4076 results for "*geneti*"

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• Long-read whole genome sequencing of gastric cancer

  Gastric cancer (GC) remains a significant health challenge globally, with a particularly high incidence in Asia, including Singapore. Understanding the genomic landscape of normal gastric and the different GC subtypes along with its precursor lesions such as intestinal metaplasia (IM) as well as GC metastatic sites is crucial for advancing diagnostics, prognostics, and therapeutics. Long-read sequencing technologies offer an opportunity to delve deeper into the genomic and epigenetic alterations underlying these conditions and to complement existing short-read omics data. By integrating these data with previously generated in-house multi-omics data (such as RNA sequencing and whole exome sequencing), we hope to better elucidate the molecular mechanism underlying GC initiation and progression.

  Study EGAS50000001607

• TMEM259 alleles modulate respiratory syncytial virus infection and ER-stress-triggered apoptosis

  Whole Exome Sequencing data for the IRIS1, IRIS2, and IRIS3 cohorts. Abstract: Respiratory syncytial virus (RSV) is a main cause of infant morbidity and mortality. Susceptibility factors for severe RSV bronchiolitis in previously healthy children are unclear. We analyze genetic variants in 5,141 genes involved in virus sensing, interferon (IFN) signaling and effector functions in a population of n=101 previously healthy infants with severe RSV bronchiolitis. Comparing the allele frequencies of the patient cohort with the Exome Aggregation Consortium (ExAC) dataset our analysis reveals 94 non-synonymous coding single nucleotide polymorphisms (SNPs) mapping to 79 potential risk genes. Follow up of genes expressed in human lung cells show that TMEM259 (also known as membralin), a protein involved in regulating endoplasmic reticulum (ER) stress and neuronal cell survival, restricts RSV infection. Analysis of engineered human airway cells endogenously expressing the TMEM259 major allele or the rs77868901 minor variant shows allele-dependent modulation of RSV infection and ER-stress induced apoptosis, but not IFN activity nor induction of IFN stimulated genes. TMEM259 abundance and polymorphisms modulate RSV infection likely by modulating the ER stress response and apoptosis. This data may aid future risk stratification and development of prevention and treatment strategies for RSV.

  Study EGAS50000001971

• Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm

  Mobile element insertions (MEIs) are a significant source of human genetic variation, yet the rates and properties of de novo MEIs are poorly characterized due to technical limitations in sequencing technology. Here, we directly sequenced individual gametes from sperm samples of 19 donors (aged 27-62) using highly accurate PacBio long-read sequencing to identify de novo retrotransposition events without familial inference. We developed a “self-alignment” strategy using personalized genome assemblies that enables high-precision, single-read detection of de novo MEIs. Using this method, we identified 43 de novo Alu insertions, revealing >9-fold variation in Alu retrotransposition rates between individuals (ranging from 0 to 0.148 insertions/gamete). We found a significant increase in Alu activity with paternal age, yielding a 4.67% increase in insertions per gamete per year of additional paternal age, representing a direct observation of age-associated increases in structural variant (SV) mutation rates. De novo Alu insertions predominantly represent evolutionarily young AluYa5 and AluYb8 subfamilies and bear characteristic molecular signatures of target-primed reverse transcription (TPRT). Our population-averaged rate of 4.52 insertions per 100 gametes aligns well with previous population genetic estimates, validating both direct observation and population approaches for estimating de novo MEI rates. These results establish direct gamete sequencing as a powerful method for characterizing germline mutation processes and reveal age as a significant determinant of de novo retrotransposition in the male germline.

  Study EGAS50000002110

• Integrating transcriptional regulatory networks with chromatin accessibility as markers of survival outcome and drug response in triple-negative breast cancer

  Patients with triple-negative breast cancer (TNBC), a highly aggressive and heterogeneous breast cancer subtype, have limited effective targeted therapy options and frequently develop resistance to chemotherapy. Transcription regulators (TRs) guided precision medicine, namely anti-estrogen receptor therapy, has proven successful in hormone-dependent breast cancer, but remains a challenge in TNBC. Here, we identified key TRs underlying TNBC identity by combining a transcriptional interaction network with chromatin accessibility and defined TR activity score metrics. We show that the activity scores of these TRs independently discriminate patient outcome across different clinical endpoints. Matching TR activity scores to drug sensitivity identified drug-TR pairs across independent datasets, including NFE2L3 and CBFB activity associated with sensitivity to mTOR inhibition, which we validated using a cohort of TNBC patient-derived xenografts. Collectively, we present methodology to promote TR-guided precision medicine that captures inter-tumor heterogeneity in TNBC and nominates drug sensitivities according to TR activity scores inferred from expression and chromatin accessibility data.

  Study EGAS50000001691

• scATAC-seq of CD4+ T cells from blood, lymph nodes and tumors of NSCLC patients

  This study explore the CD4+ T cells diversity in paired blood, lymph nodes and tumors of 2 different NSCLC patients. After FACS-sorted of Tregs (DAPI- CD45+ CD4+ CD25hi CD127lo) and Tconvs (DAPI- CD45+ CD4+CD25lo CD127lo/hi), cells were mixed in equal proportion (fifty/fifty ratio) and procesed with 10X Chromium (10X Genomics) scATAC kit and sequenced using Illumina platforms.

  Study EGAS50000000294

• Germline whole-genome sequencing (WGS) of colorectal cancer patients

  Whole-genome sequencing (WGS) data generated from matched germline blood DNA samples obtained from patients with primary or metastatic colorectal adenocarcinoma (n=37). These data were generated as part of a multiomic study integrating whole-genome sequencing with single-cell multiome profiling to investigate recurrent epigenetic alterations in colorectal cancer evolution and the tumour microenvironment.

  Dataset EGAD50000002942

• Whole Genome Sequencing (WGS) of Tumour Samples of Primary and Metastatic Colorectal Cancer

  WGS samples of primary (n=33) and metastatic (n=11) colorectal cancer tissues related to Livanova et al. manuscript 'Epigenetic evolution of colorectal cancer and its microenvironment reveals new vulnerabilities'

  Dataset EGAD50000002943

• Single-cell 10x Genomics Multiome ATAC-seq data from primary and metastatic colorectal cancers and normal colon tissues

  This dataset contains single-cell 10x Genomics Multiome ATAC-seq data from 33 primary colorectal cancer, 11 metastatic colorectal cancer, and 7 matched normal colon tissue samples generated as part of the study "Epigenetic evolution of colorectal cancer and its microenvironment reveals novel vulnerabilities."

  Dataset EGAD50000002944

• Single-cell 10x Genomics Multiome RNA-seq data from primary and metastatic colorectal cancers and normal colon tissues

  This dataset contains single-cell 10x Genomics Multiome RNA-seq data from 33 primary colorectal cancer, 11 metastatic colorectal cancer, and 7 matched normal colon tissue samples generated as part of the study "Epigenetic evolution of colorectal cancer and its microenvironment reveals novel vulnerabilities."

  Dataset EGAD50000002945

• Human breast cancer epigenetic sequencing data

  Controlled-access sequencing data generated from human breast tumor samples in the study "Epigenetic Heterogeneity in Breast Tumors with Implications for Disease Diagnosis and Monitoring". The dataset includes whole-genome DNA methylation sequencing, enzyme-mediated methylation sequencing of sorted tumor-cell populations, single-nucleus CUT&Tag, and single-cell RNA and chromatin-accessibility multiome sequencing. Raw sequencing data are provided as FASTQ files.

  Dataset EGAD50000002972

• Genetic Effects on the Skin Methylome in Healthy Older Twins

  Study EGAS00001007816

• 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

• 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

• Alterations of whole genome and extrachromosomal circular cell-free DNA fragmentomes across the cancer care continuum

  The origins and properties of cancer-associated genetic changes in cell-free DNA (cfDNA) are not fully understood. Through genome-wide analyses of 1,807 samples from 1,064 patients across eight common cancer types, we identified extrachromosomal circular DNA (eccDNA) as a source of cfDNA fragments. Characterization of eccDNA-derived cfDNA fragments along with single base substitutions, small insertions and deletions, rearrangements, and phased variants in single cfDNA molecules, revealed differences between tumor tissues and cfDNA, with an increase in tumor-derived cfDNA alterations at epigenetically repressed regions and a decrease at active promoters. Combination of variant characteristics with individual error rates and machine learning analyses enabled tumor-informed and tumor-independent measures of circulating tumor DNA for early detection, detection of minimal residual disease, and for monitoring patients during therapy. The universal nature of eccDNA and other tumor-derived characteristics of cfDNA may be broadly useful for cancer detection.

  Study EGAS50000001331

• Cryptic mRNA Splicing in FLT3 Internal Tandem Duplications

  NGS analyses of genetic material from Acute Myeloid Leukemia cases harboring FLT3 Internal Tandem Duplications to investigate the occurrence of cryptic mRNA splicing.

  Study EGAS50000002156

• A nationwide prospective randomized trial for diagnosing developmental disorders demonstrates whole-genome sequencing outperforms whole-exome sequencing.

  Whole-exome (WES) or whole-genome (WGS) sequencing are recommended as first- or second-tier molecular tests for patients with developmental disorders (DD), but the clinical utility of WGS continues to be debated. This prospective randomized trial involving all Belgian Human Genetics centers compared the standard of care (SoC) - combining WES and microarray or shallow WGS - with WGS for 567 individuals with unexplained DD. The diagnostic yield of WGS was 39.8% (113/284) vs 30% for SoC (85/283) (p=0.015), mainly due to an increased detection of single nucleotide variants and indels (+8.7%). WGS also enabled the detection of three non-coding (potential) pathogenic variants. Diagnostic yield was higher for females (45.5%, 97/213) compared to males (28.5%, 101/354) (p<0.001). De novo variants were found for 23.6% of patients. Analysis of inherited variants in genes associated with autosomal dominant phenotypes contributed more to the diagnostic yield (3.9%) than X-linked variants (1.9%), and to a similar extent as autosomal recessive variants (4.1%). This nationwide study demonstrates WGS outperforms WES for the diagnosis of patients with DD in a decentralized hospital setting and well-characterized cohort. The results also highlight the importance of evaluating autosomal dominant inherited variants in genomics analyses for DD.

  Study EGAS50000002018

• Distinct immune and genomic signatures predict resistance to ibrutinib therapy in Waldenström macroglobulinemia

  In this study, we investigate the complex interplay between tumour-acquired genetic features and the composition of the microenvironment in the promotion of ibrutinib resistance in WM patients by integrating single-cell RNA sequencing (scRNAseq) and whole-genome sequencing (WGS), to examine bone marrow tumour and immune compartments from 37 symptomatic WM patients treated with ibrutinib.

  Study EGAS50000001586

• Characterization of cell types, positional codes, and enhancers contributing to human facial individuality and pathology

  Human genetic diversity generates an astonishing variety of facial shapes, and craniofacial anomalies rank among the most common birth defects. This study generated a multimodal atlas of human embryonic craniofacial development across embryonic weeks 6–11, including single-cell transcriptomics, chromatin accessibility, and spatial transcriptomics. The dataset characterizes cell states, mesenchymal subtypes, and their gene-enhancer cis-regulatory landscapes in space and time. These data provide a resource for studying normal human facial development, craniofacial abnormalities, and the genetic mechanisms underlying facial individuality.

  Study EGAS50000002001

• Cryptic mRNA Splicing in FLT3-ITD mutated Acute Myeloid Leukemia

  NGS analyses of genetic material from Acute Myeloid Leukemia cases harboring FLT3 Internal Tandem Duplications to investigate the occurrence of cryptic mRNA splicing. DNA extracted from diagnostic bone marrow sample was used for library preparation and then NGS was performed using Sophia DDMTM Myeloid Solution Panel, Thermofisher ION S5 Platform.

  Dataset EGAD50000003093

• BeSolveRD : a nationwide randomized trial comparing whole exome vs whole genome sequencing in developmental disorders

  Whole-exome (WES) and whole-genome (WGS) sequencing of 567 patients with developmental disorders for which a prospective randomized trial involving all Belgian Human Genetics centers was done to compare the standard of care - combining WES and microarray or shallow WGS - with WGS.

  Dataset EGAD50000002905

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  Documentation discovery/metadata/search-box

• Privacy Notice for Data Access Committee Account

  Privacy Notice for EGA Data Access Committee Account This Privacy Notice explains what personal data is collected by the specific service you are requesting, for what purposes, how it is processed, and how we keep it secure. Note that this service collects personal data directly provided by the user, and also collects personal data from users that is provided by other organisations. 1. Who controls your personal data and how to contact us? European Genome- Phenome Archive - EGA offers a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects, jointly managed by European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI) and Fundació Centre de Regulació Genòmica - Centre for Genomic Regulation (CRG). EMBL-EBI and CRG represent joint Data Controllers’ of processing of your personal data. 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  Documentation data-protection/privacy-notice/ega-dac

• Data Use Ontology (DUO)

  Data Use Ontology Data Use Ontology at EGA The EGA is committed to its involvement in the work of GA4GH. In an effort to enhance data discoverability and streamline data access, EGA have implemented the use of the Data Use Ontology (DUO), based on consent codes as described in Dyke et al. 2017. The Data Use Ontology codes will be displayed on the live dataset page of your submission to advise any would be requestor on how the data can be used and also to enhance data discoverability as users will be able to search on these codes to find applicable datasets. DUO can be browsed online via the Ontology Lookup Service Learn more reading the Data Use Ontology publication and the GA4GH Machine-Readable Consent Guidance! Check our DAC Portal Take The Tour and learn how to add DUO codes to your policy! Term Shorthand Label Description DUO:0000004 NRES no restriction This data use permission indicates there is no restriction on use. DUO:0000042 GRU general research use This data use permission indicates that use is allowed for general research use for any research purpose. DUO:0000006 HMB health or medical or biomedical research This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. DUO:0000007 DS disease specific research This data use permission indicates that use is allowed provided it is related to the specified disease. DUO:0000011 POA population origins or ancestry research only This data use permission indicates that use of the data is limited to the study of population origins or ancestry. DUO:0000012 RS research specific restrictions This data use modifier indicates that use is limited to studies of a certain research type. DUO:0000015 NMDS no general methods research This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms). DUO:0000016 GSO genetic studies only This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively) DUO:0000018 NPUNCU not for profit, non commercial use only This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. DUO:0000019 PUB publication required This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000020 COL collaboration required This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000021 IRB ethics approval required This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000022 GS geographical restriction This data use modifier indicates that use is limited to within a specific geographic region. DUO:0000024 MOR publication moratorium This data use modifier indicates that requestor agrees not to publish results of studies until a specific date. DUO:0000025 TS time limit on use This data use modifier indicates that use is approved for a specific number of months. DUO:0000026 US user specific restriction This data use modifier indicates that use is limited to use by approved users. DUO:0000027 PS project specific restriction This data use modifier indicates that use is limited to use within an approved project. DUO:0000028 IS institution specific restriction This data use modifier indicates that use is limited to use within an approved institution. DUO:0000029 RTN return to database or resource This data use modifier indicates that the requestor must return derived/enriched data to the database/resource. DUO:0000043 CC clinical care use This data use modifier indicates that use is allowed for clinical use and care. DUO:0000044 NPOA population origins or ancestry research prohibited This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited. DUO:0000045 NPU not for profit organisation use only This data use modifier indicates that use of the data is limited to not-for-profit organisations. DUO:0000046 NCU non-commercial use only This data use modifier indicates that use of the data is limited to not-for-profit use. Point to Notice: For the consent code DUO:0000007 where data is restricted to use on a specific disease, please accompany it with an appropriate ontology from MONDO e.g., If the data is restricted to the use of research into juvenile idiopathic arthritis the code should be displayed as DUO:0000007; MONDO:0011429.

  Documentation access/data-access-committee/data-use-ontology