4051 results for "*geneti*"

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• cfDNA in health

  This study investigates baseline methylome and fragmentomic profiles in circulating cell-free DNA (cfDNA) from healthy individuals. Two cohorts were assembled: a diurnal cohort to evaluate temporal variation in cfDNA features, and a cross-sectional cohort to assess inter-individual variability. The project’s goal was to generate a reference dataset for plasma cfDNA to support future studies in biomarker discovery and disease detection.

  Study EGAS50000001209

• Diagnostic utility of clinical genome reanalysis in rare pediatric disorders using long-read sequencing

  More than half of presumed genetic disease cases remain undiagnosed following exome and/or short-read genome sequencing (SR-GS). Long-read genome sequencing (LR-GS) has emerged as a promising next step for uncovering etiologies missed by current standard-of-care SR genetic testing. However, structural variant (SV) interpretation remains a major challenge in LR-GS clinical pipelines, owing to limitations in SV call reliability, population allele frequency estimation, and evaluation of functional impact. To further develop strategies for the effective clinical use of LR-GS, we performed LR-GS using PacBio HiFi technology on 20 families with developmental disorders of suspected genetic origin and prior negative or inconclusive genetic testing (including exome and/or genome sequencing). Analysis was performed using a comprehensive pipeline integrating phased assembly– and read-based variant calling with LR-GS population allele frequency filtering. Phenotype-driven variant prioritization using Human Phenotype Ontology (HPO) terms was performed using a combination of tertiary analysis solutions, including publicly (SvAnna) and commercially (Illumina Emedgene) available tools. Definitive diagnostic findings were identified in 1/20 (5%) families. Variants of suspicious diagnostic significance were identified in 6/20 (30%). All findings of diagnostic significance were clinically confirmed using the proband’s prior clinical SR sequencing results, demonstrating the value of reanalysis and highlighting differences in clinical interpretation. One case harbored a homozygous ~50 kb deletion of initial interest that was only detected with LR-GS; however, it was ruled inconclusive based on frequency data from LR-GS population databases, underscoring the necessity of population filtering for structural variant clinical interpretation. Collectively, the observed increase in diagnostic yield (by 35% including suspicious findings) in this exome-/SR-GS-negative clinical cohort was driven primarily by genome reanalysis rather than identification of variants unique to LR-GS data. Additional functional studies are necessary to elucidate the clinical relevance of suspicious findings.

  Study EGAS50000001464

• Frequent Genetic Alterations in Myositis Autoantigen Genes in Cancer-Associated Dermatomyositis

  One-third of patients diagnosed with dermatomyositis harbor an occult cancer, a rare condition named cancer-associated dermatomyositis (CAD). Emerging evidence suggests that genetic alterations in autoantibody-related genes give rise neoantigens and specific autoantibodies that initiate an autoimmune response characteristic of CAD. This study evaluated the prevalence of such genetic alterations and elucidated molecular mechanisms that may underlie their role in triggering autoimmunity. We detected highly frequent genetic alterations in autoantibody-related genes, supporting their role in the CAD pathogenic mechanisms. Distinct TCR repertoire and immune signatures between tumoral and non-tumoral tissues may underlie divergent cancer and dermatomyositis outcomes. Neglected, immunotherapy may offer clinical benefit in selected cases of CAD and warrants further investigation.

  Study EGAS50000001367

• Acute Myeloid Leukemia peripheral blood samples

  Study EGAS00001004896

• Hepatoblastoma tumoroid biobank as a key resource for tumour genetics

  Study EGAS00001008251

• Personalized Medicine Based on Genomic Data

  Understanding how an individual's genetics are associated with their susceptibility to complex diseases and phenotypes is fundamental to advancing precision medicine. This study involved a series of integrative analyses of biospecimens and corresponding clinical data. This study aims to comprehensively investigate genotype-phenotype associations.

  Study JGAS000874

• WES Analysis of precancerous lesions in Lynch Syndrome

  The project focuses on identifying the genetic alterations involved in the early stages of tumor development in individuals with Lynch Syndrome. Using Whole Exome Sequencing (WES), the study aims to characterize somatic mutations and molecular pathways that drive the transformation from normal tissue to precancerous lesions. This research contributes to a better understanding of tumorigenesis in hereditary colorectal cancer syndromes.

  Study EGAS50000001546

• Single nucleus ATAC sequencing of isolated NK cells and CD56+ T cells from digested NSCLC tumor lesions

  In order to explore the intratumoral NK cell heterogeneity at an epigenetic level, we performed matched single nucleus ATAC sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Study EGAS50000001190

• Epigenetic characterization of glioblastoma stem cells

  Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary human GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In-depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival, in line with the higher invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs as shown by in vitro and in vivo assays. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

  Study EGAS50000001804

• Integrated single cell analysis identifies CD39+ tumor-associated NK cells with cytotoxic potential in NSCLC

  In order to explore the intratumoral NK cell heterogeneity at a transcriptomic and epigenetic level, we performed matched single nucleus RNA and ATAC sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Dataset EGAD50000001695

• Epigenetic characterization of patient-derived glioblastoma stem cell (GSC)

  ATAC-Seq data on 43 samples of glioblastoma stem cells mapped to hg19. Fastq files are available. PMID: 33427645

  Dataset EGAD50000002603

• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - WGS data

  This data was generated as part of the project titled "Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection." The study was carried out to investigate the genetic architecture of the Greenlandic population and the consequences it has for disease mapping, diagnosis and prediction.

  Study EGAS50000000657

• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - MEGA chip data

  This data was generated as part of the project titled "Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection." The study was carried out to investigate the genetic architecture of the Greenlandic population and the consequences it has for disease mapping, diagnosis and prediction.

  Study EGAS50000000658

• Multimodal epigenetic sequencing analysis of cell-free DNA identifies biomarkers for ALS diagnosis and progression

  The role of the circulating epigenome in ALS remains understudied. We aim to develop diagnostic and prognostic blood-based biomarkers for Amyotrophic Lateral Sclerosis (ALS) by profiling methylome signatures in circulating cell-free DNA (cfDNA) in 20 sporadic ALS cases, 10 C9orf72-associated ALS cases, 10 asymptomatic C9orf72 expansion carriers, and 21 healthy controls using targeted enzymatic methyl-sequencing (EM-seq) of ~4 million CpG loci. We detected numerous differentially methylated genes, including several implicated in ALS risk and pathobiology, and integrated multiple epigenetic features with our Multimodal Epigenetic Sequencing Analysis (MESA) algorithm, achieving an ROC AUC of 0.91 and detecting ~70% of ALS cases at ~100% specificity. Methylation at a subset of loci also correlated with clinical progression and cerebrospinal-fluid neurofilament levels, supporting the potential of cfDNA-based biomarkers for ALS diagnosis and monitoring.

  Study EGAS50000001267

• Malignant mesothelioma EWAS on European prospective study

  Study EGAS00001006432

• Cell-free DNA methylation profiling for non-invasive detection and classification of lymphoma

  Compared with traditional tissue biopsies used for lymphoma diagnosis, cell-free DNA methylation profiling offers a minimally invasive approach capable of capturing lymphoma-specific epigenetic alterations. This study investigates genome-wide methylation patterns in plasma using cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq). Differential methylation analysis of discovery samples identified lymphoma-associated hypermethylated regions that were used to develop classification models for lymphoma detection. Validation analyses demonstrated high accuracy and strong associations between cfDNA methylation scores and independent measures of tumor burden and clinical outcome. These findings support cfDNA methylation profiling as a sensitive approach for non-invasive lymphoma diagnosis.

  Study EGAS50000001463

• Shaping the Genetic Landscape of Northeast India

  The genetic landscape of South Asia is intriguing. In a vast geographical region like India, mostly genes follow geography. Moreover, at neighbouring regions like East and Southeast Asia, language is the major denominator of the genes. However, these are not just the two alternatives, in many geographical pockets, ethnicity plays a stronger role than either of these. Being a crossroad of South and Southeast Asia, the Himalayan region is mostly populated by the people speaking the Trans-Himalayan language. Archaeological and anthropological studies suggest migration and cultural diffusion in this region with the Tibetan plateau in the North. To understand this complex pattern, we have performed a fine-grained genetic analysis of the major Mizo population and its various clans living at the Himalayan geography. We have investigated 110 individuals belonging to seven different clans of Mizo people for hundred thousand of autosomal markers. In contrast to the East and Southeast Asian genetic landscape, our results suggested that the fine-scaled genetic structure of Northeast India is much more complex and mixture of interplay between languages, ethnicity and geography. Allelic frequency-based analyses indicated that a novel Trans-Himalayan ancestry unite all the populations of this region.

  Study EGAS00001008205

• Epigenetic reprogramming shapes monocytes and heterologous T cell derived cytokine responses in BCG vaccination

  Study EGAS00001007498

• Interferon-related inflammaging links epigenetic age acceleration to multimorbidity

  Study EGAS00001008029

• Interferon-related inflammaging links epigenetic age acceleration to multimorbidity

  Study EGAS00001008030

• Interferon-related inflammaging links epigenetic age acceleration to multimorbidity

  Study EGAS00001008031

• RNA sequencing data and whole exome sequencing data of genetically modified IDH1 wildtype and mutant chondrosarcoma cell lines

  This dataset contains total RNA sequencing (polyA enriched) data of early and late passages of n=5 vector-based CH2879 empty vector and IDH1mut cell lines. Total RNA sequencing (polyA enriched) using 150bp paired-end reads was performed in triplicate using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) on the NovaSeq6000 platform (Illumina). Additionally, this dataset contains whole exome sequencing data of n=15 parental, mock, and CRISPR-edited IDH1mut and IDH1wt CH2879 and JJ012 cell lines. Whole exome sequencing using 150bp paired-end reads with a minimum coverage of 100x was performed in single using the SureSelect Human All Exon V8 library (Agilent Technologies) on the NovaSeq X platform (Illumina).

  Dataset EGAD50000002703

• Screening for Prostate Cancer-Specific Differentially Methylated Regions Based on BSAC

  Bisulfite Amplicon Sequencing on tissue samples from prostate cancer, benign prostatic hyperplasia (BPH), and bladder cancer.

  Study EGAS50000001895

• Differential Wnt/β-Catenin Signaling Activities Shape Distinct Tumor Cell Phenotypes

  By profiling patient-derived hepatoblastoma organoids via single-cell transcriptomics and chromatin dynamics, we identify subtype-specific transcriptional and epigenetic profiles. Using CUT&RUN, we show that β-catenin engages distinct genomic regions, which is dictated by differential association with TCF/LEF family transcription factors. TCF7L2 binds to a motif, distinct from the classical Wnt consensus sequence, which is found in the promoter of hepatic target genes.

  Study EGAS50000001229

• Full AfricanNeo ModernDNA Study

  With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started ~4000 years ago in western Africa. We have genotyped 1,763 participants, including 1,487 Bantu speakers from 143 populations across 14 African countries. Our comprehensive genetic analysis of the expansion of people speaking Bantu languages reveals a complex history of serial founder events, variable levels of contact with local groups, and spread-over-spread events.

  Study EGAS50000000006