term HIV controllers. Furthermore, we show that the HIV-DNA levels (reflecting the HIV reservoir) are associated with the same four SNPs, but also with two additional SNPs on chromosome 17 (rs6503919; intergenic region flanked by the DDX40 and YPEL2 genes) and chromosome 8 (rs2575735; within the Syndecan 2 gene). Our data provide evidence that the MHC controls both HIV replication and HIV reservoir. They also indicate that two additional genomic loci may influence the HIV reservoir.</p></div>", "links"=>[], "tags"=>["loci", "plasma", "hiv-rna", "cellular", "hiv-dna", "levels", "hiv-1", "anrs", "genome", "01"], "article_id"=>149093, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.s001", "https://dx.doi.org/10.1371/journal.pone.0003907.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Distinct_Genetic_Loci_Control_Plasma_HIV_RNA_and_Cellular_HIV_DNA_Levels_in_HIV_1_Infection_The_ANRS_Genome_Wide_Association_01_Study/149093", "title"=>"Distinct Genetic Loci Control Plasma HIV-RNA and Cellular HIV-DNA Levels in HIV-1 Infection: The ANRS Genome Wide Association 01 Study", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-12-24 02:31:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/912492"], "description"=>"<p>Negative log<sub>10</sub> (P)-values for the score test for genome-wide association across the genome ordered from 1pter to 22qter. Adjacent chromosomes are shown in light blue and dark blue. The spacing between SNPs does not reflect actual physical distances. The false discovery rate was calculated based on a stratified approach (by chromosome) leading to chromosome-specific thresholds.</p>", "links"=>[], "tags"=>["plasma", "hiv-rna", "levels", "anrs", "primo"], "article_id"=>582935, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_wide_association_GWA_study_for_plasma_HIV_RNA_levels_in_the_ANRS_PRIMO_cohort_/582935", "title"=>"Genome wide association (GWA) study for plasma HIV-RNA levels in the ANRS PRIMO cohort.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-24 00:48:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/912661"], "description"=>"<p>Upper box shows an ideogram depicting chromosome 6 and the annotated region (transparent yellow rectangle). Lower box shows the linkage disequilibrium data matrix calculated from the European HapMap population. The colour intensity of each box is proportional to the strength of the LD property (r<sup>2</sup>) for the marker pair.</p>", "links"=>[], "tags"=>["snps", "mhc", "linkage", "disequilibrium"], "article_id"=>583096, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_the_twelve_selected_SNPs_in_the_MHC_region_6p21_and_linkage_disequilibrium_plot_/583096", "title"=>"Location of the twelve selected SNPs in the MHC region (6p21) and linkage disequilibrium plot.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-24 00:51:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/912763"], "description"=>"<p>Plasma HIV-RNA level is highly correlated with the rs2395029 (HCP5), rs3093662 (TNF), rs13199524 and rs12198173 (TNXB) genotypes.</p>", "links"=>[], "tags"=>["hiv-rna", "levels", "primo", "cohort"], "article_id"=>583205, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Boxplots_for_HIV_RNA_levels_in_the_PRIMO_cohort_for_four_major_SNPs_/583205", "title"=>"Boxplots for HIV-RNA levels in the PRIMO cohort for four major SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-24 00:53:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/912886"], "description"=>"<p>Cellular HIV-DNA level is highly correlated with the rs2395029 (HCP5), rs6503919 (intergenic DDX40 – YPEL2) and rs2575735 (SDC2) genotypes.</p>", "links"=>[], "tags"=>["hiv-dna", "levels", "primo", "cohort"], "article_id"=>583328, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Boxplots_for_HIV_DNA_levels_in_the_PRIMO_cohort_for_the_three_major_SNPs_/583328", "title"=>"Boxplots for HIV-DNA levels in the PRIMO cohort for the three major SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-24 00:55:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/912985"], "description"=>"<p>The following information is given for each SNP: <b>SNP</b> is the rs number; <b>Chr</b> is the chromosome; <b>Position</b> is the position along the chromosome (Human Genome NCBI Build 35.1); <b>PRIMO Q-values</b> are the Q-values for the genome-wide association study with HIV-RNA in the Primo cohort; <b>PRIMO P-values</b> are the P-values for the genome-wide association study with HIV-RNA in the Primo cohort; <b>Beta</b> is the slope parameter (allele indicated in bracket is used as a reference group); <b>CHAVI P-values</b> are the P-values obtained from the CHAVI study; <b>CHAVI rank</b> is the rank of the p-values (obtained from the CHAVI study) according to the Illumina 317K whole-genome single-nucleotide polymorphism arrays. The rank assigned to tied values is calculated by taking the mean of the ranks. <b>MA</b> is the minor allele in the HapMap CEU population; <b>P-values</b> are the P-values for the comparison of allele frequencies between the PRIMO and HIV controllers patients (<b>HIC</b>). The four major SNPs (printed in bold) are those being significantly associated with plasma HIV-RNA and showing enrichment in HIV-controllers for protective allelic variants.</p>*<p>NA = Not Available (SNP discarded in the Chavi study).</p>", "links"=>[], "tags"=>["snps", "plasma", "hiv-rna", "levels", "hiv-1"], "article_id"=>583425, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_list_of_the_most_significant_SNPs_FDR_lt_25_associated_with_plasma_HIV_RNA_levels_during_primary_HIV_1_infection_/583425", "title"=>"The list of the most significant SNPs (FDR<25%) associated with plasma HIV-RNA levels during primary HIV-1 infection.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-24 00:57:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/913039"], "description"=>"<p><b>SNP</b> is the rs number; <b>Chr</b> is the chromosome; <b>Position</b> is position along the chromosome (Human Genome NCBI Build 35.1); <b>Q-values</b> and <b>P-values</b> for the genome-wide association study with HIV-DNA in the Primo cohort are shown; <b>Beta</b> is the slope parameter (allele indicated in bracket is used as a reference group); <b>MA</b> is the minor allele in the HapMap CEU population; <b>P-values</b> for the comparison of allele frequencies between the PRIMO and HIV controllers patients (<b>HIC</b>) are shown. The four major SNPs are in bold.</p>", "links"=>[], "tags"=>["snps", "cellular", "hiv-dna", "levels", "hiv-1"], "article_id"=>583476, "categories"=>["Genetics"], "users"=>["Cyril Dalmasso", "Wassila Carpentier", "Laurence Meyer", "Christine Rouzioux", "Cécile Goujard", "Marie-Laure Chaix", "Olivier Lambotte", "Véronique Avettand-Fenoel", "Sigrid Le Clerc", "Laure Denis de Senneville", "Christiane Deveau", "Faroudy Boufassa", "Patrice Debré", "Jean-François Delfraissy", "Philippe Broët", "Ioannis Theodorou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003907.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_list_of_the_most_significant_SNPs_FDR_lt_25_associated_with_cellular_HIV_DNA_levels_during_primary_HIV_1_infection_/583476", "title"=>"The list of the most significant SNPs (FDR<25%) associated with cellular HIV-DNA levels during primary HIV-1 infection.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-24 00:57:56"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"16", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

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