Ontology highlight
ABSTRACT:
PROVIDER: PRJNA869779 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21072800_1.fastq.gz | Fastqsanger.gz | |||
| SRR21072800_2.fastq.gz | Fastqsanger.gz | |||
| SRR21072900_1.fastq.gz | Fastqsanger.gz | |||
| SRR21072900_2.fastq.gz | Fastqsanger.gz | |||
| SRR21072801_1.fastq.gz | Fastqsanger.gz |
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Project description:To efficiently identify genetic susceptibility variants for gastric cancer, including rare coding variants, we performed an exome chip-based array study. We found that a linkage disequilibrium (LD) block containing 2 significant variants in PSCA gene increased the risk and two blocks that included 15 suggested variants including TRIM31, TRIM 40, TRIM 10, and TRIM26 regions, and included one suggested variant and OR2H2 gene showed protective associations with gastric cancer susceptibility. In addition, the PLEC region (rs200893203), FBLN2 region (rs201192415), and EPHA2 region (rs3754334) were associated with increased susceptibility We performed an exome chip-based array study in 329 gastric cancer cases and 683 controls.
2014-06-11 | E-GEOD-58356 | biostudies-arrayexpress
Project description:Over 400 million people worldwide live with a rare disease. Whole exome and whole genome sequencing often identifies potential disease causative genetic variants that are novel, which must be classified as variants of uncertain significance (VUS). Functional laboratory assays must be performed to prove disease causation, creating major delays in patient diagnostics. Here we investigate a GATA4 (p.Arg283Cys) VUS in a with congenital heart disease. The variant was CRISPR gene edited into inducible pluripotent stem cells, followed by cardio-myocyte differentiation. Genetic variant and healthy cells were similar at the level of cardiomy-ocyte cell marker expression of troponin T (cTNNT), and GATA4 protein expression. Strik-ingly, transcriptomics profiling identified differences in differentiation consistent with the pa-tient’s disease characteristics, and elucidated changes in calcium signaling and adrenergic sig-naling in cardiomyocytes. Altered action potential changes in GATA4,p.Arg283Cys (GA-TA4_HDR) cardiomyocytes were indicative of cardiac abnormalities. Our work provides strong molecular evidence for classifying the GATA4 p.Arg283Cys variant as pathogenic. Furthermore, we demonstrate the combined utility of iPSCs, CRISPR gene edit-ing and differentiation into cardiomyocytes in assessing variants associated with cardiac pheno-types.
2023-11-23 | GSE229879 | GEO
Project description:Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type — whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.
2024-01-24 | GSE253950 | GEO
Project description:To efficiently identify genetic susceptibility variants for gastric cancer, including rare coding variants, we performed an exome chip-based array study. We found that a linkage disequilibrium (LD) block containing 2 significant variants in PSCA gene increased the risk and two blocks that included 15 suggested variants including TRIM31, TRIM 40, TRIM 10, and TRIM26 regions, and included one suggested variant and OR2H2 gene showed protective associations with gastric cancer susceptibility. In addition, the PLEC region (rs200893203), FBLN2 region (rs201192415), and EPHA2 region (rs3754334) were associated with increased susceptibility
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Project description:Dyskeratosis congenita (DC) is a complex inherited bone marrow failure syndrome which is principally a disorder of telomere maintenance. To date approximately 35% of cases remain uncharacterised at the genetic level. Whole exome sequencing on a large collection of uncharacterized DC and DC-like (DCL) families (n=167) has revealed several novel pathogenic variants within known susceptibility loci, POT1 and ZCCHC8, as well as the novel locus POLA1. Functional characterisation of identified POLA1 and POT1 pathogenic variants, uncovered their effect on protein-protein interactions that have critical implications for telomere maintenance. ZCCHC8 variants disrupt protein interactions that affect nuclear exosome targeting (NEXT) complex stoichiometry and its binding with the human silencing hub (HUSH) complex chromatin modifier MPP8. Global transcriptomic analysis revealed signatures of pervasive transcription that include several short (snRNA and snoRD) and long non-coding RNA (transposable elements; LINE-1) driving inflammation in ZCCHC8 patient blood cells. In summary, our studies inform the current genetic architecture of DC and DCL disorders, by revealing novel gene loci such as POLA1 and extend our current knowledge on disease mechanisms beyond the regulation of long non-coding RNA TERC.
2024-07-10 | GSE244915 | GEO
Project description:Congenital hypopituitarism (CH) and its associated syndromes, septo-optic dysplasia (SOD) and holoprosencephaly (HPE), are midline defects that cause significant morbidity for affected people. Variants in 67 genes are associated with CH, but a vast majority of CH cases lack a genetic diagnosis. Whole exome and whole genome sequencing of CH patients identifies sequence variants in genes known to cause CH, and in new candidate genes, but many of these are variants of uncertain significance (VUS). The International Mouse Phenotyping Consortium (IMPC) is an effort to establish gene function by knocking-out all genes in the mouse genome and generating corresponding phenotype data. We used mouse embryonic imaging data generated by the Deciphering Mechanisms of Developmental Disorders (DMDD) project and identified 51 genes that cause recessive, embryonic pituitary malformations in embryonic lethal or subviable knockout mice. These genes not only represent new candidates for CH, but also reveal new molecular pathways not previously associated with pituitary organogenesis. We used this list of candidate genes to mine whole exome sequencing data of a cohort of patients with CH, and we identified variants in two unrelated cases for two genes, MORC2A and MKS1, not previously associated with CH. This provides proof-of-principle that recessive lethal mouse mutants are an excellent source of candidate genes for congenital hypopituitarism in children
2024-05-15 | GSE246211 | GEO
Project description:<p>We investigated the cumulative contribution of rare, exonic genetic variants on the concentration of 1,487 metabolites and 53,714 metabolite ratios in urine by performing gene-based tests based on 226,233 variants from up to 4,864 participants of the German Chronic Kidney Disease (GCKD) study. There were 128 significant associations (53 metabolite-gene and 75 metabolite ratio-gene pairs) involving 30 unique genes, 16 of which are known to underlie recessively inherited inborn errors of metabolism (IEMs). Across the 30 genes, 47% of individuals carried at least one rare missense, stop or splice variant. The 30 genes were strongly enriched for shared high expression in liver and kidney (OR=65, p-FDR=3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of whole-exome sequencing data in the UK Biobank allowed for linking genes to diseases that could plausibly be explained by the identified metabolites. In silico constraint-based modeling of knockouts of the implicated genes in a virtual whole-body, organ-resolved metabolic human correctly predicted the observed direction of metabolite changes in urine and blood, highlighting the potential of linking population genetics to modeling to validate associations and to predict metabolic consequences of yet unknown IEMs. Our study extends the map of genes influencing urine metabolite concentrations, reveals metabolic processes and connected health outcomes, and implicates novel candidate variants and genes for IEMs.</p><p><br></p><p>Further links;</p><p><a href='https://www.gckd.org/' rel='noopener noreferrer' target='_blank'>German Chronic Kidney Disease (GCKD)</a></p>
2021-03-09 | MTBLS284 | MetaboLights
Project description:Background: Causative genes are mostly unknown for the mismatch repair-proficient category of familial colorectal cancers designated as FCCTX. Recent evidence suggests shared susceptibility factors between colorectal and hematological malignancies. Study design: We investigated 28 FCCTX families by exome sequencing, supplemented with whole genome sequencing, RNA-sequencing, and tumor studies to identify the predisposing genes. Guided by the findings, germline and somatic exomes of ~400 patients with acute leukemia, myelodysplastic syndrome, and myeloma were subsequently examined. Results: A family with hematological and solid malignancies revealed a truncating variant in the DEAH-box RNA helicase gene DHX40 co-segregating with disease in seven family members. Neoplastic tissues revealed no apparent “second hit”, implying a haploinsufficiency model of tumorigenesis. DHX40 siRNA-treated cell lines exhibited a 13% increase in aberrantly spliced transcripts vs. GAPDH-siRNA or non-target siRNA-treated cells. Two additional families showed truncating germline variants in the TDRD9 and TDRD5 genes encoding Tudor domain-containing RNA-binding proteins. In the hospital-based hematological series, 18% of germline and 28% of somatic exomes revealed possibly pathogenic DEAD/H box gene variants, including somatic variants of DHX40 in four. Conclusions: This study identifies DHX40, TDRD9, and TDRD5 as novel candidate genes for FCCTX predisposition. In the family segregating the truncating DHX40 variant, two carriers had hematological neoplasia, suggesting possible analogy to DDX41, a DEAD-box RNA helicase gene previously linked to myeloid malignancies. Our findings emphasize aberrant RNA metabolism behind FCCTX and hematological neoplasia.
2023-11-08 | GSE228991 | GEO
Project description:It is widely recognized that the missing heritability of many human diseases is partially due to noncoding genetic variants, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals, and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multi-granular information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell-stage-specific regulatory roles three top novel regulatory elements on our list, respectively in the RET, RASGEF1A and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the affects the binding of the gliogenesis regulator NFIA, with a corresponding down-regulation of multiple genes in the same topologically associating domain.
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