4052 results for "*geneti*"

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• Multi-omic data of subjects of FUSION study

  Finland-United States Investigation of NIDDM Genetics (FUSION) Study has sought to understand the genetic basis of type 2 diabetes (T2D) and diabetes-related traits including glucose, insulin, lipid levels, and obesity. We have performed extensive multi-omic characterization of the study subjects, including SNP array genotyping, whole genome/exome DNA sequencing of blood/tissue/iPSC cells generated from fibroblast, as well as RNAs. The study has provided crucial data for understanding molecular and cellular mechanisms of the disease-causing variants and their respective target genes. This set of data will be a valuable resource to the T2D community.

  Study EGAS00001008440

• VLAIO DenMark Project Data Access Committee

  The VLAIO DenMark Project Data Access Committee is responsible for reviewing and approving controlled-access requests for human genetic, immunological, omics, and associated phenotype data generated within the VLAIO O&O project HBC.2022.0988, titled “Use of multimodel omics technologies to study Dengue host response markers”. The project is a collaboration between Janssen Pharmaceutica NV, Universiteit Gent, and the Institute of Tropical Medicine Antwerp, covering dengue host-response data generated from human challenge, natural infection, and related biomarker studies. The DAC evaluates whether proposed data use is consistent with participant consent, applicable ethics approvals, data protection requirements, institutional policies, and the data access policy linked to the relevant EGA dataset. Access decisions should be made by the project representatives from Janssen, ITG, and UGent, including Ole Lagatie, Kevin Ariën, and Filip Van Nieuwerburgh. EGA will distribute controlled-access data only upon approval granted by this DAC.

  Dac EGAC50000001078

• Plasma Nucleosome Profiling Reports on Tumor Burden and Molecular Subtypes in Small Cell Lung Cancer

  Small cell lung cancer (SCLC) is an aggressive malignancy with dismal prognosis and marked transcriptional heterogeneity that drives distinct therapeutic vulnerabilities. The clinical translation of these molecular insights is limited by limited access to tumor biopsies. Here, we apply chromatin immunoprecipitation of cell-free nucleosomes carrying active histone modifications followed by sequencing (cfChIP-seq) to 441 plasma samples from individuals with advanced SCLC, other neuroendocrine carcinomas (NEC), non-SCLC cancers, and healthy controls. cfChIP-seq faithfully captured the epigenetic and transcriptional landscape of tumor-derived cfDNA, including SCLC tissue/cell-of-origin signatures, and yielded a quantitative score of tumor fraction that tracked radiographic burden and prognosis. Integrating plasma cfChIP-seq with matched tumor transcriptomes (n = 73, including 41 time-matched pairs), we show that cfChIP-seq levels at promoters of lineage-defining transcription factors (ASCL1, NEUROD1, POU2F3, and ATOH1) correlate strongly with tumor RNA and support noninvasive inference of SCLC transcriptional subtypes directly from plasma. These findings establish cfChIP-seq as a practical liquid-biopsy platform that reports real-time tumor state and subtype, enabling precision monitoring and laying the groundwork for subtype-informed therapeutic stratification in SCLC.

  Study EGAS50000001916

• A functional genomic links differential sperm methylation from overweight men to transposable element regulation in paternal origins of disease risk in children

  The occurrence of childhood neurodevelopmental disorders has been steadily increasing for decades yet we have little understanding of modes of inheritance implicated in these diseases. Epidemiology studies have revealed an association between an elevated paternal BMI and an increased risk for neurodevelopmental disorders in children, suggesting non-genetic modes of inheritance may be involved. Epigenetic marks –like DNA methylation at cytosines– are especially susceptible to environmental, diet and lifestyle changes. Yet, whether a man’s weight influences the sperm methylome and potentially impacts offspring development remains unresolved. Using MethylC capture (MCC)-sequencing, we identified over 38000 differentially methylated CpG (DMCs) in the sperm of men with an elevated BMI, with many occurring in regions that were enriched for neural gene and disease ontologies. Differentially methylated regions (DMRs) were enriched at transposable elements that can act as active enhancers during human zygotic genome activation, and at gene promoters for early lineage specification. These results suggest that sperm methylome alterations that are linked to elevated BMI may influence key embryonic transcriptional process, notably associated with trophectoderm and placental development.

  Study EGAS50000001028

• Cell-free DNA methylation profiling in classic Hodgkin lymphoma using cfEM-seq

  Genome-wide DNA methylation profiling using cfEM-seq and Ultima Genomics sequencing in classic Hodgkin lymphoma. The study includes plasma-derived cell-free DNA from patients with classic Hodgkin lymphoma together with classic Hodgkin lymphoma and anaplastic large cell lymphoma cell lines. The deposited data comprise original sequencing CRAM files and associated sequencing-provider QC metadata.

  Study EGAS50000002038

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• Paroxysmal neurological disorders

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of the International Headache Genetics consortium and EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000048

• PAS Pedigrees: Identification of novel genetic variants contributing to cardiovascular disease in pedigrees with premature atherosclerosis.

  The heritability of CVD has been estimated to be between 40 and 55%. Due to the low MAF, PAS-causing mutations cannot be identified by indirect genotyping because their presence cannot be inferred from common haplotypes, as has been done successfully to uncover common risk variants by GWAS. It has been shown by Ng et al that the causative gene for rare syndromes can be unequivocally identified by sequencing the exomes of only four cases and eight controls. We expect exome sequencing to result in a high number of mutations and non-causitive coding variants.

  Study EGAS00001000052

• Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP)

  The Post-Transfusion Pupura (PTP) syndrome although rare has severe side effects for 5-10 cases per annum in the UK as a result of transfusion. High quality DNA has been isolated from either whole blood or from cryopreserved mononuclear cells of 4 patients in order to study our postulation that the condition is caused by a loss-of-function mutation in a specific gene.

  Study EGAS00001000053

• An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors

  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.

  Study EGAS00001000057