Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects

ABSTRACT: Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects

OTHER RELATED OMICS DATASETS IN: GSE68127

PROVIDER: PRJNA281879 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects [glomerulus]

Project description:Glomerular expression data from human kidney biopsy in African American subjects with glomerulopathies We used microarrays to analyze the transcriptome of African American subjects with glomerulopathies and the association of expression with APOL1 risk alleles (G1 and G2)

2015-07-15 | GSE68125 | GEO

Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects [tubulointerstitium]

Project description:Tubulointersitial expression data from human kidney biopsy in African American subjects with glomerulopathies We used microarrays to analyze the transcriptome of African American subjects with glomerulopathies and the association of expression with APOL1 risk alleles (G1 and G2)

2015-07-15 | GSE68126 | GEO

Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-07-15 | GSE68127 | GEO

Integrative genomics identifies novel associations with APOL1 risk genotype in African American NEPTUNE subjects

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series. This dataset is part of the TransQST collection.

2015-07-15 | E-GEOD-68127 | biostudies-arrayexpress

Glomerular transcriptome from subjects in the NEPTUNE cohort

Project description:Glomerular Transcriptome from subjects in the NEPTUNE cohort. A number of samples profiled in this analysis were also profiled in Series GSE68127, and Series GSE108113. RNA from the glomerular compartment of was extracted and processed for hybridization on Affymetrix microarrays. Contributor: NEPTUNE Consortium. This dataset is part of the TransQST collection.

2018-05-17 | E-GEOD-104066 | biostudies-arrayexpress

African American hepatocyte genotype

Project description:African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL. These AA-specific eQTLs are less correlated to GTEx eQTL in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs). We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci. Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes. Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.

2020-03-27 | GSE147628 | GEO

Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects.

Project description: Not available

| S-EPMC4769193 | biostudies-literature

Glomerular Transcriptome from subjects in the NEPTUNE cohort

Project description:Glomerular Transcriptome from subjects in the NEPTUNE cohort. A number of samples profiled in this analysis were also profiled in Series GSE68127, and Series GSE108113.

2018-05-17 | GSE104066 | GEO

Evaluation of APOL1 ASO in a novel model of APOL1-associated renal disease

Project description:African Americans develop end-stage renal disease at a higher rate compared to European Americans due to two polymorphisms (G1 and G2 risk variants) in the apolipoprotein L1 (APOL1) gene that are common in people of African ancestry. Not all homozygous risk allele carriers, however, develop renal disease suggesting that modifying factors (“second hits”) are required. Although the compelling genetic evidence provides an exciting opportunity for personalized medicine in chronic kidney disease (CKD), drug discovery efforts have been greatly hindered by the fact that APOL1 expression is limited to humans and select nonhuman primates. We describe a novel physiologically-relevant genomic mouse model of APOL1-associated renal disease that expresses human APOL1 from the endogenous human promoter, resulting in expression in similar tissues and at similar relative levels as humans. While naïve genomic APOL1 transgenic mice did not exhibit a renal disease phenotype, a single administration of IFNγ was sufficient to robustly induce proteinuria only in APOL1 G1 transgenic mice, despite inducing kidney APOL1 expression in both G0 and G1 mice, serving as a clinically-relevant “second hit.” We also report on the discovery of the first APOL1 inhibitor, IONIS-APOL1Rx, a Generation 2.5 antisense oligonucleotide (ASO) targeting APOL1 mRNA. Treatment of APOL1 G1 mice with IONIS-APOL1Rx prior to IFNγ challenge robustly and dose-dependently inhibited kidney and liver APOL1 expression and protected against IFNγ-induced proteinuria, indicating that the disease-relevant cell types are sensitive to ASO treatment. Collectively, these data suggest that IONIS-APOL1Rx may be an effective therapeutic for APOL1 nephropathies and warrants further development.

2018-10-16 | GSE121286 | GEO

APOL1 Genotype and Kidney Transplantation Outcomes From Deceased African American Donors.

Project description: Not available

| S-EPMC4684443 | biostudies-literature