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• Targets of MEK inhibition in DIPG

  The survival of children with diffuse intrinsic pontine glioma (DIPG) remains dismal, with new treatments desperately needed. In the era of precision medicine, targeted therapies represent an exciting treatment opportunity, yet resistance can rapidly emerge, playing an important role in treatment failure. In a prospective biopsy-stratified clinical trial, we combined detailed molecular profiling (methylation BeadArray, exome, RNAseq, phospho-proteomics) linked to drug screening in newly-established patient-derived models of DIPG in vitro and in vivo. We identified a high degree of in vitro sensitivity to the MEK inhibitor trametinib in samples which harboured genetic alterations targeting the MAPK pathway, including the non-canonical BRAF_G469V mutation, and those affecting PIK3R1 and NF1. However, treatment of PDX models and of a patient with trametinib at relapse failed to elicit a significant response. We generated trametinib-resistant clones in the BRAF_G469V model through continuous drug exposure, and identified acquired mutations in MEK1/2 (MEK1_K57N, MEK1_I141S and MEK2_I115N) with sustained pathway up-regulation. These cells showed the hallmarks of mesenchymal transition, and expression signatures overlapping with inherently trametinib-insensitive primary patient-derived cells that predicted an observed sensitivity to dasatinib. Combinations of trametinib with dasatinib and the downstream ERK inhibitor ulixertinib showed highly synergistic effects in vitro. These data highlight the MAPK pathway as a therapeutic target in DIPG, and show the importance of parallel resistance modelling and rational combinatorial treatments likely to be required for meaningful clinical translation.

  Study EGAS00001004495

• Transcriptome - MBD4-deficient AML

  Transcriptome sequencing for WEHI-AML-1 and WEHI-AML-2. RNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit v2 and sequenced on an Illumina HiSeq2500.

  Dataset EGAD00001003569

• Spatially resolved cellular and molecular drivers of cardiac remodelling in healthy and failing human hearts: Adult DNA (2025-10-16)

  Human Cell Atlas - WGS Adult Heart . This dataset contains all the data available for this study on 2025-10-16.

  Dataset EGAD00001015751

• DNA methylation and transposable element landscapes define human regulatory T cells in tissues and identify their blood recirculating counterpart

  Regulatory T cells (Treg cells) in tissues can perform immunoregulatory and tissue-regenerative functions. Despite these important tasks, human-tissue Treg cells lack understanding, specifically, the epigenetic basis of their differentiation as well as re-circulating tissue-Treg cells are incompletely understood. Here, we performed genome-wide DNA methylation analysis of human Treg cells from skin and blood and embedded this in a multi-omic epigenetic framework including chromatin accessibility and gene-expression. We thereby revealed novel epigenetic programs defining human skin Treg cell differentiation and delineated how these are present on the different epigenetic levels. We discovered that transposable elements are an integral constituent of the demethylation landscape in skin Treg cells. Based on TCR-sequencing and DNA demethylation homologies, our data unveil that blood CCR8+ Treg cells are recirculatory human tissue-Treg cells. Our data provide novel insights in human tissue-Treg biology, required to harness these cells for therapeutic avenues.

  Study EGAS50000000738

• Sequencing data for oesophageal and related samples - Alex Frankell et al (RNA)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours

  Dataset EGAD00001004423

• A whole-genome sequencing study for evolutionary history of Tibetans and their genetic adaptations to high altitude

  Due to a unique adaptation to high altitude, the Tibetan Plateau population has been the subject of much research interest. In this study, we conducted whole genome sequencing of 27 Tibetan individuals. Through our analysis, we inferred a detailed history of demography and revealed the natural selection of Tibetan population. We provided evidence of genetic separation between the two subpopulations of Han and Tibetans as early as 44 to 58 thousand years ago, replicated previously reported high altitude adaptation genes, including EPAS1 and EGLN1, and reported three new candidate genes, including PTGIS, VDR, and KCTD12.

  Study phs001338

• IMI-RHAPSODY data

  Molecular data of large diabetes cohorts was generated to identify markers of diabetes progression measured as time to insulin initiation

  Study EGAS00001007041

• Amplicon sequencing of long non-coding RNA associated with gastritis and gastric carcinogenesis

  This study aimed to identify dysregulations of long non-coding RNA (lncRNA) in gastric cancer, and to reveal molecular functions of lncRNAs associated with gastritis and gastric carcinogenesis. We also aimed to reveal the correlation between clinicopathological characteristics and lncRNA alterations. To this end, we will try to develop predictive markers of gastric cancer risk, which enables prevention and early detection of gastric cancer. We will also try to develop molecular markers which enable us to select treatment strategies for gastric cancer.

  Study JGAS000353

• Methylation analysis of plasma DNA informs etiologies of Epstein-Barr virus-associated diseases

  Through whole-genome methylation analysis of plasma samples from patients with nasopharyngeal carcinoma (NPC), EBV-associated lymphoma and infectious mononucleosis, we demonstrate that EBV DNA methylation profiles exhibit a disease-associated pattern. Such observation implies significant potentials in the development of methylation analysis of plasma EBV DNA for NPC diagnostics.

  Study EGAS00001003408

• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  In many areas of oncology, we lack sensitive tools to track low burden disease. While cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low disease burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and post-operative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance, and empowering treatment optimization in low-disease burden oncology care

  Study EGAS00001004406

• Single cell atlas of large B-cell lymphoma

  Large B-cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies, shaped by complex tumor and microenvironments that play a critical role in disease progression. There has been no direct and comprehensive single-cell characterization of tumor microenvironment in LBCL that simultaneously captures lymphoid, myeloid, and stromal populations across a sufficiently large cohort to reveal reproducible and biologically meaningful patterns. Here, we performed single-nucleus multiome profiling, coupled with bulk DNA and RNA sequencing, on 232 tumor and control biopsies to comprehensively map cell subpopulations of LBCL. Through this integrative approach, we identified Lymphoma Microenvironment Archetype Profiles (LymphoMAPs)—distinct, reproducible patterns defined by the co-occurrence of functionally specialized cell subsets. We further characterized the cell-cell communication pathways that shape these transcriptional phenotypes within archetypes. Importantly, we discovered associations between specific LymphoMAPs and clinical and molecular features of LBCL, including response to CD19 CAR T-cell therapy. Our study provides a valuable resource of lymphoid, myeloid, and non-hematopoietic cell states in LBCL and offers a framework for understanding how the abundance and functional state of cells within the tumor microenvironment may drive inter-patient variability in therapeutic outcome.

  Study EGAS50000001022

• BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 Summary Statistics of Most Significant Associations

  BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 summary statistics of most significant association data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each summary statistics file contains the most significant association for each phenotype ID.

  Dataset EGAD00001005200

• The G2 gene expression signature and MYC overexpression are independent poor prognostic factors in childhood high-grade osteosarcoma

  Key objective Are the prognostic transcriptomic G1/G2 gene expression signature, MYC overexpression, and MYC amplification replicable stratifying biomarkers for future clinical trials in high-grade osteosarcoma? Knowledge gathered In an unselected cohort, the G2 gene expression signature and MYC overexpression, but not MYC amplification, were independently associated with poor event-free and overall survival. Relevance Transcriptomic biomarkers may serve as stratifying factors that guide the management of patients with high-grade osteosarcoma. Current data underlines the importance of prospective validation of the G1/G2 signature and MYC overexpression in an international, multicenter, study.

  Dataset EGAD00001015503

• Oesophageal adenocarcinoma WGS from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains whole genome sequencing (WGS) generated from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). WGS data were generated with the aim to assess previously reported (e.g. tumour mutational burden) and novel predictive genomic markers for immunochemotherapy treatment in this setting. Using these data, mutation and copy number profiles were generated for the LUD2015-005 study, which were assessed for correlation with patient outcomes from this trial.

  Dataset EGAD00001009400

• WGBS data for EGAS00001004660

  WGBS data for EGAS00001004660, "Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin"

  Dataset EGAD00001006538

• RNA data for EGAS00001004660

  RNA data for EGAS00001004660, "Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin"

  Dataset EGAD00001006539

• 10x dataset of an obese human subject

  Biopsies from visceral adipose tissue from the omental depot (OAT) were obtained from an obese individual with participant informed consent obtained after the nature and possible consequences of the studies were explained under protocols approved by the Institutional Review Boards of the Perelman School of Medicine at the University of Pennsylvania, the Children’s Hospital of Philadelphia, or the Tel Aviv Sourasky Medical Center. The obese donor underwent bariatric surgery, the lean donor underwent cholecystectomy. OAT samples were placed in 1 mL of DMEM, and finely minced under sterile conditions before digestion in 50 mL of DMEM with 3 mg/1 mL collagenase IV (Gibco). Samples were incubated at 37°C in a rotating oven for 20-60 min. Adipocyte and stromal vascular fractions (SVF) were separated by centrifugation, and red blood cells (RBCs) were removed from the SVF by histopaque gradient (Sigma). Single-cell RNA-sequencing libraries were prepared using the Chromium platform (10x genomics), and sequenced on the MiSeq 500 or HiSeq 2500 Sequencing System (Illumina).

  Dataset EGAD00001005101

• RIP-SeqRaw data

  This dataset contains the raw count matrix generated in the PTBP1 project. Sequencing data were obtained from bulk directional RNA-seq and RIP-seq experiments performed on a NovaSeq 6000 platform (2×100 bp paired-end reads). Read counts were computed using HTSeq-count, without normalization. The dataset comprises two groups of samples: controls and patients. For each group, both input and immunoprecipitated samples are available. Patient samples correspond to skin biopsies from individuals affected by a neurodevelopmental disorder associated with variable skeletal dysplasia and disproportionate short-limbed short stature.

  Dataset EGAD50000001722

• Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures

  The SARS-CoV-2 pandemic has led to increasing numbers of COVID-19 patients all over the world. Aetiopathologies range from no symptoms, mild flu-like to severe cases succumbing to respiratory failure. Reports on a dysregulated immune system in the severe cases, showing similarities to cytokine release syndrome, calls for better characterization and understanding of the changes in the immune system as well as their variance across COVID-19 patients in order to be able to design according to host-directed therapies. Here, we profiled blood transcriptomes of 39 COVID-19 patients and 10 control donors. Enriched granulocyte signatures in whole blood samples were verified in granulocyte samples from 49 COVID-19 patients in a second cohort.

  Study EGAS00001004503

• Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions

  Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions

  Study EGAS50000000773

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005920

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005921

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who mastectomies due to Breast Cancer. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005923

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who underwent mastectomies due to a breast cancer diagnosis. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005924

• Clonally heritable gene expression imparts a layer of diversity within cell types

  Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high coverage single cell RNA profiling, we asked whether long-term, heritable differences in gene expression can impart diversity within cells of the same type. Studying clonal human lymphocytes and mouse brain cells, we uncovered a vast diversity of heritable gene expression patterns among different clones of cells of the same type in vivo. We combined chromatin accessibility and RNA profiling on different lymphocyte clones to reveal thousands of regulatory regions exhibiting interclonal variation which could be directly linked to interclonal variation in gene expression. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging and disease.

  Study EGAS50000000161