13311 results for ""pdc"+"heritage+language"+census+study"

in 59.32 milliseconds.

• Cohort B tumor exome sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. Tumor DNA was isolated from FFPE tissue. Both tumor and germline DNA are present for each sample in the overall dataset.

  Study EGAS50000000955

• Alternative splicing in Shh-MB

  We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

  Study EGAS00001003220

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000802

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• GWAS data (Illumina 2.5 M SNPs) in Cuban cohorts of dengue disease

  We will have 274 individuals typed for the Illumina Human Omni 2.5 chip. The individuals are from two locations in Cuba (Havana and Guantanamo) and from four phenotype classes (asymptomatic, control dengue fever and dengue hemorrhagic fever).

  Study EGAS00001002276

• Balanced_Brain_Tumour_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000360

• Chromatin accessibility of clear cell renal cell carcinoma

  To investigate chromatin accessibility in ccRCC, we performed ATAC-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001325

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000803

• 560 whole-genome sequenced breast cancers

  A comprehensive characterisation and analysis of 560 human breast cancers through genome-wide approaches including genomics, transcriptomics and epigenomics.

  Study EGAS00001001178

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Study EGAS50000000271

• Integrated genetic and epigenetic analysis of myxofibrosarcoma

  Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

  Study EGAS00001002889

• Genetics of Microcephalic Osteodysplatics Primordial Dwarfism

  This project aims to find causal variants in 50 patients diagnosed with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD), of presumed recessive inheritance performing whole exome sequencing to ~50x mean depth. This is a collaboration with Prof A. Jackson, MRC Human Genetics Unit, Edinburgh

  Study EGAS00001000064

• Whole genome amplification and whole genome sequencing of human single cells

  Human single fibroblasts and T-lymphocytes were amplified using multiple annealing and looping-based amplification and multiple displacement amplification. Amplified products were next subjected to whole genome sequencing with the goal of performing a genetic variant analysis.

  Study EGAS00001003108

• Loss of functional mutation in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan Anemia

  We performed whole-exome sequencing analysis of 48 patients with no documented mutations/deletions involving known Diamond-Blackfan anemia genes and identified 10 mutations in previous known causative genes and 2 mutations in novel ribosomal genes.

  Study EGAS00001000875

• 3' mRNA- sequencing bams

  This project stores bam files from 3'RNA-seq from oesophageal adenocarcinoma at different timepoints during neoadjuvant treatment (prior, during, post treatment), which were used to analyse evolutionary and phenotype dynamics in oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Study EGAS50000000242

• IBDCA_Edinburgh

  In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

  Study EGAS00001001129

• Mutational_burden_in_oesophagus__nanoseq_

  We wish to accurately assess mutational burden and signature from patients of different ages using clonal oesophageal epithelium and duplex-seq. We will also attempt to look for differences between smokers and non-smokers and individuals with different levels of alcohol consumption.

  Study EGAS00001007695

• Triple_Negative_Breast_Cancer_sequencing

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

  Study EGAS00001000161

• Genomic landscape of IG-MYC positive Burkitt lymphoma with precursor B-cell immunophenotype.

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing of a rare Burkitt lymphoma subtype with precursor B-cell immunophenotype. Analysis were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002968

• Single-cell RNA seq-derived signatures define response patterns to atezolizumab + bevacizumab in advanced hepatocellular carcinoma

  FASTq files and normalised gene expression counts from bulk RNA-sequencing of pre-treatment tumour (n=39) and adjacent non-tumour tissue samples (n=13) from advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab.

  Study EGAS50000000838

• Whole exome sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. Whole exome sequencing was performed with established tumoroid models.

  Study EGAS50000000379

• RNA sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. RNA sequencing was performed with established tumoroid models.

  Study EGAS50000000380

• Genetic landscape of pediatric Rhabdomyosarcoma

  We performed whole-genome sequencing of 13 paired tumor/normal Rhabdomyosarcoma genomes and analyzed somatically acquired single nucleotide variations SNVs, insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000256

• Genetic landscape of pediatric Osteosarcoma

  We performed whole-genome sequencing of 37 paired tumor/normal OS genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000263

• Plasma pQTLs in INTERVAL cohort

  Human pQTLs using UK INTERVAL (Cambridge CEU) plasma samples. pQTL mapping of 3,283 protein analytes assayed using SomaLogic SOMAscan, across 10.6M imputed genetic variants, in 3,301 samples.

  Study EGAS00001002555

• Parallel Detections of Somatic Gene Mutations in Surgically Resected Tumor tissues and Matched Plasma Specimens in Early-Stages of Primary Breast Cancer

  We developed two panel successively, contain 68 and 136 genes respectively. Combination with ultrasound or mammography, it could be used for breast cancer early detection and avoided unnecessary surgery or other invasive detection.

  Study EGAS00001003075

• Low-coverage whole-sequencing of metastasised colorectal cancer samples treated with bevazicumab

  Low-coverage whole-genome sequencing (LC-WGS) was performed on tumor tissue, normal tissue and plasma samples collected from mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444) and the University Medical Center Mannheim (UMM).

  Study EGAS50000000131

• Lifelines NEXT

  The Lifelines-NEXT is a cohort of newborns followed up from birth up to the age of 1 year and later. The cohort includes approximately 1,500 newborns and their mothers from the 3 provinces of the Northern Netherlands.

  Study EGAS50000000133

• single cell data from HPV-positive head and neck cancer patients receiving induction CTLA-4 and PD-1 immune checkpoint blockade

  Baseline and on-treatment tumor samples from human papillomavirus-positive oropharynx cancer patients receiving anti-CTLA-4 and anti-PD-1 immune checkpoint blockade were analyzed by single-cell RNA and TCR sequencing.

  Study EGAS50000000335

• WES of paired gDNAs and PPGL tumor DNA from patients with CCHD-PPGL.

  WES of paired germline DNA (12) and PPGL tumor DNA (14) from peripheral blood/saliva and formalin-fixed paraffin-embedded (FFPE) blocks from surgery, respectively, from patients with congenital heart disease (CCHD) and pheochromocytoma and paraganglioma (PPGL).

  Study EGAS50000000815

• Coloured individuals from South Africa

  Genome-wide genotype array data (H3Africa_2017_20021485_A2 and H3Africa_2019_20037295_B1 arrays) of 152 individuals from different locations in South Africa and self-identified as Coloured. From the sites of Graaff-Reinet, Genadendal, Greyton, Nieu-Bethesda, Kranshoek, Prince Albert and Oudtshoorn.

  Study EGAS50000000352

• Whole genome sequencing of pediatric BCR-ABL1 positive acute lymphoblastic leukemia

  We performed whole-genome sequencing of 18 paired tumor/normal BCR-ABL1+ leukemia genomes and analyzed single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the tumor and normal genomes

  Study EGAS00001000253

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Non-KMT2Ar infant Acute Lymphoblastic Leukemia Sequencing

  Integrated genomic analysis of non-KMT2A rearranged infant ALL reveals clinically relevant alterations and common disease origins with childhood ALL. Whole genome and whole transcriptome sequencing from 21 infant ALL patients with no matched normal DNA sequencing.

  Study EGAS50000000405

• Analyses of transcriptome and epigenome in cardiac fibroblasts

  We report genome-wide bulk RNA- and ATAC-seq analysis of cardiac fibroblasts isolated from two patients. Cells were pre-treated with either KAT5 inhibitor or vehicle, and their fibrotic responses after TGF-β stimulation was measured.

  Study EGAS50000000835

• Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma

  Investigating the spatial architecture and microenvironment of EMD lesions in Multiple Myeloma patients using spatial whole transcriptome sequencing (10X Visium), tomography for spatially resolved transcriptomics (TOMO-seq), and single-cell RNA sequencing (scRNAseq)

  Study EGAS50000000227

• Large B cell lymphomas with CCND1 rearrangement have different immunoglobulin gene breakpoints and genomic profile than mantle cell lymphoma

  Next-generation sequencig data including whole-genome sequencing, whole-exome sequencing, and capture-based gene panels of large B cell lymphomas with CCND1 rearrangementas described in Özoğul,Montaner, Pol et al 2024.

  Study EGAS50000000564

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell RNA-sequencing (CITE-seq) and single-nucleus RNA-sequencing data were generated from neuroblastoma patient tumors to uncover transcriptional heterogeneity at a single-cell resolution. In addition, we used the data to validate our findings of the NBAtlas.

  Study EGAS50000000223

• Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

  Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

  Study EGAS00001004169

• Chromatin accessibility analysis of TFEB overexpression in LT-HSC

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus overexpressing GP91 (CTRL) or TFEB. Six days later, BFP+ transduced cells were sorted for DNA extraction, library preparation and sequencing

  Study EGAS00001004971

• MET amplification in gastric cancer

  Targeting MET in gastric and gastroesophageal junction adenocarcinoma (GC) with monoclonal antibodies or tyrosine kinase inhibitors has had limited success. We hypothesize that other prognostic and response determining genetic alterations explain the poor outcome and lack of response to MET-targeted therapies.

  Study EGAS50000000744

• TBA

  Analysis of mutational signatures arising in vivo in humans. iPS cells from control patients and100 patients carrying known mutations in DNA repair/editing genes will be generated, andsequenced.Blood from the patients will also be used to generate reference 'germline' sequence data.

  Study EGAS00001000801

• Transposome_Bisulfite_Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Study EGAS00001000751

• HCA_Heart_Disease_BHF_DZHK_RNA_

  Cell Atlas of the diseased human heart. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004566

• All available datasets of DEEP

  All available datasets of DEEP. There are several Reference Epigenomes available. For metadata check out www.deep.dkfz.de One reference epigenome represents a set of 6 ChIP-Seqs, WGBS, RNA-Seq, smallRNA-Seq and sometimes DNase1 and/or NOME-Seq.

  Study EGAS00001001608

• SPECTA__NGS_Screening_Program_for_Efficient_Clinical_Trial_Access

  SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

  Study EGAS00001000728

• Single cell RNA sequencing of lung adenocarcinoma.

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes.

  Study EGAS00001003681

• Isotype_resolved_sequencing_of_B_cell_receptor_in_measles_virus_infection

  Isotype-resolved sequencing of B cell receptor in measles virus infection 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002635

• Exome sequencing of United Kingdom Brain Expression Consortium samples

  The United Kingdom Brain Expression Consortium studies regulation of gene expression through common and rare variation. One of the main set of samples is compound by bulk brain tissue from 10 brain regions obtained from 134 controls.

  Study EGAS00001002113

• Exome_sequencing_of_UK_Birth_Cohorts___Avon_Longitudinal_Study_of_Parents_and_Children

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001005273

• STRATAA_RNAseq

  Transcriptome signatures of acute typhoid infection This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003967

• Potent neutralizing antibodies against SARS-CoV-2

  The COVID-19 pandemic urgently needs therapeutic and prophylactic interventions. Here we report the rapid identification of SARS-CoV-2 neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients.

  Study EGAS00001004412

• Myeloma WGS

  Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 tumour-normal newly diagnosed pairs and 24 matched relapse tumours from the Myeloma XI trial.

  Study EGAS00001004000

• Whole exome sequencing of Congenital Cataract

  Whole exome sequencing to identify potentially relevant mutations of congenital cataract in a Chinese girl. The novel PAX6 mutation (c.221G>A) is associated with congenital cataract, and the WFS1 mutation (c.2070_2079del) interactively aggravates this process.

  Study EGAS00001005673

• Clonal evolution and clinical implications of genetic abnormalities in blastic transformation of chronic myeloid leukaemia

  Blast crisis (BC) predicts dismal outcomes in patients with chronic myeloid leukaemia (CML). We comprehensively investigated genetic abnormalities in 136 BC and 148 chronic phase (CP) samples obtained from 216 CML patients using exome and targeted sequencing.

  Study EGAS00001005075

• Comprehensive genetic analysis of Epstein-Barr virus-associated hematological malignancy

  Comprehensive genetic analyses including whole-exome sequencing, targeted sequencing, and whole-genome sequencing of the human genome and the Epstein-Barr virus (EBV) genome were performed to reveal the molecular pathogenesis of EBV-associated hematological malignancy.

  Study EGAS00001003159

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Study EGAS00001005151

• Molecular profiling of DLBCL patients treated in the PETAL trial

  Using whole-exome sequencing and shallow whole genome sequencing for simultaneous screening of mutations, copy number alterations, and translocations, 5 biology-based risk profiles could be reproduced in an independent cohort of DLBCL patients, from the PETAL trial.

  Study EGAS00001005828

• COVID-19 Postmortem Lung snRNA-seq

  A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

  Study EGAS00001004689

• Single cell copy number and chromatin accessibility in primary multiple myeloma cells

  Multiple myeloma is characterized by inter- and intra-clonal heterogeneity. We have used single cell profiling of the genome (scCNV) and epigenome (csATAC) of clonal plasma cells to delineate the clonal heterogeneity in serially collected samples.

  Study EGAS00001005382

• SJCRH Patient-derived orthotopic xenografts of pediatric brain tumors

  Primary patient pediatric brain tumors from patients treated at SJCRH were implanted and amplified only in the brain of immunocompromised mice without tissue culture steps and referred as patient-derived orthotopic xenografts (Smith et al, Acta Neuropathologica, 2020).

  Study EGAS00001005533

• Overactivation of the IGF signalling pathway in osteosarcoma

  Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who confirmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

  Study EGAS00001004767

• cfDNA and CDX/PDX methylation profiling in SCLC

  We profiled the whole genome methylome of SCLC preclinical models and cfDNA samples. We assessed the sensitivity of cfDNA methylation profiling in detecting SCLC, especially at earlier stage of disease and the ability in discriminate among different SCLC molecular subtypes.

  Study EGAS00001005739

• Molecular and clinical effects of selective TYK2 inhibition with deucravacitinib in psoriasis

  Investigate changes in IL-23/Th17- and type I interferon-pathway biomarkers and gene responses, and measures of selectivity for TYK2 over Janus kinases (JAKs) 1–3, in patients with moderate to severe psoriasis receiving deucravacitinib.

  Study EGAS00001005875

• Whole genome sequencing of germline DNA from 8 patients with adult granulosa cell tumors (from blood or saliva)

  Whole genome sequencing BAMs of DNA obtained from blood/saliva of 8 patients with adult granulosa cell tumors. These patients come from four independent families, with each family having 2 affected family members.

  Study EGAS00001004902

• Insights from genome-wide data from Thailand and Laos

  We provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies

  Study EGAS00001006053

• Airway Dysbiosis Accelerates Lung Function Decline in Chronic Obstructive Pulmonary Disease

  This repository contains human sample derived microbiome full-length 16S rRNA sequencing data for sputum samples in COPD patients. The project goal is to understand the association of the lung microbiome with accelerated lung function decline in COPD patients.

  Study EGAS00001006444

• HLF COPD Transcriptomics

  We generated transcriptomes of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. RNA sequencing analysis demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization.

  Study EGAS00001006602

• RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 14) or with vehicle (N = 14).

  Study EGAS00001006584

• Transcriptomic analysis of MYC overexpression in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing

  Study EGAS00001004970

• Targeted sequencing of brain AVM tissues

  We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing. We have now performed targeted sequencing on AVMS, investigating genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others.

  Study EGAS00001006729

• Methylation profiles in patients with blastic plasmacytoid dendritic cell neoplasm

  We added 7 additional samples to our previous cohort (EGAS00001006166). Each samples comprises RNA-seq and whole exome sequencing data. Methylation EPIC Array data have been deposited in Gene Expression Omnibus (GEO) under accession number GSE230487.

  Study EGAS00001007201

• RNA seq before and after cold pressor test

  The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken for RNA-sequencing.

  Study EGAS00001006690

• Exome_sequencing_of_UK_Birth_Cohorts___Born_in_Bradford

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001006978

• Exome_sequencing_of_UK_Birth_Cohorts___Millennium_Cohort_Study

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001007789

• Cellular Analysis of Resistance and Evolution in IDH-mutant glioma

  We profiled a total of 75 IDH-mutant gliomas to study tumor evolution in this tumor type, among which 51 samples are presented here. These data reflect a combination of whole genome sequencing, whole exome sequencing, 10x single nucleus RNA sequencing, and 10x simultaneous single nucleus RNA and ATAC sequencing.

  Dataset EGAD50000002485

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• Sequence data for "An allele-resolved nanopore-guided tour of the human placental methylome" (Kindlova et al 2025)

  Sequence data generated for the study "An allele-resolved nanopore-guided tour of the human placental methylome" includes Illumina WGS, Illumina RNA-seq, Illumina EM-seq, and Oxford Nanopore Technologies PromethION sequence data.

  Dataset EGAD50000001850

• STimage: Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data

  This dataset comprises raw sequencing data (FASTQ files) derived from 13 Formalin-Fixed Paraffin-Embedded (FFPE) melanoma tissue samples profiled using the 10x Genomics Visium platform. These spatially resolved transcriptomic profiles serve as the primary dataset for the STimage study, enabling the development and benchmarking of deep learning models that predict gene expression directly from H&E histology images.

  Dataset EGAD50000002172

• RNA-Sequencing data of Fusobacterium nucleatum treated CAFs and HT-29 tumor spheroid exposed to Fusobacterium nucleatum treated CAFs conditioned medium.

  RNA-Sequencing data of CAFs (patient derived CAF180 and CAF181 as well as the CT5.3 CAF cell line) and HT-29 tumor spheroid samples performed in the context of the study of the interaction of Fusobacterium nucleatum with CRC CAFs. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to enhance colorectal cancer progression

  Dataset EGAD50000001614

• Whole genome sequencing data from paired tumor and normal tissue in a cohort of NSCLC patients.

  WGS data for paired tumor and normal tissue from 260 patients in the TRACERx ctDNA study. The patient cohort is comprised of NSCLC patients undergoing surgical resection of their tumour. The patients were then followed up for a median of ~5 years after surgery, and serial blood samples were collected. The WGS data here was generated to inform the manufacture of custom ctDNA panels.

  Dataset EGAD50000001693

• Shallow whole genome sequencing DETECT samples

  Shallow whole genome sequencing of samples from the paper Beddowes et al. A large-scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression-free survival. Mol. One 2025. This includes 1048 longitudinal plasma samples from 149 patients and 35 normals. Samples were sequenced with shallow whole genome sequencing for copy number estimation. All the files are single-end fastq files.

  Dataset EGAD50000001333

• Processed miRNA Counts for the miRNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed miRNA count data for the 49 Heart Failure samples profiled by miRNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001195

• Processed Total RNA Counts for the RNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed RNA count data for the 49 Heart Failure samples profiled by RNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001193

• Single-cell RNA-sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We undertook single-cell RNA sequencing to establish gene expression and lymphocyte receptor sequences of CSF and peripheral blood leukocytes derived from patients with a variety of inflammatory, infectious and non-inflammatory neurological disorders. The aim of the study was the investigation of functional changes of the cells involved in neuroinflammatory responses.

  Dataset EGAD50000001173

• SAPCS 20 Blood RNA-seq from Prostate cancer patients.

  Raw RNA-seq reads (FASTQ format) and Mapped sequencing reads (BAM format) of 20 Prostate cancer patients in Southern African Prostate Cancer Study (SAPCS). Each patient exhibit different pathogenic variations. The Illumina RNA-sequencing is performed from Blood extraction (from QIAamp RNA Blood Mini Kit). rRNA was removed prior using SortMeRNA. STAR aligner program was used for mapping to human genome GRCh38.p14, resulting in an average genome coverage of 9x.

  Dataset EGAD50000000982

• Targeted DNA sequence

  Targeted DNA sequencing files that were used in our study. The cohort was composed of 36 cases of tumor-only targeted DNA sequencing data. All files are UMI processed. The panel is designed with Agilent Sure Select and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000972

• Clinical panel sequencing of cancer of unknown primary using Comprehensive cancer panel (CCP)

  This database includes comprehensive cancer panel (CCP) on paired tumour and germline DNA from cancer of unknown primary samples, all of which are matched to WGS data under this study. This data was used to compare biomarker yield against what was achieved with WGS. This dataset contains n=34 tumour-germline paired samples. All samples are in BAM format aligned with GRCh38 reference genome.

  Dataset EGAD50000000655

• A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

  PacBio HiFi Revio WGS data from 16 individuals sequenced in the Genomic Medicine Sweden (GMS) Long read project. Each individual was sequenced on one PacBio Revio SMRT cell. The DNA was extracted from blood. The HiFi data was aligned to GRCh38 using minimap2 or the SMRT-link software.

  Dataset EGAD50000000676

• ICR TYA WES

  Whole exome sequencing of high grade gliomas occurring in teenagers and young adults between the ages of 13 and 30. This study combines methylation array profiling, whole exome sequencing and fusion panel sequencing to provide an integrated molecular description of brain tumours in this age group. Dataset contains 96 BAM files aligned with BWA to GRCh37 from 88 tumours. Tumour DNA was isolated from FFPE material in most cases. 8 germline sequences from peripheral blood DNA are also included.

  Dataset EGAD50000000904

• RNAseq from a study of MYC, BCL2 and BCL6 rearrangements in non-Hodgkin lymphoma.

  Paired-end ribodepletion RNAseq performed on 257 samples of Burkitt lymphoma, diffuse large B cell lymphoma, follicular lymphoma, and high-grade B cell lymphoma with MYC and BCL2 or BCL6 rearrangements. RNA was derived from either fresh frozen or formalin fixed/paraffin embedded (FFPE) tissues. Sequencing was performed on Illumina HiSeqX or NovaSeqX instruments.

  Dataset EGAD50000000496

• Lam-ESC&Lam-Recombination data

  This dataset includes all data produced in the study describing "Lam-ESC&Lam-Recombination", a method for sequencing of signal joints and coding joints generated from human light chain antigen receptor loci during V(D)J recombination in B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) patients. This dataset includes: - Amplicon Lam-ESC for a total of 86 BCP-ALL patients - fastq files - Amplicon Lam-Recombination for a total of 43 BCP-ALL patients - fastq files

  Dataset EGAD50000000597

• MCRI-WEHI GRREAT Ataxia Sequencing Cohort

  This study evaluated the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Long-read adaptive sequencing (LR-AS) was performed to identify pathogenic RE in 67 genes.

  Dataset EGAD50000000815

• RNA-seq of STIC lesions and adjacent normal samples

  In this study, we characterize premalignant lesions of the fallopian tube (serous tubal intraepithelial carcinomas) to explore the earliest events of tumorigenesis following mutation of the TP53 tumor suppressor gene. We conduct laser capture microdissection to isolate premalignant cells from adjacent normal cells, and subject isolated tissues to RNA-seq. Our findings reveal the earliest transcriptional changes established during premalignancy within the fallopian tube.

  Dataset EGAD50000000289

• paired-end FASTQ files from the study: Identification of the cause of juvenile parkinsonism in a case_SYNJ1

  The dataset consists of three samples: two controls and one case of juvenile Parkinsonism. Whole Exome Sequencing (WXS) was performed on these samples using hybrid selection for library preparation. Sequencing was carried out on the Illumina NextSeq 500 platform. For each sample, two FASTQ files containing paired-end reads (R1 and R2) were generated. The data deposited consists of the corresponding FASTQ files.

  Dataset EGAD50000000413

• Methylome profiling of Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) and a patient derived cell-line model

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1 using the twist human methylome panel.

  Dataset EGAD50000000040

• The chemotherapeutic CX-5461 is extremely mutagenic and may increase cancer risk

  Deposited here are whole-genome sequencing bam or fastq files from the experimental isogenic cell lines used in the study "The chemotherapeutic CX-5461 is extremely mutagenic and may increase cancer risk, Koh, Gene (2023)". The bam files were aligned to GRCh38/hg38 using BWA-MEM. The corresponding variant call data have been deposited on Mendeley Data, V2, doi: 10.17632/d58cv549v6.2

  Dataset EGAD50000000036

• SNP array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains SNP array data for tumor/normal pairs for a subset of 36 patients from the screening cohort plus an additional relapse tumor of one of those 36 patients. Data was generated on a OmniExpress-24 v1.1 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002597

• Epigenome-wide association study of cocaine use disorder in postmortem human brain tissue

  Analysis of cocaine use disorder (CUD) associated epigenome-wide DNA methylation (DNAm) alterations in human postmortem brain tissue of Brodmann Area 9. Tissue samples from N=21 CUD cases and N=21 individuals without CUD originating from the Douglas Bell Canada Brain Bank (DBCBB) were included. Epigenome-wide DNAm was investigated using the Illumina Infinium MethylationEPIC array.

  Dataset EGAD00010002396

• genotyped_bacterial_meningitis

  This study includes 1146 samples of host genotyping data (genotyped) from Illumina Omni arrays. Samples were collected from adults (>16 yrs) patients with CSF confirmed bacterial meningitis in the Netherlands between 2006 and 2015. Metadata includes patient outcome, species of bacteria, and for 467 samples a link to an ENA run with the associated bacterial genome (S. pneumoniae only).

  Dataset EGAD00010002328