8252 results for "canc*"

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• Multi-omics datasets (WES, RNA-seq) of mesothelioma NERO study, a phase II PARP inhibitor clinical trial

  Niraparib Efficacy in Patient With Unresectable Mesothelioma, NERO, this randomised phase II trial is designed to evaluating the efficacy of the PARP inhibitor Niraparib versus active symptom control.

  Study EGAS50000001825

• Liquid-based genomic profiling in high-risk localized prostate cancer.

  In this study, we evaluated the feasibility and performance of tissue and liquid-based genomic profiling in patients with high-risk localized prostate cancer. Genomic DNA from 12 FFPE tissue samples and cell-free DNA from 27 plasma samples were analyzed using Illumina TruSight Oncology (TSO) 500 panels.

  Study EGAS50000001712

• Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

  Study EGAS00001006137

• Deep whole genome ctDNA chronology of treatment-resistant prostate cancer

  Study EGAS00001005783

• Whole exome sequencing of the dMMR colorectal cancer cohort

  We leveraged the ImmunoID NeXT platform, an Immune-enhanced multiomics platform to profile a cohort of patients with dMMR CRC. This sub-study includes the whole exome sequencing data

  Study EGAS50000001744

• Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk.

  Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to lifestyle risk in the form of cigarette smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, often many years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk are unclear. CT screening of current and former smokers has been shown to reduce lung cancer mortality by up to 26%. To examine whether clinical risk stratification can be improved upon by the addition of genetic data, and to explore the mechanisms of the persisting risk in former smokers, we have analyzed transcriptomic data from accessible airway tissues of 487 subjects. We developed a model to assess smoking associated gene expression changes and their reversibility after smoking is stopped, in both healthy subjects and clinic patients. We find persistent smoking associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune and interferon related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. Our results provide initial evidence for germline-mediated personalised smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.

  Dac EGAC50000000169

• Cellular Dynamics Upon Immune Checkpoint Inhibition

  Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet most patients experience limited or no clinical benefit. To elucidate the mechanisms of response and resistance, we analyzed single-cell RNA-sequencing data from 141 patients across multiple cancer types and ICI treatment modalities, with longitudinally paired samples. Using a robust, integration-free deep phenotyping framework, we annotated 876,410 cells into 80 granular states. We identified consistent compositional changes in 17 cell subtypes following ICI treatment, including enhanced adaptive immune responses and reduced interferon-responsive cells. Co-regulated cell communities within the tumor microenvironment (TME) highlighted coordinated interplay between immune and non-immune components. Importantly, we discovered two distinct patient groups with divergent TME dynamics post-treatment: responders showed expansion of naive lymphocytes, while non-responders exhibited increased immune-experienced/suppressive cells. This dichotomy offers a potential predictive biomarker for patient stratification. Our comprehensive analysis of TME dynamics during ICI treatment advances understanding of response mechanisms and personalized cancer immunotherapy.

  Study EGAS50000000459

• WGS, DuplexSeq and NanoSeq genomic data from histologically normal tissue in cancer patients

  The extent to which mutagenic and non-mutagenic processes, including cancer treatment, contribute to somatic evolution in histologically normal tissue remains unclear. We subjected 168 cancer-free normal samples representing 16 different organs from 22 patients with metastatic cancer enrolled in the PEACE research autopsy study to high-depth duplex panel sequencing (coverage >20,000x). In every sample we identified somatic mutations (range 170 - 2,978) at exceedingly low variant allele frequencies (median VAF 0.0000323), consistent with a patchwork of mutated cells in normal tissue. By analysing the mutational spectra of each sample, we extracted 16 distinct single base substitution mutational signatures, reflecting somatic mutational processes that have moulded the genomes of normal cells. Signatures were found to be associated with diverse aetiologies, including alcohol-related mutation acquisition in liver tissue, smoking-induced mutagenesis in lung and cardiac tissue, and multiple distinct treatment-induced processes, which correlated with treatment and its duration. On average, in this cohort in which patients had each received several lines of anti-cancer therapy, exogenous sources, including treatment-related mutagenesis, underpinned >40% of mutations in liver samples, yet <10% in brain samples. Finally, we observed clear differences in the extent and effects of selection in different tissues, with positive selection in certain tissues, including lung (TP53, EGFR and PIK3CA), liver (NF2L2) and spleen (BRAF, NOTCH2), and limited selection in others, such as brain and cardiac. Over 25% of driver mutations in normal tissue exposed to systemic anti-cancer therapy, including mutations in TP53, could be attributed to treatment-induced mutagenesis. Immunotherapy, while not associated with mutagenesis, was linked to an excess of driver mutations in PPM1D and TP53, illustrating how non-mutagenic treatment can sculpt somatic evolution. Our study reveals the rich tapestry of mutational processes and driver mutations in cancer-free normal tissue, and the profound impact of cancer therapeutic and life-time environmental exposures on normal tissue somatic evolution.

  Study EGAS00001008326

• Comprehensive Genomic Profiling of a National Cohort of Pediatric Papillary Thyroid Carcinoma in Hungary

  Pediatric papillary thyroid carcinoma (PTC) is a rare childhood malignancy with increasing incidence and distinct clinicopathological features, including high rate of locoregional metastases and different molecular background compared to adult cases. Traditional treatments (surgery, radioactive iodine) are effective but pose long-term risks, prompting the exploration of targeted therapies. We performed comprehensive genomic profiling on 21 pediatric PTC patients utilising the Illumina TruSight Oncology 500 platform and detected mutations, gene fusions, copy number variations and revealed tumor mutational burden.

  Study EGAS50000001833

• WES and RNA sequencing of mesothelioma patients from CONFIRM clinical trial

  CONFIRM is a placebo controlled, double-blind randomised phase III clinical trial designed to investigate the efficacy of the anti-PD1 inhibitor nivolumab in patients with relapsed mesothelioma. This study applied the whole exome sequencing and transcriptomic sequencing to uncover determinants of efficacy in patients exhibiting the most extreme response outcomes.

  Study EGAS50000001814

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST4 study, a phase II PD-L1/VEGF blockage clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, designed to examine the efficacy and correlates of response to dual inhibition of programmed death-ligand 1 and vascular endothelial growth factor inhibition.

  Study EGAS50000001818

• Multiple Myeloma treated with anti-BCMA T-cell-redirecting therapy (1st Batch)

  Bone marrow samples were collected from patients treated with either anti-BCMA CART and/or anti-BCMA TCE. All samples were sorted using the StemCell EasySep Human CD138 positive selection kit II (StemCell, Cambridge, MA). The positive CD138+ were submitted for WGS, using peripheral blood mononuclear cells as normal matched. WGS was carried out by the Molecular Genomics Core Facility at Moffitt Cancer Center contingent on the availability of high-quality pre-treatment samples. Germline DNA was obtained from peripheral blood mononuclear cells, while tumor DNA was extracted from CD138-enriched bone marrow aspirate specimens using magnetic bead-based selection. Genomic DNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). For library preparation, 100 ng of genomic DNA was fragmented using the Covaris ML230 focused ultrasonicator (Covaris, Inc.), followed by library construction with the TruSeq DNA Nano Library Prep Kit (Illumina) in accordance with manufacturer instructions. Library quality and fragment size distribution were assessed via Agilent TapeStation, and quantification was performed using the Kapa Library Quantification Kit (Roche). Sequencing was conducted on the Illumina NovaSeq 6000 system using S4-300 reagent kits with a 2×150 bp paired-end configuration. Tumor samples were sequenced to a median coverage of 60×, and matched germline controls to 30×. Reference Genome: GRCh38.

  Dataset EGAD50000002632

• CLL Genome

  The Chronic Lymphocytic Leukemia (CLL) Genome Project aims to identify genetic alterations involved in the development and progression of the CLL, which are still unknown, with the objective of generating a comprehensive catalogue of genetic alterations in 500 independent tumours. The CLL Genome Project, as a contributing member of the International Cancer Genome Consortium (ICGC), has the purposes of creating diagnostic tools, discovering therapeutic targets and developing new strategies that will allow a customized therapy for CLL in order to make it more precise and effective. This study consists of two datasets. EGAD00001000023 described in the Nature paper (2011), Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia, and the dataset EGA00001000044 & & EGAD00001000083 described in the Nature (2011) paper, Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.Additional data generated within the ICGC-CLL genome project can be found in studies EGAS00001000374 and EGAS00001001306

  Study EGAS00000000092

• DAC for "Multimodal plasma and urinary cell-free DNA profiling improves risk stratification in newly diagnosed prostate cancer" with Dr. Anja Lisa Riediger(a.riediger@dkfz-heidelberg.de) and PD Dr. Magdalena Görtz(magdalena.goertz@dkfz-heidelberg.de)

  Dac EGAC00001003576

• MD Anderson Cancer Center HGSOC LRS Data Access Comittee

  Oxford Nanopore long-read sequencing was performed on six paired tumor-normal samples from patients with high-grade serous ovarian carcinoma. Reads were mapped to the GRCh38 reference genome, incorporating base modification information.

  Dac EGAC50000000597

• Integrated Methylation and Copy Number Analysis for Non-invasive Bladder Cancer Detection in Urine

  The molecular analysis of urine cell-free DNA (cfDNA) offers a non-invasive tool to advance bladder cancer (BC) management. Assessment of somatic copy number aberrations (SCNA) and DNA methylation, as singular or complementary analysis, have emerged as promising approaches for BC detection. Here, we developed an integrated analysis to assess both SCNA and targeted methylation changes from the same template molecules, named the iSECURE (integrated SEquencing-based Copy number and methylation analysis in URinE) method.

  Study EGAS50000001350

• Non-invasive bladder cancer cfDNA dataset

  The dataset contains 30 primary bladder cancer patients, 28 recurrent bladder cancer patients and 31 hematuria controls. Shallow WGS of cell-free DNA enzymatic methyl sequencing libraries was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD50000001935

• Non-invasive bladder cancer cfDNA dataset DAC

  Dac EGAC50000000790

• Whole-genome sequencing and H3K4me3 profiling of plasma cell-free DNA

  Epigenomic characterization of breast cancers by profiling circulating nucleosomes isolated from patient plasma using cell-free chromatin immunoprecipitation followed by sequencing (cfChIP-seq).

  Study EGAS50000001759

• Plasma cell-free whole genome sequencing

  This dataset contains whole genome sequencing data generated from plasma cell-free DNA of metastatic breast cancer patients and healthy individuals. Sequencing was performed on Illumina platforms to an average depth of approximately 10× and the dataset includes raw sequencing reads in FASTQ format.

  Dataset EGAD50000002524

• Plasma cell-free H3K4me3 chromatin immunoprecipitation sequencing

  This dataset contains plasma cell-free nucleosome H3K4me3 chromatin immunoprecipitation sequencing (cfChIP-seq) from metastatic breast cancer patients and healthy individuals. Sequencing was performed on Illumina platforms and the dataset includes raw sequencing reads in FASTQ format.

  Dataset EGAD50000002525

• Tumour tissue bulk RNA-seq

  This dataset contains bulk tissue RNA sequencing (RNA-seq) from six metastatic breast cancer patients. Sequencing was performed on Illumina platforms and includes raw FASTQ reads.

  Dataset EGAD50000002526

• A conserved enhancer in ecDNA-containing Medulloblastoma

  Extrachromosomal DNA (ecDNA) fundamentally reshapes the regulatory landscape of cancer cells by providing a platform for massive oncogene amplification and heightened chromatin accessibility. This research investigates how ecDNA-resident enhancers operate within large-scale molecular hubs to drive potent, long-range transcriptional activation that transcends standard chromosomal boundaries. By analyzing the unique structural configurations of these elements, the work identifies key mechanisms that contribute to rapid tumor evolution and significant phenotypic plasticity. These findings highlight the critical role of non-chromosomal regulatory elements in maintaining oncogenic signaling and suggest new avenues for therapeutic intervention in aggressive, ecDNA-driven malignancies.

  Study EGAS50000001609

• A conserved enhancer in ecDNA-containing Medulloblastoma

  Extrachromosomal DNA (ecDNA) fundamentally reshapes the regulatory landscape of cancer cells by providing a platform for massive oncogene amplification and heightened chromatin accessibility. This research investigates how ecDNA-resident enhancers operate within large-scale molecular hubs to drive potent, long-range transcriptional activation that transcends standard chromosomal boundaries. By analyzing the unique structural configurations of these elements, the work identifies key mechanisms that contribute to rapid tumor evolution and significant phenotypic plasticity. These findings highlight the critical role of non-chromosomal regulatory elements in maintaining oncogenic signaling and suggest new avenues for therapeutic intervention in aggressive, ecDNA-driven malignancies.

  Study EGAS50000001610

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001141

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001147

• A conserved enhancer in ecDNA-containing Medulloblastoma

  Extrachromosomal DNA (ecDNA) fundamentally reshapes the regulatory landscape of cancer cells by providing a platform for massive oncogene amplification and heightened chromatin accessibility. This research investigates how ecDNA-resident enhancers operate within large-scale molecular hubs to drive potent, long-range transcriptional activation that transcends standard chromosomal boundaries. By analyzing the unique structural configurations of these elements, the work identifies key mechanisms that contribute to rapid tumor evolution and significant phenotypic plasticity. These findings highlight the critical role of non-chromosomal regulatory elements in maintaining oncogenic signaling and suggest new avenues for therapeutic intervention in aggressive, ecDNA-driven malignancies.

  Study EGAS50000001608

• Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer

  Study EGAS00001007299

• Ultra-sensitive tumor-informed ctDNA monitoring of treatment response in advanced esophagogastric cancer patients

  To explore whether ultra-sensitive circulating tumor DNA (ctDNA) profiling enables earlier prediction of treatment response and detection of disease progression, we applied NeXT Personal, an ultra-sensitive bespoke tumor-informed liquid biopsy platform, to profile tumor samples from the KeyLargo study, a phase II trial in which metastatic esophagogastric cancer (mEGC) patients received capecitabine, oxaliplatin, and pembrolizumab. A total of 24 patients were evaluated, and all were ctDNA-positive at baseline. ctDNA levels varied from 406,067 down to 1.5 parts per million (PPM) with a median limit of detection of 2.03 PPM. ctDNA dynamics were highly correlated with changes in tumor size (ρ = 0.59, p = 7.3×10-9). Lack of early molecular response (50% or greater decrease in ctDNA levels at first available time point after 30 days, C2D1 or C4D1) was associated with worse overall survival (OS) (HR 6.6, 95% CI 1.8-24.1, p = 0.005) and progression-free survival (PFS) (HR 15.4, 95% CI 2.7-87.0, p = 0.002). Lack of molecular clearance of ctDNA was associated with worse OS (HR 6.9, 95% CI 1.5-30.8, p = 0.012) and PFS (HR 19.2, 95% CI 2.4-152.8, p = 0.005). Molecular progression (ctDNA increase) preceded imaging-derived progression by a median lead time of 65 days. These results suggest that ultra-sensitive liquid biopsy approaches could improve treatment decision-making for mEGC patients receiving chemotherapy and immunotherapy.

  Study EGAS50000001224

• Sequencing data from triple-negative breast cancer tumors

  Autoimmunity and anti-cancer immunity lie on the same biological continuum1,2, but their link remains obscure. The paraneoplastic neurological syndrome anti-NMDA receptor (NMDAR) encephalitis (ANRE) is a paradigm for their connectivity3 given that intratumoral NMDAR expression correlates with the generation of anti-NMDAR antibodies4,5. Here, we verify ectopic expression of GluN1 and GluN2B NMDAR sub-units in triple-negative breast cancer (TNBC)6 and model this using orthotopic TNBC tumors with inducible expression of GluN1-GluN2B NMDARs. We show that NMDAR expression is sufficient to induce B cell recruitment and their affinity maturation, consistent with an integrated adaptive immune response. Reconstruction of extended intratumoral B cell phylogenies and cryo-EM structural analyses demonstrated that affinity-matured hypermutated and class-switched antibodies emerged from pre-existing germline-configuration lower-affinity anti-NMDAR antibodies. Distinct matured antibodies targeted specific epitopes and induced conformational rearrangements within the NMDAR amino-terminal domain, predictive of their functional effects, ranging from inhibition to potentiation. Passive transfer of an NMDAR-potentiating antibody caused autonomic dysregulation and lowered the seizure threshold in healthy female mice, recapitulating key diagnostic criteria of ANRE4,5. We further identify a correlation between intratumoral NMDAR expression and anti-NMDAR antibody titers in TNBC patients. Taken together, our data establish a direct connection between intratumoral NMDAR expression, antibody maturation, and the onset of autoimmunity. These findings suggest that germline-encoded anti-NMDAR antibodies contribute to immune surveillance but can also trigger autoimmune disease upon maturation, revealing a mechanistic tradeoff between cancer immunity and neurotoxicity.

  Study EGAS50000001585

• 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 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS). 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.

  Study EGAS50000001619

• Sequencing data from triple-negative breast cancer tumors

  Autoimmunity and anti-cancer immunity lie on the same biological continuum1,2, but their link remains obscure. The paraneoplastic neurological syndrome anti-NMDA receptor (NMDAR) encephalitis (ANRE) is a paradigm for their connectivity3 given that intratumoral NMDAR expression correlates with the generation of anti-NMDAR antibodies4,5. Here, we verify ectopic expression of GluN1 and GluN2B NMDAR sub-units in triple-negative breast cancer (TNBC)6 and model this using orthotopic TNBC tumors with inducible expression of GluN1-GluN2B NMDARs. We show that NMDAR expression is sufficient to induce B cell recruitment and their affinity maturation, consistent with an integrated adaptive immune response. Reconstruction of extended intratumoral B cell phylogenies and cryo-EM structural analyses demonstrated that affinity-matured hypermutated and class-switched antibodies emerged from pre-existing germline-configuration lower-affinity anti-NMDAR antibodies. Distinct matured antibodies targeted specific epitopes and induced conformational rearrangements within the NMDAR amino-terminal domain, predictive of their functional effects, ranging from inhibition to potentiation. Passive transfer of an NMDAR-potentiating antibody caused autonomic dysregulation and lowered the seizure threshold in healthy female mice, recapitulating key diagnostic criteria of ANRE4,5. We further identify a correlation between intratumoral NMDAR expression and anti-NMDAR antibody titers in TNBC patients. Taken together, our data establish a direct connection between intratumoral NMDAR expression, antibody maturation, and the onset of autoimmunity. These findings suggest that germline-encoded anti-NMDAR antibodies contribute to immune surveillance but can also trigger autoimmune disease upon maturation, revealing a mechanistic tradeoff between cancer immunity and neurotoxicity.

  Study EGAS50000001598

• Single cell whole genome sequencing of 5 ovarian cancer specimens

  Single cell whole genome sequencing BAM files for five ovarian cancer specimens.

  Study EGAS50000001458

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

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

  Study EGAS50000001367

• Comprehensive genomic characterization of early stage bladder cancer - Total RNA-seq data

  This study looks at the non muscle invasive bladder cancer subtypes based on totRNAseq data of 414 bladder cancer samples collected in different European centers within the UROMOL project. All samples were sequenced using paired reads on Illumina platforms. The reads are mapped to hg38.

  Study EGAS50000000512

• Kings_Hepatoblastoma_Behjati_WGS_Managed_Access

  A study of the development of liver based tumours.

  Study EGAS00001006875

• Hepatoblastoma tumoroid biobank as a key resource for tumour genetics

  Study EGAS00001008251

• DAC for "CUT&RUN-sequencing identifies PTK7 as a direct Wnt target in patient-derived colorectal cancer organoids"

  Dac EGAC00001003592

• Plasma sequencing data for ctDNA monitoring for NSCLC in TRACERx

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project. This study captures the plasma sequencing data from the project.

  Study EGAS50000001767

• NSCLC PC9 erlotinib RAF1 study

  This Data Access Committee (DAC) oversees the controlled access to genomic sequencing data generated by Prof. Hoon Kim's laboratory at Sungkyunkwan University. The DAC is responsible for reviewing data access requests related to cancer genomics research, including the study on RAF1 ecDNA-mediated erlotinib resistance in NSCLC models.

  Dac EGAC50000001001

• Panel based plasma sequencing data for patients with NSCLC in TRACERx cohort

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project. This study captures the plasma sequencing data from the project.

  Dataset EGAD50000002534

• GCAT Hereditary Cancer Panel Sequencing Dataset

  This dataset comprises targeted sequencing data from 191 participants of the GCAT cohort generated using the I2HCP custom hereditary cancer panel. The panel is based on a custom bait library covering 122 genes associated with hereditary cancer syndromes, including genes related to hereditary colorectal cancer, hereditary breast and ovarian cancer, neurofibromatosis, and related disorders. Target enrichment was performed using a clinically validated design optimized for diagnostic accuracy. The panel and associated bioinformatic pipeline were previously validated, achieving analytical sensitivity and specificity greater than 99%. Sequencing data were processed using standardized alignment and variant calling procedures against the human reference genome. The dataset includes raw sequencing reads (FASTQ format) and processed variant call files (VCF format). All samples were pseudonymized prior to submission in accordance with ethical approvals and participant consent. Data are available under controlled access.

  Dataset EGAD50000002415

• Emergence of oncofetal plasticity is ubiquitous in early colorectal cancers

  Metastasis formation is classically considered a late-stage event in colorectal cancer (CRC) evolution. Yet, the time and patterning by which metastatic competence is acquired remain poorly understood. Here, we show that metastasis-associated oncofetal cell states already emerge at the earliest stages of CRC, concurrent with invasive front formation. However, while necessary for metastasis, we detect them ubiquitously among early non-metastatic cancers, highlighting additional bottlenecks like immune evasion. To understand how oncofetal cells first emerge, we generated multiregional organoid models that reflect successive tumor progression stages within individual early-stage CRCs. Whole-genome sequencing and growth factor-dependency assays exclude tumor cell-intrinsic acquired traits. In contrast, single-cell spatial atlases of the tumor-microenvironment before and after malignant transformation revealed stereotypic patterning of fibroblast subtypes resembling normal tissue architecture, resulting in distinct regional microenvironments. At the onset of malignant growth into the submucosa, the first cancer-associated fibroblasts (CAFs) to appear strongly resemble submucosal trophocytes and colocalize with oncofetal cell states at invasive fronts. Functionally, fibroblast-organoid co-cultures confirm that these trophocyte-like CAFs induce plastic transitioning to oncofetal states. Thus, interactions between tumor and submucosal fibroblasts directly following malignant transformation dictate the timing and location at which oncofetal plasticity first occurs during CRC progression.

  Study EGAS50000001532

• SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities

  Multiome (ATAC and GEX) sequencing for one rLN sample and one DLBCL sample

  Study EGAS50000001594

• WES Analysis of precancerous lesions in Lynch Syndrome

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

  Study EGAS50000001546

• Targeted re-sequencing of multi-region sampled tumors in PDAC

  Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).

  Study EGAS50000000239

• Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple negative breast cancer: phase 2 adaptive BELLINI trial. WES

  The adaptive BELLINI trial explored whether short combination ICI induces immune activation (primary endpoint: two-fold increase in CD8+ T cells or IFNG), providing rationale for neoadjuvant ICI without chemotherapy. In window of opportunity cohorts A (4 weeks anti-PD1) and B (4 weeks anti-PD1 + anti-CTLA4), we observed immune activation in 53% (8/15) and 60% (9/15) of patients, respectively. High tumor-infiltrating lymphocytes (TILs) correlated with response. Based on these data, we opened cohort C for patients with high TILs (≥50%) who received 6 weeks neoadjuvant anti-PD1 + anti-CTLA4 followed by surgery (primary endpoint: pathological complete response, pCR). 53% (8/15) of patients had major pathological response (< 10% viable tumor) at resection, with 33% (5/15) having pCR. All cohorts met Simon’s two-stage threshold for expansion to stage II. In conclusion, neoadjuvant immunotherapy without chemotherapy demonstrates potential efficacy and warrants further investigation in patients with early TNBC.

  Study EGAS50000000568

• Genome-Wide Variations of End Motif in Cell-Free DNA Fragments Distinguish Immunotherapy Responders from Non-Responders in Head and Neck Cancer: A Multi-Institute Prospective Study

  Genome-Wide Variations of End Motif in Cell-Free DNA Fragments Distinguish Immunotherapy Responders from Non-Responders in Head and Neck Cancer: A Multi-Institute Prospective Study

  Dac EGAC50000000753

• Epigenetic characterization of glioblastoma stem cells

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

  Study EGAS50000001804

• Peritoneal Metastasis of Gastric Cancer Data Access Committee

  Dac EGAC50000001025

• Circulating Cell-free DNA Whole Genome Sequencing from Head and Neck Cancer Patients

  This dataset contains plasma-derived circulating cell-free DNA (cfDNA) whole genome sequencing (WGS) data from patients diagnosed with head and neck squamous cell carcinoma. cfDNA was extracted from plasma collected at defined clinical timepoints.

  Dataset EGAD50000001828

• Raw transcriptomic sequencing data from peritoneal metastasis of gastric cancer

  This controlled-access dataset contains raw FASTQ files generated from single-cell RNA sequencing (scRNA-seq) and 10x Genomics Visium spatial transcriptomics. The dataset includes scRNA-seq data from four human lesions of peritoneal metastasis of gastric cancer (PMGC) and Visium spatial transcriptomics data from one human PMGC lesion. It also includes scRNA-seq data from nine PMGC lesions from humanized mouse models engrafted with human gastric cancer cells under different treatment conditions. These data are provided to support transcriptomic analysis of tumor and immune microenvironment features in PMGC.

  Dataset EGAD50000002714

• Rituximab-treated lymphoma patients show correlated deficiency in serological and T cell Spike-specific response after SARS-CoV-2 vaccination: insights from the CORSA Study.

  This study is part of the CORSA trial (NCT04345315), a prospective multicentric research project conducted by the Istituto Romagnolo per lo Studio dei Tumori “Dino Amadori” to investigate the immunologic response to mRNA SARS-CoV-2 vaccines in patients with hematologic malignancies (HM) and healthy individuals as controls (HC). The data in this repository refer to two subcohorts: 7 healthy controls and 10 lymphoma patients, randomly selected. Whole blood samples were collected to characterize T cell receptor (TCR) repertoire specificity against SARS-CoV-2 proteins before and after two BNT162b2 vaccination cycles, at baseline (before vaccination), 50 days after the first dose (V1), and 6 months after the first dose (V3). All participants were vaccinated under the Italian national campaign and provided informed consent following the Declaration of Helsinki. We investigated SARS-CoV-2-specific T cell responses through TCR repertoire profiling and examined correlations between serological and cellular responses in both patient and control groups. Using Next-Generation Sequencing (NGS) to characterize the CDR3 sequences of TCR β-chains from peripheral blood, we assessed clonal expansion (depth) and diversification (breadth) of SARS-CoV-2-specific T cell clonotypes over time, aiming to understand how cancer and its treatment influence vaccine-induced immunity in immunocompromised individuals.

  Study EGAS50000001205

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

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

  Study EGAS50000001463

• Single-cell genome and transcriptome profiling of high-grade serous ovarian cancer

  This dataset contains joint single-cell whole-genome sequencing (scWGS) and mRNA sequencing data generated using DNTR-seq from 4 high-grade serous ovarian cancer samples. Approximately 500 quality-controlled single cells per patient were profiled, with DNA and RNA libraries sequenced separately but derived from the same individual cells. Raw sequencing files are provided in FASTQ format and enable analysis of subclonal copy number alterations, gene dosage effects, and transcriptional heterogeneity.

  Dataset EGAD50000002361

• RNA-seq TPMs quantification for baseline tumor samples originating from IMpower150, and relevant clinical metadata

  This dataset includes full tumor transcriptomes from 558 advanced NSCLC tumors. These data originate from pre-treatment samples from a clinical trial for first-line non-small cell lung cancer (IMpower150). The patients in this trial were treated with the PD-L1 inhibitor atezolizumab +bevacizumab + chemotherapy or bevacizumab + chemotherapy or atezolizumab + chemotherapy.

  Dataset EGAD50000001814

• Brazilian GWAS Axiom850K Cancer Study

  Genome-wide genotyping data generated using the Affymetrix Axiom 850K PMDA Array from 2,844 Brazilian individuals enrolled in a cancer-focused biorepository. The dataset includes colorectal, breast, and cervical cancer cases as well as cancer-free controls. The data support genome-wide association studies (GWAS), replication analyses, and polygenic risk score evaluation in an admixed Brazilian population.

  Dataset EGAD00010002841

• Intratumoral Ploidy Dynamics in HCC

  Hepatocellular carcinoma (HCC) ranks as the fourth leading cause of cancer-related deaths. Effective therapies are limited, highlighting the critical need for stratification biomarkers to improve prognosis and predict treatment response. Polyploidization or hyperploidization, an early event observed in many solid cancers, may offer such potential. Here, we developed a new high throughput in situ quantitative approach to assess HCC ploidy profiles. This novel method highlights the presence of both Diploid (DP-) and Hyperploid (HP-) HCCs. RNA-seq profiling classified hyperploid HCCs as belonging to the proliferation subclass, predicting unfavourable clinical outcomes, and revealing a gene expression signature indicative of stemness. Spatially reconstructing nuclear ploidy also revealed DP/HP-HCCs with hyperploid nuclei forming discrete clusters within a predominantly diploid background. Remarkably, these emerging hyperploid foci shared a portion of their transcriptomic programme with fully developed hyperploid HCCs and displayed a signature of genomic instability, including upregulation of multiple DNA repair pathways in response to replication-associated DNA damage. Importantly, spatial transcriptomics of DP/HP HCC demonstrated that hyperploid tumor hepatocytes arise through whole-genome doubling of diploid tumor hepatocytes. Collectively, our findings underscore the prognostic value of nuclear ploidy profiling in HCC and suggest that hyperploid HCCs evolve clonally from intratumor hyperploid foci during tumor progression.

  Study EGAS00001008084

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

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

  Study EGAS50000001895

• PROMETEO

  The SOLTI-1503 PROMETEO trial was a single-arm, preoperative, window-of-opportunity phase II study conducted at four sites in Spain between December 2018 and February 2022. It enrolled female patients with operable HER2-negative breast cancer (triple-negative or Luminal B-like) and residual disease after neoadjuvant chemotherapy. Tumor biopsies were collected at five time points (baseline, post-NAC screening, C2D1, C3D1, and surgery) for translational research. This dataset includes raw paired-end RNA sequencing data (~110M reads per library) generated from the 113 biopy samples, archived in FASTQ format.

  Study EGAS50000001499

• FASTQ Files from Breast Tumor Biopsies Collected Across Five Timepoints in the PROMETEO Phase II Trial

  The dataset contains RNA sequencing raw data from tumor biopsies collected at five time points during the SOLTI-1503 PROMETEO trial: baseline (pre-NAC), post-NAC screening, Cycle 2 Day 1, Cycle 3 Day 1, and surgery. The study intervention consisted of intratumoral injections of T-VEC followed by intravenous administrations of atezolizumab prior to surgery. The data is obtained from tumor samples of patients included in the study: female breast cancer patients with residual disease after neoadjuvant chemotherapy, including both triple-negative and Luminal B-like subtypes. Each sample includes raw paired-end RNAseq reads (~110 million reads per library) aligned to the GRCh38/hg38 reference genome

  Dataset EGAD50000002165

• Xiangya Third Hospital Prostate Cancer Methylation Study

  This DAC manages the controlled access data for the prostate cancer research project from Xiangya Third Hospital. The dataset includes raw high-throughput sequencing data (PE150, MeDIP-seq & BSAS) from 19 Prostate Cancer (PCA) samples, 29 Benign Prostatic Hyperplasia (BPH) samples, and 19 Bladder Cancer tissue samples.

  Dac EGAC50000001034

• Duplex sequencing of selected breast cancer patients

  This study assessed the variant profiles of 22 samples from 11 breast cancer patients with adverse survival outcomes, including paired uninvolved mammary gland samples collected at various distances from primary lesions. Ultra-deep sequencing was performed to identify the presence of low-frequency pathogenic post-zygotic variants in PIK3CA and TP53 genes.

  Study EGAS50000000538

• LySeqST: A targeted sequencing assay for robust genomic classification of diffuse large B-cell lymphoma

  Diffuse large B-cell lymphoma (DLBCL) is a biologically heterogeneous disease. Two genomic classification systems, LymphGen and DLBclass, are capable of reproducibly classifying single tumors into subtypes with prognostic relevance in the context of standard-of-care R-CHOP chemoimmunotherapy. Preliminary data from subgroup analyses of clinical trials suggest that the distinct biological features are targetable with drugs that exploit subtype-specific vulnerabilities, and large clinical trials are being designed to test this hypothesis. Although whole exome sequencing (WES) remains the gold standard for each of these classification systems, many laboratories may opt for smaller targeted sequencing panels that reduce costs associated with sequencing, data storage, and processing. Here, we describe the design and validation of a targeted sequencing panel (LySeqST) that captures the genomic features required specifically for LymphGen classification. We perform in silico and real-world validation vs. WES data and demonstrate that LySeqST can be used to accurately classify DLBCL tumors. In an unselected population-based cohort, we determine the real-world proportions and validate the prognostic relevance of LymphGen subtypes, confirming that only tumors expressing the dark zone gene expression signature are consistently associated with inferior outcomes. Our results support the use of LySeqST for accurate genomic classification of DLBCL.

  Study EGAS50000001601

• Oropharynx cancers sequencing study (RNA-seq from FFPE)

  This is a study of transcriptomics in HPV-associated oropharynx tumors. The goals of this study were to characterize HPV+ oropharynx tumor subtypes and to examine HPV integration events and their downstream effects. HPV-host fusion transcripts and recurrent HPV integration genes were identified. Various alternative isoforms and splicing events of HPV genes were also studied. Multiple potential biomarkers of prognosis were associated with clinical outcomes.

  Study EGAS50000000893

• Liquid biopsy sequencing

  Liquid biopsy samples were collected from patients. Cell free DNA was extracted and profiled by NGS. Samples were analyzed by low pass whole genome sequencing, targeted panel sequencing using a custom hybrid capture panel, or both.

  Study EGAS50000001528

• Vaccine-Expanded Plasmablast-like B Cells Are Associated with Response to Dendritic Cell Therapy in Metastatic Melanoma

  Dendritic cells (DCs), either monocyte-derived (moDCs) or naturally circulating, have been employed in cancer treatment across both metastatic and adjuvant settings. DC vaccines (DC Vax) are capable of inducing tumor-specific immune responses, yet clinical outcomes have thus far fallen short of expectations. Here, we performed a multi-omics analysis of the apheresis product, including CD14⁺ monocytes, and the final DCVax formulation. Among all the components analyzed, the most striking finding was the unexpected presence of CD19⁺ B cells within the DC Vax formulation, which distinguished Responders from Non-Responders to moDC vaccination in metastatic melanoma. The abundance of B cells in DC Vax correlated with their peripheral frequency; however, within the vaccine, these cells acquired a CD20lowCD27hiCD38hi plasmablast-like phenotype, distinct from their autologous circulating B-cell precursors. Notably, a parallel observation was made in Responders, whose pre-treatment lesions were enriched in B cells organized as Tertiary Lymphoid Structures. These results underscore the importance of B cells in both baseline immunity and DCVax formulation, hinting at unexplored mechanisms by which they may influence vaccine effectiveness.

  Study EGAS50000001177

• Spatial transcriptomics of human meningioma samples.

  We performed spatial transcriptomic profiling of human meningioma samples to map gene expression patterns within their native tissue architecture.

  Study EGAS50000001556

• ATAC-seq of 38 TNBC Patient Derived Xenograft Models

  Chromatin accessibility profiles from 38 triple‑negative breast cancer (TNBC) patient‑derived xenograft (PDX) tumor samples generated by ATAC‑seq. Fastq files and aligned bam files are uploaded.

  Dataset EGAD50000002430

• Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes

  Current single-cell multiomics methods typically provide limited genomic information, constraining genotype-phenotype studies. To address this gap, we developed SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome), which integrates 10X Genomics barcoding with Oxford Nanopore sequencing to simultaneously profile genome, chromatin accessibility, and full-length transcriptomes in thousands of single cells. By retaining all tagmentation fragments during library preparation, SPLONGGET delivers whole-genome coverage, supports target enrichment for effective single-cell genotyping, and remains backwards compatible with existing short-read workflows. We apply SPLONGGET to longitudinal samples from a case of pediatric B-cell acute lymphoblastic leukemia (B-ALL) to reveal clonal dynamics during therapy and the phenotypic effects of somatic variation, providing valuable insights into disease progression and relapse. In conclusion, SPLONGGET enables integrated high-throughput analysis of genetic variation and molecular phenotypes using off-the-shelf kits, offering a timely and powerful tool to study genetically heterogeneous samples, such as tumours but also ageing normal tissues.

  Study EGAS50000001278

• cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Raw data for cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Study EGAS50000001539

• Proteomics of human cancer-associated T cells identifies regulators of T cell functionality

  CD8⁺ T cells in solid tumors progressively lose anti-tumor activity, yet the cell-intrinsic mechanisms driving this loss of function remain incompletely defined. Here, we performed matched proteomic and transcriptomic profiling of dysfunctional and bystander CD8⁺ tumor-infiltrating T cells isolated from primary tumors of treatment-naïve non-small cell lung cancer patients. Proteomic analysis revealed widespread discordance with mRNA expression, with 8% of differentially expressed proteins detected exclusively at the protein level. Genetic perturbation of such differentially expressed proteins identified the chromatin remodeler CHD4 and fatty acid synthase (FASN) as cell-intrinsic regulators of T cell function. CHD4 deletion promoted effector differentiation and enhanced cytokine production, whereas FASN deletion preserved mitochondrial fitness and sustained T cell functionality under chronic T cell receptor stimulation. Together, these findings demonstrate that proteomic profiling uncovers regulators of T cell functionality that are not apparent from transcriptomic analyses alone, highlighting an additional layer of regulatory control.

  Study EGAS50000001886

• scRNAseq of tumor infiltrating CD8+ T cells

  single cell mRNA sequencing of tumor infiltrating CD8+ T cells. CD8+ T cells were FACS sorted from tumor tissue obtained from 8 non-small cell lung cancer patients. Gene expression and TCR library preparation was performed using the Chromium Next GEM Single Cell 5' Kit v2, Chromium 5' Feature Barcode Kit, and Chromium Single Cell Human TCR Amplification Kit from 10x genomics. After paired-end sequencing this resulted in fastq files containing TCR sequences, gene expression, and feature barcode levels.

  Dataset EGAD50000002739

• Bulk RNAseq of cancer-associated CD8 T cell populations

  Bulk mRNA sequencing of cancer-associated CD8 T cell populations isolated from tumor and tumor-adjacent tissue from non-small cell lung cancer patients. CD8 T cell populations isolated were CD103+CD39- and CD103+CD39+ from tumor tissue, and CD103+CD39- from adjacent tissue. These populations were isolated from 5 patients, totaling 15 samples. bulk poly-A RNA was isolated and libraries were prepped using the Smart-Seq2 protocol, followed by paired-end sequencing (Illumina). Raw data are in fastq format.

  Dataset EGAD50000002740

• Multimodal analysis of rare BARD1 missense variant

  This project analyzes whole-exome sequencing data from a patient with breast cancer recurrence and endometrial cancer, as well as from the patient’s father’s colon tumor, all harboring a rare germline BARD1 missense variant (p.Gly753Val). The data reveal loss of heterozygosity and homologous recombination deficiency specific to the triple-negative breast cancer recurrence, supporting the variant’s conditional pathogenicity linked to prior treatment.

  Study EGAS50000001682

• BIOMEDE : genomic data analysis from clinical trial

  Genomics landscapte of DIPG

  Study EGAS50000001164

• Genomic Data from Patients with Advanced Rare Cancers Treated with Pembrolizumab

  Rare cancers lack effective evidence-based treatments despite contributing substantially to cancer-related mortality. The goal of this study is to identify molecular biomarkers associated with response to pembrolizumab in patients with advanced rare cancers.This dataset includes genomic profiling generated from patients enrolled in an investigator-initiated phase II basket trial of pembrolizumab.

  Study EGAS50000001508

• Transcriptomic Data from Patients with Advanced Rare Cancers Treated with Pembrolizumab

  Rare cancers lack effective evidence-based treatments despite contributing substantially to cancer-related mortality. The goal of this study is to identify molecular biomarkers associated with response to pembrolizumab in patients with advanced rare cancers.This dataset includes transcriptomic profiling generated from patients enrolled in an investigator-initiated phase II basket trial of pembrolizumab.

  Study EGAS50000001509

• Plasma cell-free small RNA sequencing comparison of Illumina and Ultima Genomics in pancreatic cancer

  This study evaluates plasma-derived cell-free small RNA sequencing in a case-control cohort of 39 pancreatic ductal adenocarcinoma patients and 39 control subjects. Cell-free nucleic acids were isolated from plasma, small RNA libraries were prepared using the SMARTer smRNA-Seq workflow, and the same libraries were sequenced on both Illumina NovaSeq 6000 and Ultima Genomics UG 100 platforms. The project aims to compare platform performance for circulating small RNA and mature microRNA profiling, including read yield, alignment, RNA biotype composition, mature miRNA detection, expression concordance, and pancreatic cancer-associated differential expression. The dataset supports benchmarking of cross-platform reproducibility and assessment of biologically relevant plasma microRNA signals in pancreatic cancer.

  Study EGAS50000001907

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ecDNAs generated from V(D)J recombination replicate and persist through many cell generations. High ecDNA copies at diagnosis of B-cell precursor acute lymphoblastic leukaemia strongly correlate with subsequent relapse.

  Study EGAS50000000401

• Plasma cell-free small RNA sequencing of pancreatic cancer and control samples

  This dataset contains plasma-derived cell-free small RNA sequencing data from 78 human samples, comprising 39 pancreatic ductal adenocarcinoma patients and 39 control subjects. Each sample was sequenced as a single-end FASTQ library on both Illumina NovaSeq 6000 and Ultima Genomics UG 100 platforms, yielding 156 submitted sequencing runs. The data were generated from SMARTer smRNA-Seq libraries to support comparative analysis of sequencing performance, mature microRNA detection, and pancreatic cancer-associated cell-free small RNA expression across the two platforms.

  Dataset EGAD50000002771

• Frequency and prognostic significance of genetic abnormalities in a subgroup of intermediate risk neuroblastoma patients: A SIOPEN study

  Intermediate risk neuroblastoma includes a rare subgroup of patients over the age of 18 months at diagnosis with unresectable, localised tumours with unfavourable histology without MYCN amplification. This group is treated differently around the world with some patients receiving upfront myeloablative therapy (MAT) in addition to standard treatment with chemotherapy, surgery, radiotherapy and 13 cis retinoic acid, but the overall 5-year patient survival with or without MAT is similar (75%). This study aimed to understand the neuroblastoma biology of this rare patient subgroup.

  Study EGAS50000001908

• DFCI Gynecological Oncology Data Access Committee

  This Data Access Committee is responsible for reviewing requests to access controlled human genomic data generated as part of the RESOLVE clinical trial at DFCI. The committee ensures that access complies with participant consent, institutional policies, and applicable data protection regulations (e.g., GDPR). Data access decisions are made by a multidisciplinary panel including clinical researchers, bioinformaticians, and data governance officers from Dana-Farber Cancer Institute. The committee reviews each access request to determine whether the proposed research aligns with the study’s consent terms and the data access policy. If approved, access is granted via the European Genome-phenome Archive (EGA) in accordance with EGA’s data use and security guidelines.

  Dac EGAC50000000712

• SPECTA RP-1759-AYA CNS cohort

  EORTC-SPECTA RP1759 study focuses on cancers in adolescent and young adult (AYA), age 12 to 29 years. This study explicitly recruited AYA patients and therefore collected empirical data to bridge the molecular gap between pediatric and adult oncology. The initial pilot study, activated in February 2019 across Europe, aimed to recruit 50 AYA patients (aged 12-29 years) with newly diagnosed or relapsed high-grade gliomas, and for which matching tumor and blood samples were collected.

  Study EGAS50000000985

• Arcagen - Gynecologic cancer (ovarian, peritoneal and/or fallopian-tube)

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files in .BAM format from 94 patients with rare ovarian cancer and primary peritoneal cancer and/or fallopian-tube cancer, including low grade serous carcinoma, mucinous adenocarcinoma, clear cell adenocarcinoma; and other rare cancers such as sex cord tumors, germ cell tumor, yolk sac tumor, and malignant/immature teratoma.

  Dataset EGAD50000001315

• Arcagen - Relapsing germ cell tumors of any origin

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files in .BAM format from 23 patients with Relapsing germ cell tumors, of any origin and of any histological type.

  Dataset EGAD50000000914

• Arcagen – Cancer of unknown Primary

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from 96 patients in .BAM format diagnosed with a locally advanced or metastatic Cancer of Unknown Primary.

  Dataset EGAD50000000256

• Arcagen - Skin cancer

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files in .BAM format from 49 patients diagnosed with adnexal carcinoma of the skin, Merkel cells cancer or malignant melanoma of the uvea.

  Dataset EGAD50000000705

• Arcagen - Head and Neck malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here were are submitting the dataset that contains NGS files in .BAM from 102 patients diagnosed with salivary gland tumors of major salivary gland; salivary gland type tumors of head and neck with a strong focus on acinic cell carcinoma (diagnostic based on morphology, but IHC can be performed for DOG1 and SOX10), NUT carcinoma (presence of NUT, cytokeratin and p40 by IHC) and sinus carcinoma.

  Dataset EGAD50000000885

• Arcagen – Adrenal and Thyroid cancers

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here were are submitting the dataset that contains NGS files in .BAM format from 103 patients with adrenocortical carcinoma, pheochromocytoma, anaplastic thyroid cancer, medullary thyroid cancer and radioiodine refractory thyroid cancer.

  Dataset EGAD50000000886

• Arcagen - Sarcoma

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files in .BAM format from 62 patients with undifferentiated sarcoma of the bone; aggressive angiomyxoma; alveolar soft part sarcoma; small round cell sarcoma without EWSR1 and CIC translocations; undifferentiated pleomorphic sarcoma; undifferentiated sarcoma; myxofibrosarcoma; or sarcoma with an incidence of less than 1 per 10 million.

  Dataset EGAD50000000902

• Whole-exome sequencing data for breast cancer patients

  This datasets contains the FASTQ files sequenced by Illumina NovaSeqX Plus, and the variants called from the sequencing data.

  Dataset EGAD50000002800

• DAC for study of Zanidatamab in breast cancer patients

  This is the DAC for manuscript "Zanidatamab in Patients with Early Stage HER2-positive Breast Cancer: The NeoZanHER Phase 2 Single-Arm Open-Label Trial"

  Dac EGAC50000001059

• Single-molecule nanopore sequencing of plasma and cerebrospinal fluid cell-free DNA from paediatric patients with brain and extracranial solid tumours.

  Cell-free DNA (cfDNA) profiling enables minimally invasive cancer detection and monitoring. Here, we report single-molecule nanopore sequencing data generated using the SIMMA assay for 792 plasma and cerebrospinal fluid cfDNA samples from 277 paediatric patients with diverse brain and extracranial tumours. SIMMA is a low-input single-molecule sequencing approach that enables multimodal whole-genome and high-depth targeted sequencing of the same cfDNA sample for both tumour-agnostic and tumour-informed liquid biopsy analysis (Sauer et al. 2026).

  Study EGAS50000001839

• Detection of high-grade serous ovarian cancer using TP53 mutation burden in uterine lavage

  In total, 436 DNA samples from the 278 patients were processed for TP53 ultradeep duplex sequencing: 278 lavages, 86 tissue samples (some patients had multiple tissue samples), and 72 blood samples. Duplex sequencing was performed on an Illumina NovaSeq 6000 by TwinStrand Biosciences using a capture panel targeting the coding regions of the TP53 gene. Data were processed by TwinStrand Biosciences and .bam files were created for each sample.

  Dataset EGAD50000002776

• Single-cell RNA sequencing of liver metastasis-derived colorectal cancer organoids profiling cellular heterogeneity and lineage dynamics across time

  The objective of this analysis was to identify, at single-cell resolution, trasncriptionally distinct subpopulations in untreated metastatic colorectal cancer organoids with diverse genetic backgrounds and to investigate their temporal dynamics.

  Study EGAS50000001927

• Transcriptome profiling of liver metastasis-derived colorectal cancer organoids to dissect pro-differentiative effects of TGFB1 and IL-6

  Bulk RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to test the effect of IL-6 and TGFbeta1 on mCRC organoid cell differentiation. Transcriptomic profiling was conducted following cytokine treatments to investigate molecular changes associated with treatments. Three biological replicates were included for each experimental condition (control, IL-6, and TGF-beta1 treatments).

  Study EGAS50000001914

• Bulk RNA sequencing of metastatic colorectal cancer PDX-derived organoids - untreated and treated with IL-6 or TGF-beta1

  Bulk RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to test the effect of IL-6 and TGF-beta1 on mCRC organoid cell differentiation. Transcriptomic profiling was conducted following cytokine treatments to investigate molecular changes associated with treatments.

  Dataset EGAD50000002782

• Single-cell transcriptomic profiling of metastatic colorectal cancer organoids maintained in growth medium.

  Single-cell RNA sequencing was performed on metastatic colorectal cancer (mCRC) organoids derived from patient-derived xenograft (PDX) models. Organoids were seeded in 12-well plates, embedded in 200 µL of Matrigel or BME diluted 1:1 with culture medium, and maintained with EGF-supplemented growth medium. After 7 days (or 11 days) of growth, organoids were harvested, dissociated, and live single cells were sorted for single-cell RNA sequencing using the 10x Genomics platform.

  Dataset EGAD50000002797

• IRCCS Candiolo - Quantitative Cancer Cell Biology (QCCB)

  DAC for Quantitative Cancer Cell Biology (QCCB) datasets

  Dac EGAC50000001019