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• Single nucleus RNA sequencing of squamous cell carcinoma arising from mature teratoma of the ovary

  Squamous cell carcinoma arising from mature teratoma is one of the rare ovarian cancers. Therefore, the detailed molecular background of this disease has not been elucidated. The purpose of this study is to investigate the single-cell transcriptional landscape of this disease.

  Study JGAS000521

• DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism

  Plasma samples derived from a study population of control participants (DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism) were used to profile miRNA circulating in plasma. RNA was isolated from plasma samples using the Qiagen miRNeasy kit. Libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit. Libraries were sequenced on a HiSeq. Data from this sequencing project will be available through dbGaP.

  Study phs003223

• Molecular portraits of breast cancer diagnosed during pregnancy

  The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology.

  Dataset EGAD00001004353

• STAT1 AM RNAseq

  The transcriptome of peripheral blood cells (PBMCs) from control or patients with an activation mutation on the STAT1 gene was analyzed. This analysis aimed to identify the major changes in the circulating immune cells of patients with STAT1 mutation and compare this with the result of the perturbation prediction tool huva (human variation, R).

  Dataset EGAD00001006962

• Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

  This whole-section GeoMx Digital Spatial Profiler (DSP) dataset was a part of the discovery cohort in the study. The dataset contains raw FASTQ files from Regions of Interest (ROIs) across complete tumor tissue sections, enabling detection of 18,000 protein-coding genes. GeoMx DSP data from 1063 ROIs (after QC) from 15 GCs were included in the datasets.

  Dataset EGAD50000000500

• Exploring the Genomic Dark Matter of Neurodevelopmental Disorders

  Neurodevelopmental Disorders (NDDs) are a group of disorders that typically manifest early in development and may give rise to impaired cognition, communication, adaptive behavior, and psychomotor skills. This study aims to take a more comprehensive view into the genomic landscape of structural variants implicated in NDDs with intellectual disability (ID). We have evaluated the genome of families with a genetically unsolved severe NDD via optical genome mapping. This study identified likely pathogenic or pathogenic structural variants in known NDD genes, including BCL11A, OPHN1, PHF8, SON, and NFIA. Data is available in VCF format, following the standard filtering settings in Bionano Access and available as "variants_combine_filters_inMoleRefine1.vcf" files.

  Study phs002937

• Systems genetics in human endothelial cells identifies non-coding variants modifying enhancers, expression, and complex disease traits

  Identification of causal variants and mechanisms underlying complex disease traits in humans requires strategies to locate and fine-map functional regulatory variants in disease-relevant cell types. To discover functional regulatory variants in primary aortic endothelial cells (ECs) from humans, we collected genetic, transcriptomic, and four epigenomic phenotypes in a population of 153 human donors representing individuals of both sexes and three major ancestries. We found thousands of EC eQTLs that were not present in GTEx at all ranges of effect sizes, indicating novel functional variants not observable from tissue data. We performed several epigenetic assays across 53 donors' EC to enable molecular QTL mapping, which included chromatin accessibility, histone modification, and transcription factor binding of proteins ERG and NF-kB/p65 in two activation states. We discovered over 3000 regulatory elements where cis-regulatory variants associated to significant differences in epigenetic marks. Co-localization with our eQTLs, TF motif mutations, and 3D confirmation capture data in ECs enabled our discovery of hundreds of high-confidence functional regulatory elements that perturb endothelial molecular phenotypes. Furthermore, this set of variants is enriched at GWAS loci for Coronary Artery disease and other disease traits, with some SNPs demonstrating pleiotropic effects. Together, our dataset and analytical approach provide the genetics and vascular biology communities with specific variants affecting EC biology and serves as a proof-of-principle for how to detect functional regulatory variants in human cells with relevance to complex traits.

  Study phs002057

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• A single-cell atlas of human glioma

  Although tumor-propagating cells can be derived from glioblastomas (GBMs) of the proneural and mesenchymal subtypes, a glioma stem-like cell (GSC) of the classical subtype has not been identified. It is unclear if mesenchymal GSCs (mGSCs) and/or proneural GSCs (pGSCs) alone are sufficient to generate the spectrum of cellular heterogeneity observed in GBM. This study sheds light on a long-standing debate regarding lineage relationships among GSCs.

  Study EGAS00001003845

• UK_ReplicationChip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC Replicationchip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.

  Dataset EGAD00010002118

• UK_exomechip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC exomechip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper

  Dataset EGAD00010002019

• Whole exome sequencing identifies clinically relevant mutational signatures in resected hepatocellular carcinoma

  We conducted a multicentre pilot study on patients with localized HCC following complete radiological response to surgical resection. Patients received 250 mg oral gefitinib once daily as adjuvant therapy, up to a maximum of 6 months. The clinical endpoints included recurrence-free survival (RFS) and overall survival (OS), and correlative genetic analyses were conducted from whole exome sequencing data (n=33). All statistical analyses were carried out on an intention-to-treat basis. The study is registered with ClinicalTrials.gov (NCT00282100).

  Study EGAS00001004371

• Copy number profiles detected by shallow coverage WGS

  We performed shallow coverage whole genome sequencing on 147 glioma samples and analyzed their copy number profile. The coverage of each sample is about 2. Data are presented as VCF files which describe the copy number segments and their log2 ratio.

  Dataset EGAD00001005062

• Multi-omics profiling of paired primary and recurrent glioblastoma patient tissues

  Despite maximal therapy with surgery, chemotherapy and radiotherapy, glioblastoma multiforme (GBM) patients have a median survival of only 15 months. Almost all patients inevitably experience symptomatic tumor recurrence. A hallmark of this tumor type is the large heterogeneity between patients and within tumors itself which relate to failure of standardized tumor treatment. In this study, tissue samples of paired primary and recurrent GBM tumors were investigated to identify individual factors related to tumor progression.

  Study EGAS00001004345

• Integration of genomics and metabolomics in acute myeloid leukemia

  Although targeting of cell metabolism is a promising therapeutic strategy in acute myeloid leukemia (AML), metabolic dependencies are largely unexplored. We aimed to classify AML patients based on their metabolic landscape and map connections between metabolic and genomic profiles. The intracellular metabolome distinguished three AML clusters, correlating with distinct genomic profiles: NPM1-mutated(mut), chromatin/spliceosome-mut and TP53-mut/aneuploid AML that were confirmed by biofluid analysis.

  Study EGAS00001005422

• Dynamics of Genomic and Immune Responses During Primary Immunotherapy Resistance in Mismatch Repair Deficient Tumors

  We study a patient with dMMR lung cancer refractory to immunotherapy. Post-treatment tumor demonstrated compound heterozygous frameshift deletions located upstream of the kinase domain in the gene encoding JAK1 protein, downregulation of JAK1 and mediators of its signal transduction, and total loss of JAK1 phosphorylation. Importantly, one of the JAK1 mutations, despite not being detected in the pre-treatment tumor, was found at low variant allele frequency in the pre-treatment circulating tumor DNA, suggesting clonal selection of the mutation. This report provides the most detailed look yet of defective JAK1 signaling in the context of dMMR and immunotherapy-resistance. Together with observations of JAK1 frameshift indels being enriched in dMMR compared with MMR-proficient tumors, our findings demonstrate the critical function of JAK1 in immunological surveillance of dMMR cancer.

  Study phs002089

• Genomic and transcriptomic landscape of T-cell lymphoblastic lymphoma compared to T-cell acute lymphoblastic leukemia: similar subtypes and different fusions

  Due to the lower incidence of T-LBL and difficulties in obtaining diagnostic T-LBL material, extensive research on T-LBL has been hampered whereas genetic aberrations in T-ALL are thoroughly characterized. Given the similarities and differences between T-LBL and T-ALL, the question has been raised whether T-LBL and T-ALL represent two different diseases or different manifestations of the same disease. This study aims to identify the genomic and transcriptomic landscape of T-LBL and compare the findings to what is found T-ALL. Comparison of the molecular aberrations between T-LBL and T-ALL can provide insights into the overlap and differences in malignant development between the two entities, which could lead to improved risk stratification in T-LBL in order to eventually adapt T-LBL treatment protocols based on molecular-genetic prognostic factors.

  Study EGAS00001007767

• analysis of immune infiltration in colorectal cancer metastasis

  Metastatic colorectal cancer (mCRC) is the main cause of CRC mortality, with limited treatment options. Although immunotherapy has benefited some cancer patients, mCRC typically lacks the molecular features that respond to this treatment. However, recent studies indicate that the immune microenvironment of mCRC may be modified to enhance the effect of immune checkpoint inhibitors. This study aimed to explore the metastatic immune microenvironment by comparing immune cell populations in colorectal liver (CLM), lung (mLu) and peritoneal (PM) metastases.

  Study EGAS50000000652

• DNA Double Strand Breaks in KMT2A-Rearranged AML patients

  DNA breakage at specific rearrangement-participating genes, which are more sensitive to a range of environmental and chemotherapeutic agents than other regions of the human genome, contributes to the generation of leukemia-causing rearrangements, and can be used as a predictor of susceptibility to cancer caused by gene rearrangements. As a direct proof-of-principle regarding the feasibility of employing fragile site breakage to identify and monitor high-risk populations to allow personalized treatments, genome-wide DNA break mapping/sequencing was used to determine whether preferential DNA breaks are generated at the major breakpoint regions of KMT2A in AML remission patients with previously diagnosed KMT2A rearrangement. We are submitting break mapping data from three patients with KMT2A rearrangements and three non-fusion patients, with and without etoposide treatments.

  Study phs002804

• Single Duplex DNA Sequencing with CODEC Detects Mutations with High Sensitivity

  Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules (single duplexes) to discern the true mutations on both strands. Here, we present Concatenating Original Duplex for Error Correction (CODEC) which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than Duplex Sequencing. CODEC revealed mutation frequencies of 2.72 x 10-8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability (MSI) with 10-fold greater sensitivity, and mutational signatures and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations which are commonly obscured by NGS errors. We applied CODEC to clinical colon and breast neoplasm samples and uncovered expected mutational signatures including homologous recombination deficiency (HRD) and MSI.

  Study phs003255

• Identification_of_rare_variants_associated_with_cardiovascular_traits_in_Cilento_isolates

  The aim of this project is to identify rare genetic variants of large effect implicated in complex diseases by focusing on the study of cardiovascular diseases and related quantitative traits in a well characterized isolated population in Cilento area, Italy.The reference panel has been selected carefully in order to maximize the imputation coverage and quality on the all population samples. The selected individuals should meet three criteria: selected individuals should be chip-genotyped and closely related to the maximum number of chip-genotyped individuals so as to maximize imputation coverage; relatedness between selected individuals should be minimal, so as to minimize redundancy in genetic information of the reference panel.We perform exome sequencing on samples from 250 individuals from the Campora and Gioi-Cardile populations.

  Study EGAS00001000620

• Single cell analysis reveals new evolutionary complexity in uveal melanoma

  Uveal melanoma (UM) is a rare eye cancer that is highly aggressive and leads to metastatic death in up to half of patients. Here, we conduct droplet-based single-cell RNA sequencing of 59,915 neoplastic and non-neoplastic cells from 8 primary and 3 metastatic UMs. Single-cell VDJ sequencing of RNA is conducted to determine clonally expanded B/T- cell populations. Single-cell DNA sequencing of 1 primary and 1 metastasis is utilized.

  Study phs001861

• Prime editing for functional repair in patient-derived disease models

  Prime editing is a novel genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct a wide variety of genetic defects. We succeeded in efficient prime editing and functional recovery of disease-causing mutations in patient-derived liver and intestinal stem cell organoids. Whole genome sequencing of did not detect off-target mutations or a mutational signature induced by prime editing.

  Study EGAS00001004611

• Transcriptome profiling of head and neck squamous cell carcinomas with paired patient-derived xenografts

  This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.

  Dataset EGAD50000000995

• Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors

  Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors. The sequencing was done on HiSeq 4000 with the SmarTer Ultra Low Input RNA v4 and NEBNext ChIP-Seq Kit. The TAMs were treated with GW2580, BLZ945 and PLX3397 and DMSO as control.

  Dataset EGAD00001011273

• Low Density Genotyping from the Fragile Families and Child Wellbeing Study

  The Fragile Families and Child Wellbeing Study (FFCWS) is based on a stratified, multistage sample of 4898 children born in large U.S. cities (population over 200,000) between 1998 and 2000, where births to unmarried mothers were oversampled by a ratio of 3 to 1. This sampling strategy resulted in the inclusion of a large number of Black, Hispanic, and low-income families. The project “Low Density Genotyping from the Fragile Families & Child Wellbeing Study” uses saliva collected from a subset of FFCWS children at Year 9 and from teens at Year 15 to examine genetic variation using a genome-wide assay (Illumina PsychChip). In addition to the genotype data, a limited set of self reported and anthropomorphic measures are included.

  Study phs002417

• Study of 5'UTR Mutations in Prostate Cancer

  The 5' untranslated region (5' UTR) of mRNA controls the translation of specific transcripts through encoded cis-regulatory elements. Yet exceedingly little is known about the prevalence and function of 5' UTR mutations in cancer. We have uncovered many 5' UTR mutations in our analysis of localized and castration resistant prostate cancer patients, and hypothesize that systematic mutations in critical 5' UTR regulatory regions perturb gene expression to drive prostate cancer progression. To elucidate the functional 5' UTR regulatory landscape of prostate cancer, we have taken a multi-faceted approach including ribosome profiling, in vitro reporter assays and the development of a novel high throughput method to functionally access the impact of recurrent 5' UTR mutations on both transcription and translation.

  Study phs001825

• Multicenter International Cross-Sectional Evaluation of Pulmonary Alveolar Proteinosis (MICEPAP) Trial

  The purpose of this study is to (1) compare a technically improved assay with an existing assay used to measure serum anti-GM-CSF antibodies in stored serum samples previously obtained from patients diagnosed with either primary, secondary, congenital or idiopathic pulmonary alveolar proteinosis (PAP), other chronic diseases or disease-free, healthy individuals; (2) determine the prevalence and levels of anti-GM-CSF autoantibodies and (3) define the breadth of the autoimmune antibody responses in primary PAP patients from the United States, Japan, Australia, and Europe using previously collected serum samples; and (4) using a chart review approach, compare the clinical, radiologic and laboratory features of primary PAP patients to determine if differences exist among patients in these globally geographically distributed regions.

  Study phs001309

• RNAseq and genotypes from pancreatic islets (InsPIRE study).

  This is the data from the eQTLs InsPIRE study. This dataset includes RNAseq and genotypes from pancreatic islets and FAC sorted beta-cells, as well as RPKM values, covariates and cell count estimates.

  Dataset EGAD00001006149

• Patient-derived organoids model treatment response of metastatic gastrointestinal cancers (targeted and whole-genome sequencing)

  Patient-derived organoids (PDOs) have recently emerged as robust pre-clinical models, however, their potential to predict patient clinical outcomes remain unclear. We report a living biobank of PDOs from metastatic, heavily-pretreated colorectal and gastroesophageal cancer patients recruited in phase I/II clinical trials. Phenotypic and genotypic profiling of PDOs showed a high-degree of similarity to the original patient tumor. Molecular profiling of tumor organoids was matched to drug screening results, suggesting PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared ex vivo organoid responses to anticancer agents, and PDO-based orthotopic mouse tumor xenograft models to the response of the patient in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic, and have the potential to be implemented in personalized medicine programs.

  Study EGAS00001002784

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 51pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003392

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 23pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003405

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 45pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003431

• Endothelium-derived stromal cells contribute to bone marrow niche formation

  Comprehensive transcriptional characterization of bone marrow stromal cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during niche formation.Here, we identify a rare subset of cells in the human fetal BM that co-express endothelial and stromal markers, including low-affinity nerve growth factor receptor (LNGFR/CD271). They display transcriptional reprogramming consistent with endothelial-to-mesenchymal transition (EndoMT), reflected in their potential to generate stromal cells with in vivo BM niche forming capacity.

  Study EGAS00001004946

• CSER: North Carolina Clinical Genomic Evaluation by Next-Gen Exome Sequencing 2

  The North Carolina Clinical Genomic Evaluation by Next-gen Exome Sequencing, 2 (NCGENES 2) study is part of a larger consortium project investigating the clinical utility, or net benefit of an intervention on patient and family well-being as well as diagnostic efficacy, management planning, and medical outcomes. A clinical trial will be implemented to compare (1) first-line exome sequencing to usual care and (2) participant pre-visit preparation to no pre-visit preparation. The study will use a randomized controlled design, with 2x2 factorial design, coupled with patient-reported outcomes and comprehensive clinical data collection addressing key outcomes, to determine the net impact of diagnostic results and secondary findings.

  Study phs002110

• WES Analysis of CRC and UC samples from a cohort of Lynch Syndrome carriers

  Whole-exome sequencing (WES) was performed on 73 tumors, including 58 colorectal cancers (CRC) and 15 urothelial cancers (UC), derived from 58 individuals with Lynch syndrome (LS). The cohort comprised both primary and metachronous tumors.

  Dataset EGAD50000001915

• Breast Cancer TNBC Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of five TNBC primary breast cancers from Wu et al. (2020) EMBO J study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001006981

• Pilocytic Astrocytoma RNA sequencing

  This dataset contains RNA sequencing samples from the Duesseldorf/LIsbon pilocytic astrocytoma cohort which was profiled using Proteogenomics (RNA Sequencing, proteomics and methylation). There are 48 samples which were sequenced using paired-end sequencing at the University Hopstial Dusseldorf.

  Dataset EGAD00001009053

• Nanopore medulloblastoma data

  Nanopore data from 3 medulloblastoma samples of which 2 are tumor-normal pairs sequenced with the MinIon and one is tumor only data sequenced on the PromethIon. The data consists of BAM files aligned using minimap2

  Dataset EGAD00001010851

• Chromatin activation profiling of stereotyped chronic lymphocytic leukemias reveals a subset #8 specific signature

  The chromatin activation landscape of major subsets of chronic lymphocytic leukemia (CLL) with stereotyped B-cell receptor immunoglobulin is currently unknown. Here, we report the results of a whole-genome chromatin profiling of histone 3 lysine 27 acetylation of 18 CLLs from subsets #1, #2, #4, and #8 which were compared against non-stereotyped CLLs and normal B cell subpopulations. Although subsets #1, #2, and #4 were similar to their non-stereotyped CLL counterparts with concordant somatic hypermutation status, subset #8 displayed a remarkably different chromatin activation profile.

  Study EGAS00001006457

• smRNA-seq of human post-mortem brain data of frontal lobe (Tuebingen part)

  This dataset contains smRNA-seq data from post-mortem human brain tissue of the frontal lobe of patients with FTD and healthy controls. The smRNA-sequencing was done in two parts, this dataset depicts the data generated at the DZNE Tübingen.

  Dataset EGAD00001006846

• CIRdb: Array genotype data

  The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (>20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. In addition, here we describe the overall design and the methods that are being implemented to develop CIRdb.

  Study EGAS00001006050

• Fecal microbiome subtype affects the clinical and genomic aberrations of colorectal cancer

  Colorectal cancers (CRCs) have been categorized based on histopathological characteristics or genomic abnormalities, such as gene expression. These classifications have gained widespread acceptance and application in clinical practice. It has become evident in recent times that there is a connection between gut bacteria and CRC. However, the extent to which the diversity of CRC and the gut microbiota are linked has not been extensively investigated. We conducted a comprehensive analysis that integrated whole genome and whole transcriptome data of CRC tissues, along with stool-derived whole genome metagenome analysis. Our approach to accurately stratify CRC involved the utilization of explainable AI, which allowed us to classify the disease into four distinct subtypes based on the composition of gut microbiota.

  Study JGAS000696

• COVID-19 GWAS in Japanese

  The Japan COVID-19 Task Force (JCTF) was established in early 2020 as a nation-wide multicenter consortium to overcome the COVID-19 pandemic in Japan. We conducted a genome-wide association study (GWAS) involving 2,393 Japanese COVID-19 cases collected in initial pandemic waves with 3,289 controls. GWAS genotyping was performed using Infinium Asian Screening Array (Illumina, USA).

  Study EGAS00001006284

• danMAC5

  Three whole genome sequecing of three independent cohorts. The three cohorts derives from projects including samples of inviduals with Danish origin. Data is deviden into males and female and compiled.

  Dataset EGAD00001009756

• A GWAS meta-analysis on severe acne on a European population of 26,722 individuals

  Acne vulgaris is a highly heritable common, chronic inflammatory disease of the skin. We performed a genome-wide association study of 3,823 cases and 16,144 controls followed by meta-analysis with summary statistics from a previous study, with a total sample size of 26,722. We identified 20 independent association signals at 15 risk loci, 12 of which have not been previously implicated in the disease.

  Study EGAS00001003278

• Somatic L1 retrotranspositions in normal human cells

  Genomic mutations accumulate in normal cells during lifetime; however, somatic mosaicism generated by mobilization of transposable elements is not well understood. Here, we explored whole-genome sequences of single-cell expanded clones to illustrate the mutational landscape produced by L1. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 and read-through RNA expression profiles to investigate the epigenetic regulation of L1 activity.

  Study EGAS00001006213

• GEOCODE data access policy

  The GEOCODE Data Access Policy ensures the responsible use, security, and compliance of GEOCODE data. Access to GEOCODE data is restricted to authorized users based on role-based permissions, ensuring compliance with data protection regulations.

  Dac EGAC50000000574

• MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells

  Despite the established role of the transcription factor MYC in cancer, little is known about the involvement of lncRNAs in mediating MYC’s function. Here we have intersected RNA-sequencing data from MYC-inducible cell lines, from a cohort of 91 mature B-cell lymphomas and from sorted germinal-center B-cells. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, showing a strong correlation with MYC expression in MYC-positive lymphomas and in pancreatic ductal adenocarcinomas. RNAi experiments showed that MINCR controls cellular viability by influencing the expression of MYC-regulated cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR acts as a modulator of MYC transcriptional control of cell cycle genes.

  Study EGAS00001001199

• DIAMOND PCR : plasma DNA LINE-1 targeted bisulfite sequencing, a new non-invasive multi-cancer detection marker

  The detection of circulating tumor DNA, which allows non-invasive tumor molecular profiling and disease follow-up, promises optimal and individualized management of patients with cancer. However, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge. We developed a PCR-based targeted bisulfite method coupled to deep sequencing to detect methylation patterns of L1PA elements,which we named DIAMOND (for Detection of Long Interspersed Nuclear Element Altered Methylation ON plasma DNA). We used sodium bisulfite chemical conversion to achieve base-pair resolution analysis and designed a multiplexed PCR based on 8 amplicons covering L1PAs .

  Dataset EGAD50000000646