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• Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

  This dataset contains CLCNKA/CLCNKB locus alignment data from 27 patients with Bartter syndrome and structural variants encompassing the CLCNKB gene. Due to data protection regulations and in accordance with the patient consent, only relevant alignments from the following regions are shared: hg19: chr1:16,300,000-16,400,000 hg38 (linked read dataset only): chr1:16,000,000-16,100,000 Methods to generate libaries were: long-range amplicon PCR (24 samples), targeted long-fragment enrichment (Samplix/Xdrop technology, 4 samples), long-read whole genome (PacBio Sequel II HiFi reads, 3 samples), 10X linked read short read whole genome (1 sample).

  Dataset EGAD00001011064

• Whole genome sequencing of EBV Associated Nasopharyngeal Carcinoma

  Interplay between EBV infection and acquired genetic alterations during nasopharyngeal carcinoma (NPC) development remains vague. Here we report a comprehensive genomic analysis of 70 NPCs, combining whole-genome sequencing (WGS) of microdissected tumor cells with EBV oncogene expression to reveal multiple aspects of cellular-viral co-operation in tumorigenesis. Genomic aberrations along with EBV-encoded LMP1 expression underpin constitutive NF-κB activation in 90% of NPCs. A similar spectrum of somatic aberrations and viral gene expression undermine innate immunity in 79% of cases and adaptive immunity in 47% of cases; mechanisms by which NPC may evade immune surveillance despite its pro inflammatory phenotype. Additionally, genomic changes impairing TGFBR2 promote oncogenesis and stabilize EBV infection in tumor cells. Fine-mapping of CDKN2A/CDKN2B deletion breakpoints reveals homozygous MTAP deletions in 32-34% of NPCs that confer marked sensitivity to MAT2A inhibition. Our work concludes that NPC is a homogeneously NF-κB-driven and immune-protected, yet potentially druggable, cancer.

  Study EGAS00001004705

• SC_DDD-G-4

  Post-QC (pre-imputation) genotype data for N=6,983 DDD probands included in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Consists of filtered set of samples and variants from EGAD00010001598 and EGAD00010001600. Includes patient HPO phenotype terms and GWAS summary statistics (including imputed variants). Samples were genotyped on the Illumina HumanCoreExome BeadChip and Illumina InfiniumCoreExome Beadchip

  Dataset EGAD00010001604

• HipSci RNA sequencing for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNA sequencing on commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines.

  Study EGAS00001001727

• Transcriptome profiling for Korean Diffuse Gastric cancers

  Gastric cancers in young patients are aggressive and predominantly of diffuse histology. Also, they are more frequent in female. To identify transcriptome profile in this unique subset of gastric cancers, RNA-seq analyses were performed using frozen cancer tissue. Adjacent normal tissue of the same patients were used in differently expressed gene selection and fusion gene prediction.

  Study EGAS00001001859

• Timing the Philadelphia chromosome and trajectory to chronic myeloid leukaemia

  We sequence >1000 whole genomes from 9 patients with CML, providing the largest sequencing dataset for this cancer. We reconstruct phylogenetic trees using somatic mutations and infer BCR::ABL1 timing and tumour growth rates. We correlate mutation landscapes and clonal trajectories with clinical features.

  Dataset EGAD00001015353

• Integrated whole-genome and transcriptome sequencing reveals divergent evolutionary processes across biliary tract cancer subtypes (WGS data from biliary tract cancer molecular subtype study)

  WGS data for biliary tract cancer samples (Consensus molecular subtypes define distinct evolutionary trajectories of biliary tract cancers). The dataset includes tumour bam files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=97 tumour normal pairs)

  Dataset EGAD50000002530

• Survival Benefit and Genetic Profile of Pemetrexed as Initial Chemotherapy in Selected Chinese Patients with Advanced Lung Adenocarcinoma

  NGS data of 12 patients enrolled in the Chinese Patient Assistance Program from multiple centers who received pemetrexed alone or combined with platinum as initial chemotherapy and continued pemetrexed maintenance therapy for advanced lung adenocarcinoma from November 2014 to June 2017.

  Dataset EGAD00001006287

• Primary_DIPG_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

  Dataset EGAD00001011080

• RNA-seq dataset of Ewing and Ewing-like-sarcoma tumoroid biobank reveals distinct drug sensitivities: translocation makes the difference

  Creation of living organoid biobank for ewing and ewing-like sarcomas

  Dataset EGAD00001015419

• Low-coverage whole-genome sequencing (lcWGS) data of Genome in a Bottle (GIAB) reference samples

  This dataset contains low-coverage whole-genome sequencing (lcWGS) data generated from three GIAB reference samples (HG001–HG003) for method benchmarking and concordance analysis in FFPE-GWAS workflows. The data were generated using Illumina NovaSeq with paired-end 150bp reads and downsampled to 2x coverage.

  Dataset EGAD00001015533

• Whole-genome array data for 42 Roma and 52 non-Roma from Czech Republic

  This dataset contains one VCF file with 94 individuals genotyped with the Human Origins Array.

  Dataset EGAD50000001103

• Discordant_Monozygotic_Twins_ALS (Epigenetics)

  We conducted a multi-omics study on a monozygotic twin pair discordant for amyotrophic lateral sclerosis. Data refers to 7 samples that are technical replicates from biological samples collected from the twins at two different time points (T1 and T2).

  Dataset EGAD00010002716

• GATCI_Oncoscan_Data

  This dataset contains files generated from Affymetrix Oncoscan Arrays. For each sample there are two paired cel files containing the raw data from AT and GT channels. Raw data has been transfromed to OSCHP signal files also within this dataset.

  Dataset EGAD00010001579

• WGS/RNA-seq pair of an inflammatory hepatocellular adenoma (IHCA)

  This study contain the WGS and RNA-seq aligned bam files for this particular inflammatory hepatocellular adenoma sample.

  Dataset EGAD00001004141

• BRIDGE Bleeding and Platelet Disorders

  Whole exome sequencing BAM files for samples from the BRIDGE Consortium with pathogenic or likely pathogenic variants on genes linked to bleeding or platelet disorders.

  Dataset EGAD00001001333

• Target capture sequence for Primary-recurrent HCC study

  This dataset contains target capture sequence data from 255 samples, including 154 tumors and 101 normal samples. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.

  Dataset EGAD00001005450

• Sequencing data for the manuscript "Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer"

  This submission contains gzipped fastq files from paired-end targeted sequencing.

  Dataset EGAD00001010105

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) monitoring shows promise for risk stratification and decision-making in cancer patients. However, factors like background noise from non-tumor DNA, clonal haematopoiesis, and non-shedding tumors may complicate manual interpretation and limit its clinical application. In this proof-of-concept study in advanced non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), we developed an algorithm that automatically classifies serial cell-free DNA (cfDNA) samples, thereby enabling reliable and reproducible interpretation, and preventing time-consuming manual interpretation in approximately 75% of patients. Importantly, application of the algorithm allowed early risk stratification and decision-making, specifically identifying approximately 35% of patients with short-term clinical benefit and approximately 25% of patients who may potentially benefit from treatment escalation. Simultaneous serum tumor marker (STM) monitoring further improved risk stratification and decision-making in our study, enabling accurate identification of all patients with a clinical benefit of at least one year.

  Study EGAS50000001554

• Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

  The dataset contains Whole Exome Sequencing data (BAM files) of 22 samples from HER2+ metastatic breast patients. For 9 of the 13 tumours samples there are paired controls available from normal tissue. There are 8 tumours samples that are from treatment-responder patients and 5 tumours samples from non responder patients.

  Dataset EGAD00001006217

• DNA Replication Speed controls Epigenome Integrity and T Cell Fate

  Epigenetic mechanisms maintain cellular identities by enforcing stable, cell type-specific transcriptional programs while also allowing regulated plasticity for adaptations to environmental cues like differentiation signals. Dysregulation of this dual capacity has been linked to cancer and chronic inflammation, with the regulatory mechanisms remaining poorly understood. Here, we identify DNA replication speed as a physiological regulator controlling epigenome stability and plasticity. Using T-lymphocytes as a model, we demonstrate that fast DNA replication speed impaired epigenome stability, causing DNA methylation maintenance errors at cell type-specific enhancers and heterochromatin, ultimately leading to compromised cell function. However, accelerated DNA replication speed supported epigenome plasticity during differentiation, promoting successful cell-type transitions

  Study EGAS50000001273

• Single-cell RNA sequencing of sorted regulatory T cells

  Single-cell RNA sequencing of flow cytometry enriched CD4+ CD127- CD25+ regulatory T cells from 8 systemic lupus erythematosus patients (SLE_001 to SLE_007, and SLE_009) collected at baseline (day 0, before interleukin-2 immunotherpay) and day 5 (after 1 treatment cycle of interleukin-2 immunotherapy). Sorted immune cells were hash tagged and then stained with TotalSeq Human Universal Cocktail (Biolegend) before further processing for single-cell RNA sequencing using the 10X-Genomics platform (incl. generation of TCR libraries). Samples from patients SLE_001, SLE_002, SLE_004, SLE_006 were collected and processed on the first day of experiment (Day 1), and samples from patients SLE_003, SLE_005, SLE_007, SLE_009 on the second day of experiment (Day 2). On each day, samples were pooled and distributed to four lanes on the chromium controller. Run ID 245269 and ID 245270 identify samples sequenced on separate flow cells. Provided are raw sequencing files.

  Dataset EGAD50000000663

• NIHR BioResource Rare Diseases WGS project - Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Ehler-Danlos (ED) and ED-like Syndromes (EDS) Rare Disease domain.

  Dataset EGAD00001005123

• mRNA-Seq on single human MII oocytes collected from gonadotropin stimulated women

  This dataset contains 11 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from gonadotropin stimulated women undergoing fertility treatments. M-II stage oocytes were collected and flash frozen prior to lysis followed by RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina.

  Dataset EGAD00001006863

• Sequencing data for oesophageal and related samples - Black et al (WES)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)

  Dataset EGAD00001011188

• ChIP-seq for 10 samples

  This dataset contains ChIP-seq data generated from two patient-derived xenograft (PDX) models. For each model, sequencing data are provided from input control (n=1), IgG control (n=2), and FOXF1 immunoprecipitation (n=2). All the 10 samples are in bam file type.

  Dataset EGAD50000001786

• GeoMx DSP of NGS mRNA expression in pre-treatment biopsies from patients with metastatic triple-negative breast cancer treated with PARP inhibitors.

  This dataset contains GeoMx digital spatial profiling (DSP) data from 12 FFPE pre-treatment biopsies of metastatic HR-altered breast cancer patients subsequently treated with PARP inhibitors (Olaparib or Talazoparib). Samples were collected from primary breast tumors (n=7) and metastatic sites including lymph nodes (n=2), bone (n=2), and brain (n=1). Tissue sections were stained for pan-cytokeratin (PANCK) to selectively profile tumor cells, with NGS-based transcriptome data generated for both PANCK+ and PANCK- regions. The dataset includes raw data files (176 fastq files) along with clinical annotations.

  Dataset EGAD50000001932

• ANGIOPREDICT - an FP7-funded project enabling personalised medicine for patients with metastatic colorectal cancer.

  In ANGIOPREDICT, academic cancer biologists and industry-based biotechnology researchers will work together with clinicians to identify biomarkers to predict whether individual metastatic colorectal cancer patients will respond positively to Avastin® combination therapy. Diagnostic tests using these biomarkers will also be developed to provide clinicians with the means to predict patient treatment responses in the future.

  Study EGAS00001005423

• Leukemia Data Access committee for the deposited data. The committee consists of the principal investigators for the data set.

  Dac EGAC00001003565

• Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

  Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.

  Study EGAS00001003190

• 160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN.

  160 WES and 25 WGS for HBV related HCC, and 15 WES for ICC belongs LICA-CN.

  Study EGAS00001002331

• Whole genome sequencing generated from metastatic gliosarcoma patient samples

  This dataset contains whole genome sequencing data aligned to the b37 reference genome for 4 spatially and temporally distinct tumors from one patient with a matched normal blood sample.

  Dataset EGAD00001005745

• Bulk RNAseq fastq files

  RNAseq FASTq files from 15 samples from patients with ovarian cancer, 5 samples for each of the 3 tumor immune phenotypes (Infiltrated, Excluded and Desert).

  Dataset EGAD00001006975

• Combined PDCD1, BRAF and MAP2K7 Inhibition in BRAFV600E Colorectal Cancer: A Phase 2 Trial

  In this study, we evaluated the clinical efficacy of combined PDCD1, BRAF, and MAP2K7 inhibition in metastatic BRAFV600E Colorectal Cancer (CRC) patients (NCT03668431). We performed bulk whole exome sequencing (WXS) and bulk RNA sequencing (RNA-Seq) in 35 pre-treatment tumor biopsies and matching germline for tumor mutational burden (TMB), BM1/BM2 transcriptional subtypes, and consensus molecular subtypes (CMS) analysis, which were previously reported to affect prognosis and response to therapy (PMIDs: 32047001, 27354468, and 26457756). Analysis of bulk data showed that TMB, BM1/BM2 subtypes, and CMS did not correlate with clinical response in this study. Analysis of single cell RNA sequencing (scRNA-Seq) data of tumor epithelial cells from 23 paired day 0 and day 15 tumor biopsies revealed greater induction of tumor cell-intrinsic immune programs and more complete MAPK inhibition in patients with better clinical outcome.

  Study phs003178

• atrial appendage RNA-seq in non-, paroxysmal and persistent atrial fibrillation

  64 left atrial appendages from patients without atrial fibrillation (AF) undergoing cardiac surgery, patients with paroxysmal AF and with persistent AF (~20 per group). Trizol RNA isolation, rRNA depletion, paired transcriptome sequencing on illumina NovaSeq 6000. Provided are FastQ and BAM files. Additional data (e.g. clinical characteristics, RIN values etc.) can be provided upon reasonable request. The same RNA samples (62 out of 64) were used for miRNA sequencing. Results from miRNA seuqencing are stored in the EGA database managed by the same DAC.

  Dataset EGAD00001007693

• Dataset for gynecologic_cancer-RNA

  Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008856

• Dataset for melanoma-RNA

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008858

• Dataset for hematopoietic_malignancy-RNA

  Rare cancer sequencing data of 47 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008860

• Dataset for soft_tissue_tumor-WHOLE_GENOME

  Rare cancer sequencing data of 142 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008900

• Dataset for leiomyosarcoma-RNA

  Rare cancer sequencing data of 87 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008849

• Lineage-specific genome architecture links disease variants to target genes

  Long-range interactions between DNA regulatory elements and their target genes play major roles in gene regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary haematopoietic cell types. We show that long-range promoter interactions are highly cell-type specific, preferentially linking active promoters and enhancers. Patterns of promoter interactions reflect cell lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched for expression quantitative trait loci with effects on their interacting target genes. We exploit this rich resource of interactome maps to connect non-coding disease variants to their target promoters, identifying thousands of new disease-candidate genes, and implicating a number of gene pathways in disease susceptibility. Our results demonstrate the power of promoter interactomes from primary cells to reveal insights into genomic regulatory mechanisms underlying common diseases.

  Study EGAS00001001911

• Genetic regulation of RNA splicing in human pancreatic islets

  Here we provide access to newly generated RNA-seq data for 101 human islet samples used to map genetic effects on gene expression and alternative splicing (eQTLs and sQTLs) in a total of 399 human islets. We also make publicly available genotyping array data for 128 human islets, including the fraction of 101 human islet samples with existing RNA-seq data.

  Dataset EGAD00001009102

• Targeted panel data for newly diagnosed myeloma patients.

  Genomic abnormalities in MM are common and can affect a patients outcome. Here we have performed targeted sequencing on xx patient tumor samples and matched control DNA. The targeted panel consists of ~160 genes and copy number regions, as well as key regions of chromosomal translocation including IGH, IGK, IGL and MYC. Using mutation, copy number, and translocation information we have been able to identify abnormalities that affect prognosis including bi-allelic inactivation of TP53 and rearrangements involving MYC.

  Study EGAS00001002859

• Establishment and Genomic Validation of Novel Patient-Derived Xenograft Models for Drug Discovery in Gastrointestinal Stromal Tumor

  This dataset contains targeted next-generation sequencing data generated with the Illumina TruSight Oncology 500 (TSO500) assay from six gastrointestinal stromal tumors (GIST) and matched patient-derived xenograft (PDX) models established at Fox Chase Cancer Center (Philadelphia, PA). GIST are most commonly driven by activating mutations in KIT or PDGFRA, and this study focused on KIT-mutant tumors. All PDXs were derived from metastatic patient tumors previously treated with one or more tyrosine kinase inhibitors (TKIs). PDXs were maintained through series of passages and represents in vivo models of differential TKI sensitivity. The dataset represents a detailed comparison of mutational profiles between primary tumors and corresponding PDXs across passages, enabling studies of genomic stability, resistance mechanisms, and the evaluation of novel therapeutic strategies in GIST.

  Study phs004185

• Project for Development of Innovative Research on Cancer Therapeutics; Identifiying the predictive factors for response to chemoherapy in ovarian cancer

  To identify novel predictive biomarkers of response to chemotherapy for clear cell carcinoma of the ovary

  Study JGAS000076

• Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment

  Genomic data from FFPE tumor samples of 258 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS) at 1x. The study aimed to characterize somatic copy number alterations (SCNAs) and SCNA burden to assess their clinical relevance for patient stratification across different first-line treatments.

  Dac EGAC50000000929

• Integrated whole-genome and transcriptome sequencing reveals divergent evolutionary processes across biliary tract cancer subtypes (WTS data from biliary tract cancer molecular subtype study)

  WTS data for biliary tract cancer samples (Consensus molecular subtypes define distinct evolutionary trajectories of biliary tract cancers). The dataset includes tumour bam files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=85 tumours)

  Dataset EGAD50000002529

• RNA_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in either glucose or lactate, in the presence and absence of DCA or BRD4 inhibition (JQ1). Samples were collected and processed for bulk RNA-seq.

  Dataset EGAD50000000089

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 241 tumour samples

  Dataset EGAD00001005388

• CITE-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to assess RNA expression and surface antigen expression of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level. For this purpose, we performed cellular indexing of transcriptomes and epitopes (CITE-seq) of primary leukemia samples from four CK-AML patients.

  Dataset EGAD00001011171