5522 results for "*oma"

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• Predictive value of genomic, transcriptomic and epigenetic biomarkers in patients with recurrent and/or metastatic HNSC treated with PD-1/PD-L1 inhibitors

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Study EGAS50000001746

• A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies

  Pineoblastoma is a clinically aggressive childhood brain tumor composed of distinct molecular subgroups with divergent driver genes, demographics, and clinical outcomes. To identify developmental origins and mechanisms governing disease pathogenesis, we derive single-cell transcriptomes from pineal parenchymal tumors, aligning malignant cells with our atlas of pineal gland development to retrace cellular origins. Integrative computational analyses maps pineoblastoma origins to transient cycling pinealocyte progenitors during development. Lineage-specific perturbation of suspected drivers in the early pineal gland yields preclinical models representative of consensus molecular subgroups. Multi-omic characterization of patient tumors and these models uncovers a tumor-associated photoreceptor signature common to pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this signature within respective cellular origins establishes a developmental basis for molecular similarities between entities. Photoreceptor signature constituents are selective dependencies across these anatomically distinct central nervous system malignancies, motivating future studies evaluating developmentally encoded programs of malignancy as potential therapeutic liabilities.

  Study EGAS50000001457

• ecDNA copy number heterogeneity

  Neuroblastoma exhibits significant inter- and intra-tumour genetic heterogeneity and varying clinical outcomes. Here, we used DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. We reveal extensive intercellular ecDNA copy number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells.

  Study EGAS50000000509

• Single cell RNA sequencing of relapsed/refractory multiple myeloma

  Study EGAS00001004805

• Whole-exome sequencing of HPV-negative HNSCC to identify pathway alterations

  This study applies whole-exome sequencing (WES) to characterize genomic alterations in HPV-negative head and neck squamous cell carcinoma. Tumors were analyzed to derive pathway-level alteration scores, enabling stratification into Hedgehog-high and Hedgehog-low groups. The genomic data were integrated with imaging, transcriptomic, and functional analyses to investigate tumor-intrinsic Hedgehog signaling. The study aims to identify molecular features associated with biologically distinct tumor subgroups.

  Study EGAS50000001550

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST2 study, a phase II CDK4/6 (abemaciclib) clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, to to assess potential sensitivity to CDK4/6 inhibition in p16ink4A-negative mesothelioma.

  Study EGAS50000001823

• 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

• RNA sequencing dataset of of explants treated with PRX3 inhibitor thiostrepton in mesothelioma

  This dataset includes 66 RNA sequences datasets of mesothelioma explants under three conditions: baseline, untreated control and thiostrepton treatment.

  Dataset EGAD50000002650

• Transcriptome profiling of HNSCC treated with PD1/PDL1

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Dataset EGAD50000002506

• Transcriptomic profiling of Hedgehog-high and Hedgehog-low HPV-negative HNSCC

  This study investigates transcriptomic differences between Hedgehog-high and Hedgehog-low HPV-negative head and neck squamous cell carcinoma (HNSCC). Tumors were stratified based on pathway-level genomic alteration scores and imaging-associated Hedgehog activity. RNA sequencing was performed on archival FFPE tumor samples to assess pathway activation and transcriptional programs associated with Hedgehog signaling. The dataset supports integrative radiogenomic and functional analyses of tumor-intrinsic signaling pathways.

  Study EGAS50000001549

• Anaplastic Large Cell Lymphoma Tumor Gene Expression Profiling

  Anaplastic large cell lymphoma tumor RNA-Seq

  Study EGAS50000001011

• Anaplastic Large Cell Lymphoma Gene Expression

  Anaplastic Large Cell Lymphoma Gene Expression Study

  Dataset EGAD50000001478

• Mayo Anaplastic Large Cell Lymphoma Gene Expression

  Dac EGAC50000000633

• scRNAseq data of primary and metastatic melanoma samples

  Paired-end 10x single-cell RNA sequencing data from 13 melanoma samples. Sequencing was performed on the Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single-Cell 5 Reagent Kits v2.

  Dataset EGAD50000000665

• 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

• 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 applying Illumina TruSight Oncology 500 platform and detected mutations, gene fusions, copy number variations and revealed tumor mutational burden.

  Dataset EGAD50000002659

• WGS - germline - oral squamous cell carcinoma

  We conducted a retrospective, single-center Canadian cohort study of patients who underwent primary surgery for OSCC between 2010 and 2024. Nucleic acid quality was assessed using the 4150 TapeStation System (Agilent) prior to library preparation. WGS was performed on germline DNA, following Genome Analysis Toolkit’s (GATK) Best Practices and procedures, with a target of 30X deduplicated coverage per sample, using an Illumina NovaSeq 6000 instrument.

  Dataset EGAD50000002608

• 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

• WES dataset of mesothelioma MIST4 study

  This dataset includes bam files from WES of 20 tumor samples and 18 matched normal samples.

  Dataset EGAD50000002633

• RNA sequencing dataset of mesothelioma MIST4 study

  This dataset includes BAM files from RNA-seq of 20 tumor samples.

  Dataset EGAD50000002634

• 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

• SV-based ctDNA detection in soft tissue sarcoma

  33 patients with localized soft tissue sarcoma consented for ctDNA tracking in the peri-operative and surveillance periods. WGS at a target of 15x coverage was performed from DNA extracted from FFPE of localized soft tissue sarcoma. Structural variants were identified from WGS and ddPCR assays were designed for tumor informed tracking of SV for ctDNA.

  Study EGAS50000001811

• SV Based ctDNA detection in localized soft tissue sarcoma

  WGS from FFPE for "Detecting ctDNA Using Personalized Structural Variants to Forecast Recurrence in Localized Soft Tissue Sarcoma." study. 33 patients had whole genome sequencing through the Illumina platform at an average depth of 15x. Tumor informed structural variants were identified and ddPCR assays were designed for individualized structural variant-based ctDNA detection.

  Dataset EGAD50000002614

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Epithelioid sarcoma (EpS) is an aggressive sarcoma, characterized by the loss of SMARCB1 expression. EpS is traditionally classified as distal or proximal according to clinicopathological features, but its molecular characteristics remain largely unknown. To establish an EpS molecular classification and uncover determinants of inter- and intra-patient heterogeneity in EpS, we used multi-omics profiling and integrated the genomic, transcriptional and methylome landscapes with single-cell RNA sequencing on fresh samples as well as spatial transcriptomics. We identified two molecular subtypes of EpS: “distal-like” and “proximal-like”, which were distinct from the histological subtypes. Distal-like tumors include all morphological distal subtypes and a subset of proximal and hybrid EpS. They express a specific molecular single-cell derived epithelial-to-mesenchymal transition signature, which associates with improved patient survival and includes Desmoglein 2 (DSG2), which we identify as a potential routine immunohistochemical biomarker to improve diagnosis. Distal-like EpS also display increased peri-tumoral CD8+ T cell infiltrates and specific tumor-immune cell interactions. Conversely, proximal-like EpS harbor a higher inter-tumoral molecular heterogeneity with some cases resembling other SMARCB1-deficient tumors by DNA methylation profiling, and increased intra-tumoral pro-tumoral macrophage infiltrates. Our study introduces a novel molecular classification of EpS with prognostic value, associated diagnostic biomarkers and distinct tumor immune microenvironments, which extends beyond traditional clinicopathological classification. This paves the way for precision medicine-based therapeutic strategies for patients with EpS.

  Dac EGAC50000000552

• Multiregional whole exome sequencing of mesothelioma tumors of MEDUSA cohort

  MEDUSA (Mesotheliomaevolution: deciphering druggable somatic alterations) is a translational research platform to build predictive models to stratify existing therapies. This study utilizes multiregional mesothelioma exome sequencing to infer a human evolutionary model of MPM tumorigenesis and understand the inter-relationships that exist between genomic ITH, host immune surveillance and clinical phenotype.

  Study EGAS50000001865

• 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

• MEC/SEF rhabdomyosarcoma mRNA sequencing

  This project was undertaken to sequence and analyze mRNA expression in these tumor subtypes. We intended to discover distinctive patterns of tumor subtype gene expression in these subtypes. In addition, we used this data to discover expression differences between ESWR fusion positive and fusion negative MEC tumors.

  Study EGAS50000000535

• ASPSCR1-TFE3 gene fusion panel deep amplicon sequencing data

  Dataset contains compressed, paired-end Fastq files of deep amplicon sequencing data from a custom ASPSCR1-TFE3 gene fusion panel for three alveolar soft part sarcoma cases described in "Development and first-in-human CAR T therapy targeting the pathognomonic MiT-fusion driven protein GPNMB".

  Dataset EGAD50000002438

• 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

• 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

• Whole exome RNA sequencing of FFPE material from 49 pediatric BCP-LBL patients.

  This study contain the results of whole exome-targeted transcriptome analyses of FFPE material from 49 pediatric B-cell precursor lymphoblastic lymphoma patients. Data are provided as Fastq files.

  Study EGAS50000000289

• Single-cell multi-omic profiling of glioblastoma-associated myeloid cells

  Study EGAS00001004871

• Immune activation in the tumor microenvironment of renal cell carcinoma

  Study describes immunological responses to immunotherapy (anti-PD-1, pembrolizumab) and targeted therapy (VEGFR inhibition, axitinib) as well as anti-CD3/CD28/CD2 (Immunocult) in a patient-derived ex vivo tumor model of renal cell carcinoma. Patient-derived ex vivo tumor models were established and their treatment response studied using material from eight renal cell carcinoma patients. Samples were collected under informed consent in HUS Helsinki University Hospital, Finland. The study aims to understand immunological treatment responses in the patient tumor microenvironment.

  Study EGAS50000001349

• Hepatoblastoma tumoroid biobank as a key resource for tumour genetics

  Study EGAS00001008251

• Non-Hodgkin Lymphoma WES Data Access Committee

  DAC for controlled access to whole exome sequencing (WES) data from NHL patients at University of Tabuk

  Dac EGAC50000000998

• Whole Exome Sequencing of Non-Hodgkin Lymphoma Patients in Tabuk, Saudi Arabia

  This study presents whole exome sequencing (WES) data from 20 Non-Hodgkin Lymphoma (NHL) patients. Samples represent diverse histopathological subtypes including Diffuse Large B-Cell Lymphoma (DLBCL), Follicular Lymphoma, and other NHL variants. Both nodal and extranodal disease origins are represented. Sequencing was performed to investigate the genomic landscape of NHL in a Saudi Arabian patient cohort.

  Study EGAS50000001776

• Whole Exome Sequencing of Non-Hodgkin Lymphoma Patients

  This dataset contains whole exome sequencing data from 20 Non-Hodgkin Lymphoma patients sequenced on the Illumina NovaSeq 6000 platform. Data includes paired-end FASTQ files (2×150 bp) for all samples representing diverse histopathological subtypes including DLBCL, Follicular Lymphoma, and other NHL variants from a Saudi Arabian cohort.

  Dataset EGAD50000002551

• 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

• 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

• Chromatin profiling using Cut&Run technique of hepatoblastoma organoids

  CUT&RUN LoV-U profiling of b-catenin, LEF1 and TCF7L2 binding in biological replicates (Replicate A, Replicate B) of hepatoblastoma organoids: 10F, 13F, 13E, 17E, 22E and 135F.

  Dataset EGAD50000001749

• Single-cell RNA/ATAC multiome profiling of hepatoblastoma resection samples

  10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression data of hepatoblastoma tissue samples. BAM files containing sequencing data of resection material of PT13 and PT17.

  Dataset EGAD50000001750

• 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

• Epigenetic characterization of patient-derived glioblastoma stem cell (GSC)

  ATAC-Seq data on 43 samples of glioblastoma stem cells mapped to hg19. Fastq files are available. PMID: 33427645

  Dataset EGAD50000002603

• 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

• Malignant mesothelioma EWAS on European prospective study

  Study EGAS00001006432

• 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

• Cell-free MeDIP-seq of plasma samples from lymphoma patients and healthy controls

  This dataset contains cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) data generated from plasma samples of lymphoma patients and healthy controls. The study aims to characterize genome-wide methylation patterns of circulating cell-free DNA and identify hypermethylated regions associated with lymphoma. Sequencing libraries were prepared using cfMeDIP with anti-5-methylcytidine antibody enrichment and sequenced on an Illumina platform. The dataset supports differential methylation analyses and the development of classification models for lymphoma detection.

  Dataset EGAD50000002108

• 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

• Pineoblastoma Single-Nuclei RNA-seq Data Access Committee (St. Jude)

  Committee responsible for reviewing and approving external access requests to controlled-access pediatric brain tumor transcriptomic datasets from St. Jude Children's Research Hospital, ensuring alignment with patient consent and institutional ethics policies.

  Dac EGAC50000000839

• IFNγ Drives Long-Term Bone Marrow Niche Dysfunction Following Doxorubicin-Based Chemotherapy

  To understand the impact of chemotherapy treatment on the bone marrow microenvironment, we acquired paired bone marrow (BM) aspirate samples from patients with acute lymphoblastic leukemia (ALL) collected at diagnosis and 4w later (end of induction therapy) at the Princess Margaret Hospital. The BM stroma was obtained by expanding BM aspirates in culture, and profiled by RNA-sequencing.

  Study EGAS50000001621

• Leicester Mesothelioma Research Omics Dataset Committee

  This Data Access Committee consists of the mesothelioma research group led by Professor Dean Fennell.

  Dac EGAC50000000965

• Targeting vulnerabilities in IDH mutant tumours: The model matters RNAseq study

  Introduction: Synthetic lethal interactions with IDH1 and IDH2 (IDH) mutations were identified in non-endogenous IDH mutant (IDHmut) AML and glioma models, but are absent in endogenous IDHmut chondrosarcoma cell lines. The translation into successful clinical applications has remained challenging, implying artificially created models do not fully recapitulate endogenous IDHmut tumour biology. The aim of this study was to elucidate if the model system is indeed an important factor to consider when studying therapeutic vulnerabilities in IDHmut tumours. Methods: Vector-based and CRISPR-Cas9 approaches were used to introduce or revert the IDH1 mutation in chondrosarcoma cell lines. These isogenic cell line pairs were used to examine the presence of known therapeutic vulnerabilities and their underlying biological mechanisms. Results: Vector-based IDHmut chondrosarcoma models showed the previously reported synthetic lethal interactions, but these treatment sensitivities were absent in the CRISPR-edited models. Interestingly, not all vector-based IDHmut cell lines displayed the same therapeutic vulnerabilities. Differences in treatment response were associated with multiple factors, including IDHmut protein expression and D-2-HG levels, in line with the fact that therapeutic vulnerabilities could be induced in the CRISPR-edited models by enhancing D-2-HG levels. Conclusion: Our findings demonstrate that synthetic lethal interactions observed in vector-based models are often a consequence of IDHmut protein overexpression and supra-physiological D-2-HG levels. These results highlight that relying on artificially created IDHmut models may lead to the identification of therapeutic vulnerabilities that are not present in IDHmut tumours, potentially explaining the poor translation of preclinical findings to clinical trials.

  Study EGAS50000001871

• RNA sequencing data and whole exome sequencing data of genetically modified IDH1 wildtype and mutant chondrosarcoma cell lines

  This dataset contains total RNA sequencing (polyA enriched) data of early and late passages of n=5 vector-based CH2879 empty vector and IDH1mut cell lines. Total RNA sequencing (polyA enriched) using 150bp paired-end reads was performed in triplicate using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) on the NovaSeq6000 platform (Illumina). Additionally, this dataset contains whole exome sequencing data of n=15 parental, mock, and CRISPR-edited IDH1mut and IDH1wt CH2879 and JJ012 cell lines. Whole exome sequencing using 150bp paired-end reads with a minimum coverage of 100x was performed in single using the SureSelect Human All Exon V8 library (Agilent Technologies) on the NovaSeq X platform (Illumina).

  Dataset EGAD50000002703

• TR T Cell and Melanoma Study Data Access Committee

  This Data Access Committee (DAC) governs access to controlled human genomic and transcriptomic data generated from melanoma patients enrolled in studies investigating tumour-resident immune cells and mechanisms of resistance to immune checkpoint inhibitors. The dataset includes bulk and single-cell RNA sequencing, TCR sequencing, and associated clinical metadata derived from metastatic melanoma samples. Access to these data will be granted to qualified researchers for ethically approved studies, in accordance with patient consent, institutional guidelines, and applicable data protection regulations. Requests will be evaluated based on scientific merit, data security measures, and compliance with the intended use of the data. All approved users must agree to a Data Access Agreement outlining conditions for data use, storage, and publication.

  Dac EGAC50000000974

• Bulk RNA-seq (FASTQ) – melanoma samples

  This dataset comprises raw FASTQ files from bulk RNA sequencing of metastatic melanoma lymph node samples collected from patients with differential responses to immune checkpoint inhibitor therapy. RNA was extracted from tumour tissue, enriched for polyadenylated transcripts, and libraries were prepared using standard Illumina protocols. Sequencing was performed on an Illumina platform to generate high-quality paired-end reads. The dataset includes multiple patient samples with associated clinical annotations, enabling analysis of tumour-intrinsic transcriptional programs linked to immunotherapy response and resistance.

  Dataset EGAD50000002475

• Single-cell RNA-seq (10x) – melanoma samples

  This dataset comprises raw FASTQ files generated from single-cell RNA sequencing of metastatic melanoma lymph node samples using the 10x Genomics Chromium platform. Single-cell suspensions were prepared from tumour tissues, and libraries were constructed using 5′ or 3′ gene expression kits following the manufacturer’s protocol. Sequencing was performed on an Illumina platform to obtain high-throughput single-cell transcriptomic profiles. The dataset includes samples from patients with differing responses to immune checkpoint inhibitor therapy, enabling characterisation of tumour-resident immune cell populations and tumour–immune interactions associated with treatment response and resistance.

  Dataset EGAD50000002476

• Nanostring – melanoma samples

  This dataset comprises gene expression data generated using the Nanostring nCounter platform from metastatic melanoma samples. RNA extracted from tumour tissues was analysed using targeted gene expression panels, including immune-related and tumour-resident T cell signatures. The dataset includes RCC files and associated normalised counts derived from patients with differing responses to immune checkpoint inhibitor therapy. These data enable targeted profiling of immune and tumour transcriptional programs associated with treatment response and resistance.

  Dataset EGAD50000002477

• TCR-seq (10x VDJ) – melanoma samples

  This dataset comprises raw FASTQ files generated from T cell receptor (TCR) sequencing of metastatic melanoma samples using the 10x Genomics V(D)J platform. Single-cell suspensions were processed to generate paired gene expression and V(D)J libraries, with this dataset containing the V(D)J-enriched libraries targeting TCR α and β chains. Sequencing was performed on an Illumina platform to enable reconstruction of TCR clonotypes and analysis of clonal expansion. The dataset includes samples from patients with varying responses to immune checkpoint inhibitor therapy, supporting investigation of T cell clonality, antigen specificity, and immune dynamics associated with treatment response and resistance.

  Dataset EGAD50000002478

• 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

• 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

• Differential Wnt/β-Catenin Signaling Activities Shape Distinct Tumor Cell Phenotypes

  By profiling patient-derived hepatoblastoma organoids via single-cell transcriptomics and chromatin dynamics, we identify subtype-specific transcriptional and epigenetic profiles. Using CUT&RUN, we show that β-catenin engages distinct genomic regions, which is dictated by differential association with TCF/LEF family transcription factors. TCF7L2 binds to a motif, distinct from the classical Wnt consensus sequence, which is found in the promoter of hepatic target genes.

  Study EGAS50000001229

• 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

• A single-cell atlas of meningioma.

  In this study, we examined the breadth of cell types and states in meningioma using the largest single-cell cohort of meningioma by generating more than 7.5 million total cells from meningioma and surrounding dura, profiled using single-nuclear RNA sequencing and high-resolution spatial transcriptomics.

  Study EGAS50000001589

• 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

• 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

• 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

• VIVO Biobank Neuroblastoma Project Data Accession Committee

  Access to neuroblastoma sample data for VIVO Biobank projects.

  Dac EGAC50000000977

• 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

• TNGS data for SIOPEN intermediate-risk neuroblastoma subgroup study

  Targeted next-generation sequencing data for a SIOPEN intermediate-risk neuroblastoma subgroup (age >18 months, localised, unresectable, non-MYCN-amplified neuroblastoma with unfavourable histology), with a total of 31 cases analysed. All but one sample have been analysed using the same workflow, with the exception being NB32. VCF files for the analyses are included in this dataset.

  Dataset EGAD50000002773

• WES data for SIOPEN intermediate-risk neuroblastoma subgroup study

  Whole exome sequencing (WES) data analysed for the SIOPEN intermediate-risk neuroblastoma subgroup (age >18 months, localised, unresectable, non-MYCN amplified neuroblastoma with unfavourable histology), data for a total of 30 cases available. Four samples were analysed as part of another relapse neuroblastoma study (NB02 to NB05), of which two have germline comparison available. The remaining 26 cases had a different analysis workflow, with all but one having germline comparison available. VCF files from WES analyses are included in this dataset.

  Dataset EGAD50000002774

• 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

• Hit counts dataset from RNAseq and single-cell mutiple myeloma analysis

  Hit counts from 60 samples from multiple myeloma patients. The sample were sequenced by bulk RNAseq and/or single cell RNAseq.

  Dataset EGAD50000002713

• Multiple Myeloma Microenvironement Leukemia Canther DAC

  Dac EGAC00001003566

• 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

• Transcriptome analysis of 32 pheochromocytoma and paraganglioma samples

  Pheochromocytomas and sympathetic paragangliomas (PPGL) are rare neuroendocrine tumors derived from chromaffin tissue of the adrenal medulla and sympathetic paraganglia, respectively. There is at the moment a lack of accurate biomarkers to predict the biologic behavior of a PPGL. The aim of this study was to investigate the biological behavior of localized and metastatic PPGL by comparing the genomic and transcriptomic landscapes of localized and metastatic PPGL, including PPGL samples with a non-metastatic phenotype at initial diagnosis that developed metachronous metastases during follow-up. The dataset presented here contains the RNA-seq data of 32 tumor samples (n=17 localized, n=15 metastatic).

  Study EGAS50000000988

• RNA-seq of 32 pheochromocytoma and paraganglioma samples

  This dataset contains RNA-seq data of 32 pheochromocytoma and paraganglioma samples (n=17 localized, n=15 metastatic). A NEXTflex Rapid Directional qRNA library preparation kit (Perkin Elmer) was used for RNA quantification. Samples were sequenced on a NextSeq 500 sequencer (Illumina). The files have the FASTQ format (paired; 2 x 32 files).

  Dataset EGAD50000001447

• Germline variants in patients with five cutaneous melanoma

  Skin melanoma arises from a complex interplay between UV radiation exposure and inherited genetic susceptibility. A subset of invidiuals experience multiple independent tumours, suggestingh a stronger underlying genetic component. In this study, we investigate the germline contribution to melanoma development in individuals diagnosed with five or more primary melanomas.

  Study EGAS50000001361

• RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs

  Methods: We compared the efficacy of B7-H3 CAR T-cells between SJ-DIPGX7c (DMG) and U87-MG (adult glioblastoma) patient-derived cell lines and showed impaired efficacy both in vitro and in vivo. We performed live-cell imaging and single-cell RNA sequencing to investigate deficiencies in immune synapse (IS) formation between CAR T-cells and DMGs. Lastly, we genetically deleted RASA2, a negative regulator of T cell activation, and evaluated the resulting impact on IS formation and quality, as well as in vitro and in vivo functionality. Sample preparation and sequencing For single cell RNA sequencing, two sets of co-culture arrays were prepared: (1) 2.5×106 Ctrl T cells were co-cultured with 2.5×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG) and (2) 1×106 CAR T-cells were co-cultured with 4×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG). Both co-culture arrays were incubated at 37°C 5% CO2 for 16 hours. Co-cultures were enzymatically digested with Accutase (Thermofisher; A1110501) for 10 min at room temperature, and cells were filtered by using Miltenyi dead cell removal kit (Miltenyi; 130-090-101). Highly viable cells were recovered and prepared using the Fixation Kit (PARSE Bioscience) according to manufacturer ‘s protocol. After fixation, the cell count was determined by using a Neubauer hemocytometer. A total of 1.14×105 cells from 12 coculture conditions were used, resulting in approximately 9.5×104 cells per condition. These cells were subjected to the Single Cell Whole Transcriptomic kit v2 (PARSE Bioscience) for library construction. Libraries were subsequently sequenced using the Illumina NovaSeq 6000 platform, generating paired-end 200 bp reads.

  Dataset EGAD50000002785

• CUP-COMP DAC

  The Carcinoma of Unknown Primary (CUP): A comparison across tissue and liquid biomarkers (CUP-COMP) study (NCT: NCT04750109) was sponsored by The Christie NHS Foundation Trust and funded by Innovate UK. Data generated include: A) Whole genome sequencing* of paired germline blood and tumour tissue B) Whole genome sequencing *of germline blood only C) Next-generation sequencing of circulating tumour DNA (FoundationOne Liquid CDX) D) Next-generation sequencing of tumour tissue (FoudationOne CDX) *Whole genome sequencing - germline sample at 30x coverage and somatic sample at 75x coverage performed by Illumina NovaSeq 6000 instrument in the 150bp PE read mode.

  Dac EGAC50000000610

• DAC policy The Kids Research Institute Australia

  DAC policy related to the study: Visium CytAssist Spatial Gene Expression analysis for FFPE glioblastoma samples. Committee: Raelene Endersby raelene.endersby@thekids.org.au Anya Jones anya.jones@thekids.org.au Emma Stone emma.stone@thekids.org.au

  Dac EGAC50000000734

• Multi-omic signatures in multiple myeloma

  Multiple myeloma (MM) is a genetically and clinically heterogeneous plasma-cell malignancy. Quadruplet therapy, combining anti-CD38 antibodies, immunomodulatory drugs, proteasome inhibitors, and dexamethasone, is now the standard induction treatment for newly diagnosed multiple myeloma (NDMM). To gain a comprehensive view of molecular changes in MM and their association with treatment response in this new standard care, we performed a multi-omic study of 423 NDMM from the MIDAS trial.

  Study EGAS50000001573

• Investigating adaptive immune responses in MM patients treated with belantamab mafodotin

  We used single-cell CITE + VDJ sequencing and CapTCRseq to investigate the adaptive immune response, specifically the role of T cells and tumor-reactive gamma delta T cells, in multiple myeloma patients treated with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Study EGAS50000001889

• Identification of broadly tumor-reactive γδ TCRs from multiple myeloma

  We used single-cell CITE + TCR sequencing to identify tumor-reactive gamma delta TCR sequences from multiple myeloma patient bone marrow samples.

  Study EGAS50000001888

• Single-cell sequencing of Belamaf treated MM patients

  Single-cell CITE + VDJ sequencing of bone marrow samples from relapsed/refractory multiple myeloma patients prior to and following one round (28 days) of treatment with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Dataset EGAD50000002742

• Targeted bulk TCR sequencing of Belamaf treated MM patients

  Targeted bulk TCR sequencing from peripheral blood mononuclear cell (PBMC) and plasma cell-free DNA (cfDNA) samples from relapsed/refractory multiple myeloma patients being treated with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Dataset EGAD50000002743

• Targeted bulk TCR sequencing of MM patients

  Targeted bulk TCR sequencing of longitudinally collected peripheral blood buffy coat samples from two multiple myeloma patients.

  Dataset EGAD50000002744

• Single-cell sequencing MM patients

  Single-cell CITE + VDJ sequencing of bone marrow samples collected from a mix of diagnosis and relapsed/refractory multiple myeloma patients undergoing standard of care treatment which were used for the development of PreGame.

  Dataset EGAD50000002745

• Single-cell tracking reveals tumor-reactive T cell plasticity during melanoma TIL therapy

  Using 10x genomics 5' Single Cell Immune Profiling kit for single-cell RNA and TCR sequencing, we tracked the transcriptional alterations and fate decisions of tumor-reactive T cells through longitudinal sample obtained from patients undergo-ing TIL therapy. We performed single-cell RNA and single-cell TCR sequencing (scRNA-seq and scTCR-seq) of CD45+ CD3+ tumor-infiltrating lymphocytes from the baseline tumor (pre-ACT), during and after TIL expansion protocol (intermediate product and TIL product, respectively), as well as after cell transfer in blood (PBMC 7dpt) or from metastatic lesions (post-ACT). Samples were derived from patients enrolled in a phase I clinical trial (NCT04165967) that inves-tigated ACT-TIL therapy in combination with nivolumab therapy for metastatic melanoma. Additionally, we established a tumor reactivity assay by co-culturing TIL products with autologous single-cell suspensions of tumor material or short cultured primary melanoma cell lines derived from the tumor material. Reactive T cells were identified by IFNɣ and TNF⍺ expression and sorted to sequence TCRβ genes.

  Study EGAS50000000967

• Single cell RNA and TCR sequencing of adoptive cell transfer using tumor infiltrating lymphocyte.

  This dataset contains two experiments. 1) Single cell RNA and TCR sequencing of tumor infiltrating lymphocites from 7 patients across 5 timepoints: from the baseline tumor (pre-ACT, 7), during and after TIL expansion protocol (intermediate product and TIL product, respectively, 7 each), as well as after cell transfer in blood (PBMC 7dpt, 7) or from metastatic lesions after therapy (post-ACT, 1 patient with one leason and 4 patient with two lesions). Samples were derived from patients with metastatic melanoma which were enrolled in a phase I clinical trial (NCT04165967). The raw reads are available as compressed fastq files. 2) TCRb sequences of the bulk TIL product or TCRb reads derived from an in vitro coculturing assay of TIL product with autologous tumor material and subsequent isolation of IFNɣ and TNF⍺ positive T cells. For some patients multiple autologous tumor material sources could be tested including pre-ACT, post-ACT or tumor lesion derived cell lines. The raw reads are available as compressed fastq files.

  Dataset EGAD50000001408

• MDACC GBM Data Access Committee

  Retrospective global-omics analyses of an anti-PD-L1 treated cohort of newly diagnosed glioblastoma.

  Dac EGAC50000000477

• Transcriptomic characterization of breast cancer cells in a luminal-hybrid state

  Background: We have previously identified a subset of early human breast epithelial progenitors that, despite their luminal affiliation, are enriched for basal markers, including CD146 and keratin 14 (K14). This simultaneous presence of both lineages thus defines a luminal-hybrid state. As luminal progenitors are generally proposed as a cell of origin of breast carcinoma, we examined how cells within this luminal hybrid state relate to breast cancer malignancy. Findings: We first analyzed two patient-derived xenograft (PDX)-derived breast cancer cell lines by dividing cell populations based on CD146-expression by FACS and found that this marker defines a cellular state with increased expression of a selection of luminal hybrid markers, including KRT14. When subjecting the sorted cells to in vitro transwell filter analysis, CD146HI/K14HI luminal hybrid state cells were less invasive. Knocking out either CD146- or K14-expression by CRISPR/Cas9 on a CD146/K14-positive background did not affect the in vivo tumorigenic potential, nor the differentiation state. However, when subjecting the respective sorted populations to a soft agar colony formation assay or as in vivo xenografts, CD146HI/K14HI cells exhibited more growth and metastasis, suggesting that the luminal hybrid state contributes to malignant properties. Conclusions: Our findings demonstrate that multiple components of the luminal hybrid state provide distinct properties to tumor malignancy. The fact that breast cancer can reflect a significant part of the original breast gland differentiation hierarchy may add weight to the argument that the search for novel strategies for treating basal-like breast cancer should include manipulation of cellular differentiation states.

  Dataset EGAD50000002857

• Transcriptomics analysis of biopsy and resected material from HCC and matched non-tumor

  We hypothesize that pre-analytical handling such as surgery procedure and cold ischemia have significant effects on omics data derived from liver and liver tumor tissue that may confound classification of tumor subtypes of hepatocellular carcinoma. This study is aimed at revealing such effects by comparing resection samples with patient matched biopsy samples in a multi-omics analysis.

  Study EGAS50000001602

• FGFR2b Prevalence in Biliary Tract Cancers

  Patients with intrahepatic cholangiocarcinoma (iCCA) often have limited effective treatment options after first-line therapy. Actionable driver mutations are present in only a small subset of patients with iCCA; therefore, therapeutic strategies such as antibody–drug conjugates (ADCs) that do not exclusively rely on presence of specific oncogenic mutations may be particularly attractive. However, there is a critical lack of knowledge regarding prevalent and actionable cell-surface targets in iCCA. We applied a novel isoform-resolved proteogenomic discovery framework for profiling cell surface targets and identified FGFR2b, a splicing isoform of FGFR2, as a therapeutic target in iCCA that is highly-expressed, tumor-enriched, localized to the membrane, and associated with prognosis. FGFR2b is the dominant isoform in iCCA, and it was present in all patients with FGFR2 fusions. These findings provide a strong rationale for further research and therapeutic development of FGFR2b-targeted biologics, including therapeutic antibodies and ADCs, in iCCA.

  Study EGAS50000002012

• Tumoral immune microenvironment profiling in B-cell non-Hodgkin lymphoma stratifies patients in different prognostic groups

  Dac EGAC50000001065

• RNAseq and WES of CHC patients years before HCC development

  We conducted a nested case–control study within a prospective liver biopsy biobank at the University Hospital Basel. Patients with chronic hepatitis C (CHC) who developed hepatocellular carcinoma (HCC) during follow-up (index cases, CHC-HCC) were identified and 1:2 propensity score-matched to CHC controls without HCC (controls, CHC-nonHCC). Matching included clinical, demographic, and virological risk factors for HCC. Liver biopsies were analyzed using RNA and whole-exome sequencing.

  Dataset EGAD50000001591