EGAS00001000057-sc-20120125 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001000087 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53.
| EGAD00001000047 | EGA
Project description:exome sequence data for 57 HIV elite long term non-progressors and rapid progressors. Complete dataset of improved BAMs mapped to hs37d5 and including phenotype information.
| EGAD00001003345 | EGA
Project description:HIV-infected long-term non-progressors (LTNPs) are a special group of people who can naturally control HIV and maintain good host immunity. Their mechanism is related to viruses, host genetic characteristics, immune response and other factors, but the relationship between the activation level of innate immunity and long-term non-progression is not clear. Therefore,we hypothesize that LTNPs may have some founction to control the HIV replication in vivo.In this study, we used RNA-seq to investigate the transcription（lncRNA, miRNA and mRNA) profiles of LTNPs and typical progressors (TPs).This study is showing expression spectrum of mRNA and non-coding RNA between HIV-infected long-term non-progressors and typical progressors, and analyze the role of mRNA,IncRNA and miRNA in the HIV infected long-term non-progression based on whole transcriptome level.This study reveals the mechanism of different disease progression between LTNPs and TPs through functional enrichment analysis and differentially expressed genes(DEGs) analysis.
2021-02-10 | E-MTAB-9997 | biostudies-arrayexpress
Project description:A pilot study examining genetic determinants associated with elite long term non progression and rapid progression using exome sequencing of individuals at the extremes of the distribution of HIV control and progression. Data can only be used for HIV related research.
| EGAS00001000057 | EGA
Project description:Elite Long-Term Nonprogressors are asymptomatic HIV-infected individuals who display long-term virtually undetectable viremia, stable CD4 T cell counts and extremeley low levels of HIV reservoir, in the absence of antiretroviral therapy. We conducted a whole-genome transcriptional profiling study of sorted resting CD4 T cell subsets (naive, central memory, transitional memory and effector memory) in 7 Elite Long-Term Nonprogressors, 7 HIV-infected viremic and 7 uninfected individuals. HIV-1 cellular DNA levels were quantified in each sorted CD4 T cell subset
2015-01-10 | E-MTAB-1480 | biostudies-arrayexpress
Project description:Background: A rare subgroup of HIV infected individuals naturally controls infection without
treatment. These ?elite controllers? constitute an important model for the natural control of
HIV infection. Indeed, the study of these individuals may provide insights into strategies for
the development of HIV vaccines. Although several HLA and chemokine alleles are known
to be over-represented in elite controllers, only a small portion of HIV phenotypic variation is
explained by known genetic variants. The elite controller phenotype is rare and distinct,
representing the extreme of an infectious disease trait. As such, this phenotype may be partly
explained by variation in host immune control, which may be characterized by differences in
rare functional genetic variants. Genomic regions underlying elite control can be potentially
identified by comparing the presence or frequency of variants in this group to that
representing the opposite extreme. In this context, ?rapid progressors? is a group defined by
its rapid immunological and clinical disease progression.
Aim: To extend an existing study, in order to identify DNA sequence variants involved in the
control of HIV infection with greater statistical resolution. Specifically, we aim to sequence up
to 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (a
collaboration of 25 HIV seroconversion cohort studies across Europe).
| EGAS00001000522 | EGA
Project description:Background: A rare subgroup of HIV infected individuals naturally controls infection without
treatment. These ?elite controllers? constitute an important model for the natural control of
HIV infection. Indeed, the study of these individuals may provide insights into strategies for
the development of HIV vaccines. Although several HLA and chemokine alleles are known
to be over-represented in elite controllers, only a small portion of HIV phenotypic variation is
explained by known genetic variants. The elite controller phenotype is rare and distinct,
representing the extreme of an infectious disease trait. As such, this phenotype may be partly
explained by variation in host immune control, which may be characterized by differences in
rare functional genetic variants. Genomic regions underlying elite control can be potentially
identified by comparing the presence or frequency of variants in this group to that
representing the opposite extreme. In this context, ?rapid progressors? is a group defined by
its rapid immunological and clinical disease progression.
Aim: To extend an existing study, in order to identify DNA sequence variants involved in the
control of HIV infection with greater statistical resolution. Specifically, we aim to sequence up
to 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (a
collaboration of 25 HIV seroconversion cohort studies across Europe).
| EGAD00001002179 | EGA
Project description:In our cohort study for HIV, we have classified patients in 3 different groups, primarily on the basis latency period- Long term non-progressors (LTNP), Long term non-progressors NON-controllers (LNC), and regular progressors. individuals in these groups differ phenotypically as well as have significantly different levels of CD4+T cell counts and viral loads. Goal of the study is to explore the underlying novel mechanisms behind the differences in different patient classes of HIV using Next-Generation sequencing.
2022-12-31 | GSE200462 | GEO
Project description:High levels of HIV-1 replication during the chronic phase of infection are usually associated with rapid disease progression (RP). However, a minority of HIV-infected individuals remain asymptomatic and show persistently high CD4+ T cell counts despite high viremia for many years (viremic non progressors, VNP). The latter profile is reminiscent of the non-pathogenic model of SIV infection in natural hosts such as the sooty mangabey. We used various genomic approaches to examine 66 RP and 6 VNP defined according to strict criteria. RP were characterized by depletion of protective HLA alleles, enrichment of HLA alleles associated with disease progression, and a characteristic transcriptome profile of CD4+ and CD8+ T cells similar to that observed in pathogenic SIV infection of rhesus macaque. In contrast, VNPs presented lower expression of interferon stimulated genes than RP, and shared with SIV-infected sooty mangabeys a common profile of regulation of a set of genes that includes CASP1, CD38, LAG3, TNFSF13B, SOCS1 and EEF1D. The estimated 8% of RP and 0.1% of VNP in human cohorts represent two subsets of HIV-infected individuals whose analysis may inform our understanding of HIV pathogenesis. Selection criteria rapid progressors (RP): HIV seroconversion window <1 year WITH documented negative and positive serology or biological proof of primary infection. AND One of A) or B) A) >2 CD4+ T cell counts below 350 cells/µl within 3 years of seroconversion AND no subsequent rise of CD4+ T cells above 350 cells/µl in the absence of ART. B) ART initiated within 3 years of seroconversion AND CD4+ T cell count within 1 month of ART-start <350 cells/µl. Selection criteria viremic non progressors (VNP): > 3 years of follow-up AND median HIV viremia from >3 measurements >100'000 viral RNA copies/ml AND HIV viremia consistently above 10’000 copies/ml AND CD4+ T cell count above 350 cells/µl AND no ART during follow-up. Selection criteria elite/viremic controllers (EC): see Casado et al. 2010. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS ONE 5:e11079. Total RNA from 41 samples obtained from CD4 T cells from HIV infected individuals to identify associations between gene expression and different distinct patterns of disease progression Total RNA from 38 samples obtained from CD8 T cells from HIV infected individuals to identify associations between gene expression and different distinct
2011-06-03 | E-GEOD-28128 | biostudies-arrayexpress
Project description:The relationship between host microRNAs (miRNA), viral control and immune response has not been elucidated in the field of HIV yet. The aim of this study was to assess the differential miRNA profile in CD8+ T-cells between HIV-infected individuals who differ in terms of disease progression. A total of 136 RNAs (miRNAs) were analyzed: 68 RNAs from resting CD8+ T-cells and the respective 68 RNAs from stimulated CD8+ T-cells from Elite Controllers (EC, n=15), Viremic Controllers (VC, n=15), Viremic Progressors (VP, n=13), Treated Patients (ART, n=14) and Uninfect Donors (HIV-, n=11).
2015-08-04 | E-GEOD-71650 | biostudies-arrayexpress