8252 results for "canc*"

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• 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