Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of human and EBV genetic variants

ABSTRACT: A Comprehensive Risk Score for Effective Risk Stratification and Screening of Nasopharyngeal Carcinoma

INSTRUMENT(S): MassARRAY iPLEX

ORGANISM(S): Homo Sapiens

SUBMITTER: Sun Yat-sen University Cancer Center

PROVIDER: PRJEB46183 | EVA | 2021-07-23

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	3EBV_SNP_20210630.vcf.gz	Vcf
	3EBV_SNP_20210630.vcf.gz.csi	Vcf
	3EBV_SNP_20210630.vcf.gz.tbi	Vcf
	7human_SNP_20210630.vcf.gz	Vcf
	7human_SNP_20210630.vcf.gz.csi	Vcf

Items per page:

1 - 5 of 6

Similar Datasets

Investigation of cattle genetic variants

Project description:An investigation into a sub set of cattle genetic variantion

| PRJEB75603 | ENA

Investigation of barley genetic variants

Project description:IBGV

| PRJEB59111 | ENA

A multi-level investigation of the genetic relationship between endometriosis and ovarian cancer histotypes

Project description:Endometriosis is associated with increased risk of epithelial ovarian cancers (EOCs). Using data from large endometriosis and EOC genome-wide association meta-analyses we estimate the genetic correlation and evaluate the causal relationship between genetic liability to endometriosis and EOC histotypes, and identify shared susceptibility loci. We estimate a significant genetic correlation (rg) between endometriosis and clear cell (rg=0.71), endometrioid (rg=0.48) and high-grade serous (rg=0.19) ovarian cancer, associations supported by Mendelian randomization analyses. Bivariate meta-analysis identify 28 loci associated with both endometriosis and EOC, including 19 with evidence for a shared underlying association signal. Differences in the shared risk suggest different underlying pathways may contribute to the relationship between endometriosis and the different histotypes. Functional annotation using transcriptomic and epigenomic profiles of relevant tissues/cells highlights several target genes. This comprehensive analysis reveals profound genetic overlap between endometriosis and EOC histotypes with valuable genomic targets for understanding the biological mechanisms linking the diseases.

2022-03-07 | GSE197928 | GEO

APOL1 renal-risk variants induce mitochondrial dysfunction (Affymetrix 2)

Project description:To assess differential gene expression by APOL1 renal-risk (2 risk alleles) vs. non-risk (G0G0) genotypes in primary proximal tubule cells (PTCs), global gene expression (mRNA) levels were examined on Affymetrix HTA 2.0 arrays in primary PTCs cultured from non-diseased kidney in African Americans without CKD who underwent nephrectomy for localized renal cell carcinoma. To detect differentially expressed gene profiles attributable to APOL1 renal-risk genotypes, African American primary proximal tubule cells with two APOL1 renal-risk alleles (N=5) and lacking renal-risk alleles (N=25) were included in comparisons of global gene expression.

2016-08-23 | E-GEOD-85920 | biostudies-arrayexpress

A study of genetic variants associated with skin traits in the Vietnamese population

Project description:Background: Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. Objectives: We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health. Results: The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst=0.036, CHB: Fst=0.031, CHS: Fst=0.027, CDX: Fst=0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p =1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)).

2023-11-26 | GSE248483 | GEO

Genetic Risk Variants for Autoimmune Diseases that Influence Gene Expression in Thymus

Project description:Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most of the risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. We have performed a cis expression quantitative trait locus (eQTL) screen to investigate whether single nucleotide polymorphisms (SNPs) associated with AIDs influence gene expression in thymus. Genotyping was performed using the Immunochip and 353 AID associated SNPs were tested against expression of surrounding genes (+/- 1 Mb) from human thymic tissue (N=42). We identified eight genes where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.57x10-5). Five genes (FCRL3, RNASET2, C2orf74, SIRPG and SYS1) displayed cis eQTL signals also in other tissues, while for two loci (NPIPB8 and LOC388814), the eQTL signal appear to be thymus-specific. Since many AID risk variants from GWAS have been subsequently fine-mapped in recent Immunochip projects, we explored the overlap between these novel AID risk variants and the thymic eQTL regions. Moreover, we examined the functional annotation of the seven expression altering SNPs (eSNPs). Our study reveals autoimmune risk variants that act as eQTLs in thymus. We have highlighted functional variants within these genetic regions that potentially can represent causal autoimmune risk variants. Total RNA from 42 human thymic samples were obtained from children undergoing cardiac surgery.

2016-01-21 | E-GEOD-77052 | biostudies-arrayexpress

Genetic variants associated with development of pseudoexfoliation syndrome

Project description:Pseudoexfoliation syndrome (PEXS) is a late-onset disorder in which fibrillar material accumulates at abnormally high concentrations mainly in the anterior segment of the eye. PEXS is the most common cause of secondary glaucoma, which can ultimately lead to blindness and is associated with a higher risk of cataract and serious complications following different types of intraocular surgery. Although PEXS clearly has a genetic component, it remains poorly explored. In our genome-wide association study, we searched for an association of genetic variants with this disorder among older Poles with PEXS without glaucoma.

2018-01-31 | GSE93205 | GEO

APOL1 renal-risk variants induce mitochondrial dysfunction (Affymetrix 2)

2016-08-23 | GSE85920 | GEO

Genetic lineage analysis in intramucosal gland-forming gastric neoplasms

Project description:To predict the progression risk of non-invasive gland-forming gastric neoplasms to invasive carcinoma, we assessed lineage continuity or discontinuity between the non-invasive and invasive neoplasms by applying hierarchical clustering analysis to the gene copy-number profiles of individual tumours.

2014-08-06 | GSE60116 | GEO

IRF5 genetic risk variants drive myeloid-specific IRF5 hyper-activation and pre-symptomatic SLE

Project description:The IRF5-SLE risk haplotype is associated with SLE disease severity. We hypothesized that neutrophils from healthy risk donors would carry a pathogenic gene signature compared to non-risk donors. To compare basal neutrophil gene signature between risk and non-risk healthy individuals, fresh whole blood was collected from healthy donors, and granulocytes were extracted from the remaining pellet following Ficoll purification. RNA-seq libraries were prepared from globin-reduced RNA extracted from the granulocytes using the Qiagen RNA preparation kit.

2020-04-07 | GSE137067 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data