4051 results for "*geneti*"

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• Molecular Landscape of Hypertrophic Cardiomyopathy Across Disease Stages and Genotypes

  Hypertrophic Cardiomyopathy (HCM) is marked by asymmetric cardiac wall thickening, enhanced contractility, diastolic dysfunction, and fibrosis. Pathogenic sarcomere gene variants cause HCM, but comparable abnormalities occur in patients with unexplained disease albeit with fewer adverse events. We applied single-nucleus RNA sequencing to investigate how genetic and unexplained HCM affect early disease mechanisms and to contrast HCM with dilated cardiomyopathy (DCM). This EGA dataset contains HCM and control data. DCM and additional control snRNA-seq data, integrated in this study, are available under the EGA dataset accession number: EGAD00001009292.

  Study EGAS50000001411

• Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes

  Current single-cell multiomics methods typically provide limited genomic information, constraining genotype-phenotype studies. To address this gap, we developed SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome), which integrates 10X Genomics barcoding with Oxford Nanopore sequencing to simultaneously profile genome, chromatin accessibility, and full-length transcriptomes in thousands of single cells. By retaining all tagmentation fragments during library preparation, SPLONGGET delivers whole-genome coverage, supports target enrichment for effective single-cell genotyping, and remains backwards compatible with existing short-read workflows. We apply SPLONGGET to longitudinal samples from a case of pediatric B-cell acute lymphoblastic leukemia (B-ALL) to reveal clonal dynamics during therapy and the phenotypic effects of somatic variation, providing valuable insights into disease progression and relapse. In conclusion, SPLONGGET enables integrated high-throughput analysis of genetic variation and molecular phenotypes using off-the-shelf kits, offering a timely and powerful tool to study genetically heterogeneous samples, such as tumours but also ageing normal tissues.

  Study EGAS50000001278

• Raw fastq files (not trimmed) from RNAseq sequencing

  Samples from infants diagnosed with KMT2A-r B-ALL confirmed by comprehensive immunophenotypic and molecular/cytogenetic features. Mononuclear cells containing >87% blasts were isolated by density gradient centrifugation. Immunophenotyping was performed using the monoclonal antibodies CD45-FITC, CD19-APC, and NG2-PE. NG2POS (NG2 positive) and NG2NEG (NG2 Negative) B-ALL blasts (CD45dimCD19+) were sorted by fluorescence-activated cell sorting (FACS) using a FACS-Aria Fusion cell sorter (BD Biosciences).

  Study EGAS50000001244

• Proteomics of human cancer-associated T cells identifies regulators of T cell functionality

  CD8⁺ T cells in solid tumors progressively lose anti-tumor activity, yet the cell-intrinsic mechanisms driving this loss of function remain incompletely defined. Here, we performed matched proteomic and transcriptomic profiling of dysfunctional and bystander CD8⁺ tumor-infiltrating T cells isolated from primary tumors of treatment-naïve non-small cell lung cancer patients. Proteomic analysis revealed widespread discordance with mRNA expression, with 8% of differentially expressed proteins detected exclusively at the protein level. Genetic perturbation of such differentially expressed proteins identified the chromatin remodeler CHD4 and fatty acid synthase (FASN) as cell-intrinsic regulators of T cell function. CHD4 deletion promoted effector differentiation and enhanced cytokine production, whereas FASN deletion preserved mitochondrial fitness and sustained T cell functionality under chronic T cell receptor stimulation. Together, these findings demonstrate that proteomic profiling uncovers regulators of T cell functionality that are not apparent from transcriptomic analyses alone, highlighting an additional layer of regulatory control.

  Study EGAS50000001886

• Frequency and prognostic significance of genetic abnormalities in a subgroup of intermediate risk neuroblastoma patients: A SIOPEN study

  Intermediate risk neuroblastoma includes a rare subgroup of patients over the age of 18 months at diagnosis with unresectable, localised tumours with unfavourable histology without MYCN amplification. This group is treated differently around the world with some patients receiving upfront myeloablative therapy (MAT) in addition to standard treatment with chemotherapy, surgery, radiotherapy and 13 cis retinoic acid, but the overall 5-year patient survival with or without MAT is similar (75%). This study aimed to understand the neuroblastoma biology of this rare patient subgroup.

  Study EGAS50000001908

• Reduced platelet formation associated with serine metabolic dysregulation in integrin αIIbβ3-deficient megakaryocytes

  Glanzmann Thrombasthenia (GT) is characterized by absent platelet aggregation in response to all agonists except ristocetin and is caused by recessive inactivating variants in ITGA2B or ITGB3. While GT patients typically are described as having normal platelet counts, autosomal dominant activating variants in ITGA2B or ITGB3 cause macrothrombocytopenia. Interestingly, in our cohort of 16 GT patients, eight consistently exhibited platelet counts at the lower end of the normal range. We studied the role of integrin αIIbβ3 in platelet formation using megakaryocytes (MKs) derived from genetically modified immortalized megakaryocyte cell lines (imMKCLs), focusing on two modifications of ITGB3: ITGB3-/- (inactivating) and ITGB3WT/D673_E713del (activating). In static differentiation cultures, ITGB3-/- and ITGB3WT/D673_E713del imMKCLs exhibited normal MK differentiation but reduced proplatelet formation. Platelet production was also impaired in a 3D silk-based bone marrow system and in shaking cultures, confirming a quantitative role for ITGB3 in platelet production, independent of the type of variant. While TRAP-activated in vitro-generated platelets lacking αIIbβ3 failed to bind the activation-dependent PAC-1 antibody, ITGB3WT/D673_E713del platelets bound PAC-1 prior to activation mimicking the patient’s phenotype. Transcriptome profiling and metabolomic analyses ofintegrin αIIbβ3 deficient MKs revealed impaired serine metabolism and downregulation of SLC3A2 (CD98hc), an amino acid transporter chaperon known to interact with the β3 subunit. Flow cytometry confirmed decreased CD98hc in mutant MKs, while re-expression of wild-type ITGB3 in ITGB3-/- MKs restored αIIbβ3 and CD98hc expression, normalized proplatelet formation, and enhanced serine uptake. These results uncover a previously unrecognized role of integrin αIIbβ3 in coupling serine metabolism to platelet biogenesis.

  Study EGAS50000001711

• RNA sequencing of genetically modifed immortalized megakaryocytes

  The dataset contains bulk RNAseq samples from 7 ITGB3 mutants (3 with ITGB3 knock-out and 4 with an ITGB3 splice variant) compared to 4 wildtypes. The ITGB3 mutants and WT_1 and WT_2 are from the same batch; WT_3 and WT_4 are from another sequencing batch. The library was performed using the TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold kit and the read length is 100 bp.

  Dataset EGAD50000002462

• Germline variants in patients with five cutaneous melanoma

  Skin melanoma arises from a complex interplay between UV radiation exposure and inherited genetic susceptibility. A subset of invidiuals experience multiple independent tumours, suggestingh a stronger underlying genetic component. In this study, we investigate the germline contribution to melanoma development in individuals diagnosed with five or more primary melanomas.

  Study EGAS50000001361

• RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs

  Methods: We compared the efficacy of B7-H3 CAR T-cells between SJ-DIPGX7c (DMG) and U87-MG (adult glioblastoma) patient-derived cell lines and showed impaired efficacy both in vitro and in vivo. We performed live-cell imaging and single-cell RNA sequencing to investigate deficiencies in immune synapse (IS) formation between CAR T-cells and DMGs. Lastly, we genetically deleted RASA2, a negative regulator of T cell activation, and evaluated the resulting impact on IS formation and quality, as well as in vitro and in vivo functionality. Sample preparation and sequencing For single cell RNA sequencing, two sets of co-culture arrays were prepared: (1) 2.5×106 Ctrl T cells were co-cultured with 2.5×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG) and (2) 1×106 CAR T-cells were co-cultured with 4×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG). Both co-culture arrays were incubated at 37°C 5% CO2 for 16 hours. Co-cultures were enzymatically digested with Accutase (Thermofisher; A1110501) for 10 min at room temperature, and cells were filtered by using Miltenyi dead cell removal kit (Miltenyi; 130-090-101). Highly viable cells were recovered and prepared using the Fixation Kit (PARSE Bioscience) according to manufacturer ‘s protocol. After fixation, the cell count was determined by using a Neubauer hemocytometer. A total of 1.14×105 cells from 12 coculture conditions were used, resulting in approximately 9.5×104 cells per condition. These cells were subjected to the Single Cell Whole Transcriptomic kit v2 (PARSE Bioscience) for library construction. Libraries were subsequently sequenced using the Illumina NovaSeq 6000 platform, generating paired-end 200 bp reads.

  Dataset EGAD50000002785

• Single-cell RNA sequencing of liver metastasis-derived colorectal cancer organoids profiling cellular heterogeneity and lineage dynamics across time

  The objective of this analysis was to identify, at single-cell resolution, trasncriptionally distinct subpopulations in untreated metastatic colorectal cancer organoids with diverse genetic backgrounds and to investigate their temporal dynamics.

  Study EGAS50000001927

• Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes

  Sri Lanka has played a key role in the peopling of South Asia, with archaeological evidence for human presence on the island dating back to ⁓40,000 years ago. Present-day Indigenous peoples of the island, the Adivasi, are proposed to have descended from early inhabitants of the region, while urban populations like the Sinhalese, the major ethnic group on the island, migrated from India in historical times. Using whole genomes from 19 Adivasi individuals belonging to two clans and from 35 Sinhalese, we find that the Adivasi and Sinhalese share high genetic similarities with each other and with other Sri Lankan and Indian populations, especially those with greater genetic affinity to Ancestral South Indians (ASI). Admixture modeling of the Sri Lankan groups reveals that despite shared ancestral components, the Adivasi retain higher genetic contributions from ancient hunter-gatherers compared with the Sinhalese. Additionally, in contrast to the Sinhalese, the Adivasi have maintained low effective population size and undergone strong founder events, which is consistent with their hunter-gatherer lifestyle, historic relocations, and habitat fragmentation. While the two Adivasi clans are genetically more similar to each other than to any other populations, we observe differing demographic histories, with the Interior Adivasi experiencing a stronger bottleneck than the Coastal Adivasi since their split. This whole-genome-based study addresses gaps in our understanding of the demographic and migratory history of two key Sri Lankan groups and, consequently, of broader South Asia by illuminating complex population structure that has been shaped by both demographic and socio-cultural factors.

  Study EGAS50000001928

• Plasma CTCF ChIP-seq Reveals Cancer-Associated cfDNA Binding Profiles

  Cell-free DNA (cfDNA) in plasma predominantly exists as nucleoprotein complexes. Although circulating CTCF-bound cfDNA (cfCTCF-DNA) has previously been reported, the occupancy of individual CTCF binding sites in plasma has not been systematically characterised. This study describes the isolation of endogenous plasma cfCTCF-DNA by chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) in samples obtained from cancer patients and healthy individuals. A two-step enrichment strategy was employed, combining physical removal of background cfDNA by immunoprecipitation with bioinformatic filtering to remove residual non-CTCF-derived sequences. Sequencing reads were aligned to the UCSC hg38 reference genome using BWA-MEM v0.7.17 and processed to generate CRAM files containing alignments restricted to the primary chromosomes (chr1–chr22, chrX, chrY and chrM). CTCF-associated cfDNA fragments were classified according to their similarity to a consensus CTCF binding motif, enabling discrimination between low-affinity and high-affinity CTCF binding sites. Comparative analyses identified quantitative and qualitative differences in plasma cfCTCF-DNA profiles between healthy individuals and patients with cancer. The deposited dataset comprises plasma cfCTCF-DNA ChIP-seq data from four clinical cohorts and includes both CTCF-enriched and total cfDNA samples where applicable. These data support the investigation of CTCF occupancy patterns as a novel class of liquid biopsy biomarkers for cancer detection and monitoring.

  Study EGAS50000001937

• Urine cfDNA workflow for epigenomic profiling.

  Urine cell-free DNA (cfDNA) holds great promise as a non-invasive biomarker for diagnosis, prognosis and treatment monitoring of diseases. However, its clinical utility is challenged by high nuclease activity and rapid degradation, necessitating an optimized urine cfDNA workflow. We evaluated a workflow for urine cfDNA methylation and fragmentation profiling, comparing PAXgene Urine Technology, with Streck Urine Preserve and unstabilized urine, using enzymatic methyl sequencing of cfDNA from healthy individuals, across multiple urine storage time points (immediate, 6 h, and 72 h). Urine stabilization significantly improved cfDNA yield and preserved cfDNA fragment sizes, while unstabilized samples exhibited marked degradation and reduced sequencing quality. Methylation analysis revealed high concordance between stabilized samples, with subtle divergence after 72 h. In contrast, unstabilized samples showed widespread methylation changes. Biological patterns were retained in stabilized urine cfDNA. Our study underscores the importance of well-designed (pre)analytical urine workflows to allow urine cfDNA (epi)genomic analyses.

  Study EGAS50000001535

• Circulating cell-free DNA methylation profiles as noninvasive multiple sclerosis biomarkers: A proof-of-concept study

  In chronic neurodegenerative diseases such as multiple sclerosis (MS), there is a critical unmet need for cost-effective non-invasive blood biomarkers to concurrently classify disease subtypes, monitor disability severity, and predict long-term progression. In this proof-of-concept study, we performed low-coverage whole-genome bisulfite sequencing (WGBS) on 75 plasma cell-free DNA (cfDNA) samples collected from a well-characterized real-world prospective clinic cohort with longitudinal disability outcome measurements. We assessed the clinical utility of cfDNA methylation profile for differentiating MS patients from non-MS controls, classifying MS subtypes, estimating disability severity, and predicting disease trajectories.

  Study EGAS50000001277

• INTEGRATIVE MOLECULAR ANALYSIS OF SKIN TUMORS FROM CYLD CUTANEOUS SYNDROME PATIENTS

  CYLD cutaneous syndrome (CCS) is a rare autosomal dominant disorder characterized by germline CYLD mutations and by multiple benign skin tumors dependent on NF-kB pathway. We assembled a large cohort of CCS rare skin tumors that was profiled with whole exome or genome sequencing, RNA sequencing and methylation arrays to better understand genetic mechanisms of CCS tumorogenesis.

  Dataset EGAD50000000362

• Multi-omic signatures in multiple myeloma

  Multiple myeloma (MM) is a genetically and clinically heterogeneous plasma-cell malignancy. Quadruplet therapy, combining anti-CD38 antibodies, immunomodulatory drugs, proteasome inhibitors, and dexamethasone, is now the standard induction treatment for newly diagnosed multiple myeloma (NDMM). To gain a comprehensive view of molecular changes in MM and their association with treatment response in this new standard care, we performed a multi-omic study of 423 NDMM from the MIDAS trial.

  Study EGAS50000001573

• Epigenetic and Transcriptomic profiling of hiPSC- and UCB-HSC derived CD4+CD8+ T progenitors

  Generation of T cell subsets from human induced pluripotent stem cells (hiPSCs) in defined in vitro systems could provide a valuable model to study the mechanisms of human T cell development in the thymus and serve as a scalable source for therapeutic cell products. We generated a unique DNA methylation (DNAmeth) and RNA-seq dataset of in vitro generated hiPSC-derived and umbilical cord blood (UCB-) derived T cell progenitor subsets from a feeder-free differentiaion system and integrated them with data from primary human thymocyte populations.

  Study EGAS50000001929

• Genotyping data from low-coverage whole genome sequencing (lc-WGS) for 90 Asian individuals

  A uniquely comprehensive genetic profile of 90 "healthy" Asian individuals who are representative of the diverse multi-ethnic population of Singapore, with 65 females and 25 males, aged 21 to 61 years, from the major ethnic groups (63 Chinese, 9 Malay, 18 Indian). This is a subset of the 92 participants described in PMID 41387625 (DOI: 10.1038/s43856-025-01298-4), who agreed to share their genetic data for future research beyond the original study. Replicates for one female (Coriell Cat# GM18592, RRID:CVCL_P195) and one male (Coriell Cat# GM18609, RRID:CVCL_P207) control cell line of type B-Lymphocyte, ethnicity Han Chinese from the NHGRI Sample Repository for Human Genetic Research were also included in each of the four flowcell lanes. This dataset consists of individual-level genetic data from low-coverage whole genome sequencing (lc-WGS, read length 2X150bp). Data from 4 commercially available genotyping arrays for the same samples is also available on EGA (EGAD00010002834).

  Dataset EGAD50000002806

• Genotyping data from four arrays for 90 Asian individuals (Illumina GDA, Illumina GSA, Illumina OncoArray, and ThermoFisher Axiom)

  A uniquely comprehensive genetic profile of 90 "healthy" Asian individuals who are representative of the diverse multi-ethnic population of Singapore, with 65 females and 25 males, aged 21 to 61 years, from the major ethnic groups (63 Chinese, 9 Malay, 18 Indian). This is a subset of the 92 participants described in PMID 41387625 (DOI: 10.1038/s43856-025-01298-4), who agreed to share their genetic data for future research beyond the original study. Replicates for one female (Coriell Cat# GM18592, RRID:CVCL_P195) and one male (Coriell Cat# GM18609, RRID:CVCL_P207) control cell line of type B-Lymphocyte, ethnicity Han Chinese from the NHGRI Sample Repository for Human Genetic Research were also included. This dataset consists of individual-level genetic data from 4 genotyping arrays -- the Illumina Infinium Global Diversity Array (GDA) v1.0, the Illumina Infinium Global Screening Array (GSA) v3.0, the Illumina Infinium OncoArray-500K v1.0, and a custom ThermoFisher Scientific's Applied Biosystems Axiom array. Data from low-coverage whole genome sequencing (lc-WGS read length 2X150bp) for the same samples is also available on EGA (EGAD50000002806).

  Dataset EGAD00010002834

• Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

  SMART-PTA single-cell whole-genome and full transcriptome sequencing form normal esophagus samples

  Dac EGAC50000000968

• Telomere variant sequences encode a heritable genetic blueprint for allele-specific telomere length

  Long read sequencing of 195 blood samples for allele-specific telomere detection

  Dataset EGAD50000002360

• Telomere variant sequences encode a heritable genetic blueprint for allele-specific telomere length

  A high-resolution workflow combining PacBio and Nanopore long-read sequencing platforms has been developed to map allele-specific telomere length in clinical patient samples. By tracing allele-specific telomeric sequence in family members across multiple generations, we show that telomeric variant sequences (TVSs) interspersed throughout the canonical repeat region are heritable (with mean similarity score > 0.95), allele-specific, and account for the extreme heterogeneity of telomere length between alleles.

  Study EGAS50000001642

• DAC of telomere variant sequences encode a heritable genetic blueprint for allele-specific telomere length

  DAC of telomere variant sequences encode a heritable genetic blueprint for allele-specific telomere length

  Dac EGAC50000000943

• Multi-omics analysis of chronic active EBV infection.

  Here we performed a comprehensive multi-omics analysis (genome, transcriptome, epigenome, and single-cell transcriptome and surface proteome) to elucidate the pathogenesis of CAEBV. Our multi-omics approach highlighted the complex interplay between genetic and epigenetic factors in the pathogenesis of CAEBV and suggest novel avenues for therapeutic strategies.

  Study JGAS000735

• Genetic analysis of nevus spilus-type congenital melanocytic nevus

  We performed whole-exome sequencing (WES) of lesional dermis and SNP array of peripheral blood, lesional epidermis, lesional dermis, and/or cultured melanocytes from individuals with nevus spilus-type congenital melanocytic nevus.

  Study JGAS000929