Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic association between ancestry and IBD phenotypes in Chilean Population

ABSTRACT: Genotyping IBD patients

INSTRUMENT(S): Illumina iScan

ORGANISM(S): Homo Sapiens

SUBMITTER: Pontificia Universidad Catolica

PROVIDER: PRJEB87649 | EVA | 2026-01-01

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	file_final_tr_march25th.vcf.csi	Other
	file_final_tr_march25th.vcf.gz	Vcf
	file_final_tr_march25th.vcf.gz.csi	Vcf

Items per page:

1 - 3 of 3

Similar Datasets

Genomic polymorphism is genotyped to determine the association between genotypes and treatment outcomes

Project description:The Illumina GoldenGate Genotyping Assay is a flexible, pre-optimized assay that uses a discriminatory DNA polymerase and ligase to interrogate 96 SNP loci simultaneously. This Assay utilizes the BeadArray Reader. Using this assay, we examined the distribution of the patients` genotypes to determine which genotype tends to have a better outcomes for cancer treatment.

2015-05-30 | GSE52072 | GEO

Association Between Population Density and Genetic Risk for Schizophrenia.

Project description: Not available

| S-EPMC6142911 | biostudies-literature

Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population

Project description:Background & Aims: Most inflammatory bowel diseases (IBDs) are classic polygenic disorders represented by common alleles. However, multiple determinants of very early-onset IBD characterized by a more extensive disease course remain largely unknown. The present study aimed to define the genetic architecture of pediatric and adult-onset IBDs in the Polish population. Results: Of 82 SNPs validated/replicated for association with IBD, a novel BRD2 (rs1049526) association was found in both pediatric (OR= 2.35) and adult (OR= 2.66) patients. Thirty SNPs were shared between pediatric and adult patients; 22 and 30 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare/infrequent, potentially deleterious variants in IBD-associated or innate immunity-associated genes. Both groups of variants were over-represented in affected children. Two highly deleterious homozygous variants, HLA-DRB1 c.565_566insC and NCF4 p.Arg8Trp, were found in two affected children, and WAS p.Glu131Lys was found in one child and one adult patient. Conclusions: Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare/low frequency deleterious variants in affected children suggests a contribution by yet unexplained genetic components.

2017-01-01 | GSE79094 | GEO

Genotyping of hundreds of individuals from Kazakh population in Kazakhstan

Project description:Genotyping of hundreds of healthy individuals with Kazakh ethnicity as a reference cohort for further genetic investigations

2024-10-04 | GSE199322 | GEO

Population structure and ancestry of Qinchuan cattle by GeneSeek HD Bovine 77k Genotyping BeadChip

Project description:GeneSeek HD Bovine 77k Genotyping array is used to estimate population structure and ancestry of bovine and evaluate loci responsible for complex traits. Further, copy number variation of bovine can be estimated by GeneSeek HD Bovine 77k Genotyping array. Here, we estimate population structure and ancestry of Qinchuan cattle.

2017-06-15 | GSE100038 | GEO

Genome-wide association study on Tuberculosis in the Chinese Population

Project description:We perform the first two-stage GWAS on TB in the Chinese population. We examined 900,015 genetic variants in 1,008 TB patients using the HumanOmniZhongHua-8 v1.1 BeadChip.

2019-06-01 | GSE83397 | GEO

Population genetic properties of differentiated human copy number polymorphisms

Project description:Copy number variants (CNVs) can reach appreciable frequencies in the human population, and several of these copy number polymorphisms (CNPs) have been recently associated with human diseases including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. Developing a novel method based on single channel intensity data and benchmarking against copy numbers determined from sequencing read-depth, we successfully obtained CNP genotypes for 1489 CNPs from 487 human DNA samples from diverse ethnic backgrounds. This customized microarray was enriched for segmental duplication-rich regions and novel insertions of sequences not represented in the reference genome assembly or on standard single nucleotide polymorphism (SNP) microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that bi-allelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although bi-allelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multi-copy CNPs do not (40% with r >0.8). We selected a subset of CNPs for further characterization in 1873 additional samples from 62 populations (947 samples analyzed by microarray; 926 samples analyzed with PCR based assays); this revealed striking population-differentiated structural variants in genes of clinical significance such as the OCLN gene, a tight junction protein involved in hepatitis C viral entry. Our new microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that are not in linkage disequilibrium with SNPs) may have contributed disproportionately to human diversity and selection.

2011-02-01 | GSE26450 | GEO

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

Association between lncRNAs in plasma exosomes and diabetic retinopathy

Project description:Long noncoding RNA (lncRNA) in plasma exosomes is a potential non-invasive diagnostic biomarker for diabetic retinopathy (DR). However, the changes in plasma exosomal lncRNAs and diagnostic relevance in patients with DR patients remain unclear. A case–control study with type 2 diabetes mellitus (T2DM) and patients with comorbid DR were enrolled, and their clinical information and blood samples were collected.

2022-09-06 | GSE212594 | GEO

Genetic Association between Akt1 Polymorphisms and Alzheimer's Disease in a Japanese Population.

Project description: Not available

| S-EPMC3139182 | biostudies-literature