16764 results for "sec+and+unspecified+malignant+neoplasm"

in 80.22 milliseconds.

• ​Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002417

• University College London, Department of Genetics and Genomic Medicine (UCL GGM)

  Dac EGAC00001002813

• DAC - Liquid biopsy: Reference materials and patient with overgrowth syndrome

  Dac EGAC00001002998

• Longitudinal dynamics in relapsed and refractory Hodgkin lymphoma Data Commitee

  Dac EGAC50000000108

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002159

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002781

• Single cell data Multiple Sclerosis and other neurological diseases

  Dac EGAC50000000083

• Total proteome and phosphoproteome profiling of Diffuse Midline Glioma

  Study EGAS00001007341

• Transcriptome and epigenome characterization of BMP signaling effects on H3.3K27M DIPG

  Study EGAS00001005374

• Low-C on Human CB-derived LT-HSC and ST-HSC

  Study EGAS00001004744

• Gene expression in CSF and blood of patients with pneumococcal meningitis

  Study EGAS00001003355

• GBM stem cell lines and PRMT5 inhibitor

  Study EGAS00001004397

• Cell of Origin and Early Evolution of Leukemia in Down Syndrome

  Study EGAS00001004780

• Molecular analysis of inflammatory myofibroblastic tumor (WGS and WES)

  Study EGAS00001005081

• Microbiota, Appetite, and Malnutrition in Dutch Community-dwelling older adults

  Study EGAS00001005319

• Human subsistence and signatures of selection on chemosensory genes

  Study EGAS00001007307

• EGAD00010000468

  Uveal melanoma matched Tumour and blood samples

  Dataset EGAD00010000468

• Comprehensive genomic analysis of colorectal cancer with microsatellite instability

  Microsatellite instability-high (MSI-H) colorectal cancers (CRCs) account for 10?15% of all CRCs. MSI-H CRC is characterized by a large number of somatic insertions/deletions (indels) resulting from either mutations within or the silencing of genes involved in the DNA mismatch repair (MMR) system. A subset of MSI-H CRCs is associated with Lynch syndrome (LS), which is caused by germline MMR gene mutations, leading to hereditary cancer predisposition. Other than frequent somatic mutations in BRAF, the transformation mechanisms underlying MSI-H CRC are largely unknown. Here, genomic DNA from 149 MSI-H CRC specimens was analyzed using whole-exome sequencing, and 93 of these samples were subjected to genome-wide DNA methylation analysis. Furthermore, transcriptome sequencing was conducted on 111 samples. Genomic/epigenomic analyses identified three subgroups within our cohort: (1) MSI-H CRCs with silenced MLH1 that share frequent indels, a specific mutation/copy number alteration profile and promoter DNA methylation; (2) LS-associated MSI-H CRCs with MMR genes containing germline mutations; and (3) the remaining MSI-H CRCs with frequent somatic disruptive mutations of MLH1 or MSH2. Unexpectedly, only the first group was found to frequently carry fusion-type protein kinases (15% of this group and 9.9% of all MSI-H CRCs) that are promising therapeutic targets. Thus, MSI-H CRCs can be classified into three subgroups with distinctive genomic as well as epigenomic statuses, probably reflecting the oncogenic processes of these cancers. Fusion-type kinases are enriched in MSI-H CRCs, shedding new light on potential treatment strategies.

  Study JGAS000113

• Genome-Wide Association Study of aspirin-induced PUD in a UK cohort

  Aspirin is a widely prescribed non-steroidal anti-inflammatory drug used as an effective analgesic and at low doses as anti-platelet drug for the prevention of cardiovascular diseases. However, aspirin is associated with a significant incidence of upper gastrointestinal (GI) complications, notably peptic ulceration. This study aims to identify genetic risk factors associated with the pathogenesis of aspirin-induced upper GI ulceration.A cohort of 248 patients with aspirin-induced, endoscopiclly confirmed GI ulceration and 491 controls (ulcer, without aspirin or aspirin without ulcer) were genotyped for 1.524,956 SNPs using the Illumina Omni 2.5 SNP array. A replication cohort (206 NSAID-induced ulcer cases [of which 87 were aspirin] and 309 controls) was subsequently genotyped for identified SNP association signals using Sequenom iPLEX Massarry. Logistic regression analysis of identified two SNP signal with suggestive association with aspirin-induced GI ulceration. A SNP within the EYA1 locus (rs12678747) was found to be associated with aspirin GI ulceration in both the discovery cohort (p=3.79x10-7, OR=2.06 ([1.55-2.73]) and, to a lesser extent, in the replication cohort (p=.0005, OR=1.71[1.17-2.50]. Combined analysis of both cohorts yielded a genome wide significant association (p=1.46x10-8). The rs12678747 genotype was found to be associated with significantly higher EYA1 transcript in ulcer biopsy tissue (p<0.05).Data suggest that EYA1 may represent a risk locus for aspirin-induced GI ulceration. Though it is thought that EYA1 may play a key role in mediating cell death/ survival

  Study EGAS00001002052

• Confirmation of a founder effect in a Northern European population (FRL) of a new beta-globin variant: HBB:c.23_26dup (codons 8/9 (+AGAA))

  Beta-thalassemia is a genetic disease caused by a defect in the production of the beta-like globin chain. More than 200 known different variants can lead to the disease and are mainly found in populations that have been exposed to malaria parasites. We recently described a duplication of 4 nucleotides in the first exon of beta-globin gene in several families of patients living in Nord-Pas-de-Calais (France). Using the genotypes at 12 microsatellite markers surrounding the beta-globin gene of four unrelated variant carriers plus an additional one recently discovered, we found that they shared a common haplotype indicating a founder effect that was estimated to have taken place 225 years ago (9 generations). In order to determine whether this variant arose in this region of Northern-Europe or was introduced by migrants from regions of the world where thalassemia is endemic, we genotyped the first 4 unrelated variant carriers and 32 controls from Nord-Pas-de-Calais for 97 European ancestry informative markers (EAIMs). Using these EAIMs and comparing with population reference panels, we demonstrated that the variant carriers were very similar to the controls and were closer to North European populations than to South European or Middle-East populations. Rare beta-thalassemia variants have already been described in patients sampled in non-endemic regions but it is the first proof of a founder effect in Northern Europe. The new genetic panel FRL is under registration in EGA.

  Study EGAS00001000980

• Breast cancer DNA repair

  Tumors of germline BRCA1/2 mutated carriers show homologous recombination (HR) deficiency (HRD), resulting in impaired DNA double strand break (DSB) repair and high sensitivity to Poly-(ADP-Ribose)-Polymerase (PARP) inhibitors. Although this therapy is expected to be effective beyond germline BRCA1/2 mutated carriers, a robust validated test to detect HRD tumors is lacking. In the present study we therefore evaluated a functional HR assay exploiting the formation of RAD51 foci in proliferating cells after ex vivo irradiation of fresh breast cancers (BrC) tissue: the RECAP test.Methods Fresh samples of 170 primary BrC were analyzed using the RECAP test. The molecular explanation for the HRD phenotype was investigated by exploring BRCA deficiencies, mutational signatures, tumor infiltrating lymphocytes (TILs) and microsatellite instability (MSI).Results RECAP was completed successfully in 148 out of 170 samples (87%). 24 tumors showed HRD (16%), while 6 tumors were HR intermediate (HRi) (4%). HRD was explained by BRCA deficiencies (mutations, promoter hypermethylation, deletions) in 16 cases. Several non-BRCA deficient HRD tumors showed BRCAness mutational signatures, suggesting that they are also bona fide HRD cases. HRD tumors showed an increased incidence of high TIL counts (p=0.023) compared to HR proficient (HRP) tumors and MSI was more frequently observed in the HRD group (2/20, 10%) than expected in BrC (1%) (p=0.017).Conclusion The RECAP test is a robust assay detecting both BRCA1/2 deficient and BRCA1/2 proficient HRD tumors, suggesting that this test identifies approximately 50% more patients that may benefit from PARPi treatment than BRCA gene testing only.

  Study EGAS00001002792

• Clonal fitness inferred from timeseries modeling of single cell cancer genomes

  Progress in defining genomic fitness landscapes in cancer by copy number alterations (CNA) has been impeded by lack of single cell and timeseries sampling. We generated 42,000 single cell whole genomes (scWGS) from breast epithelium and primary triple negative breast cancer (TNBC) patient-derived xenografts (PDX) collected during multi-year time series. Using a Wright-Fisher population genetics model, we inferred reproducible CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy, with accurate forecasting of experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDX resulted in cisplatin resistant clones that had shown low fitness in the untreated setting. By contrast high fitness clones from treatment naive controls were eradicated reflecting an inversion of the fitness landscape. Upon drug release selective pressure dynamics were reversed indicating a fitness cost of treatment resistance. Taken together, our findings reveal clonal fitness dynamics linked to CNA and therapeutic resistance in polyclonal tumours.

  Study EGAS00001004448

• Localised colon cancer WES study contaning WBCs, tissue and plasma samples at different time points

  Decision-making based on circulating tumor DNA (ctDNA) status following curative-intent surgery in stage II-III colon cancer (CC) is where the strongest clinical evidence lies. Commercial or academic assays are predominantly used to detect ctDNA, aiming to reveal minimal residual disease (MRD) and identify patients at high risk of recurrence. However, while current tests demonstrate exceptional specificity in detecting MRD among patients who later experience recurrence, their sensitivity is notably limited, particularly immediately after surgery when decisions regarding ACT are crucial. Additionally, up to 70% of patients with stage II-III colon cancer fail to clear ctDNA after standard adjuvant treatment (ACT) and subsequently experience recurrence. In this study, we performed whole exome sequencing (WES) of ctDNA at different timepoints in relapsed CC patients using two independent cohorts, alongside transcriptomic and proteomic analyses of metastases to gain a deeper understanding of progression mechanisms. An assay based on a tumor-agnostic approach from WES could enhance sensitivity in detecting MRD disease compared to current assays. Immune evasion appears to be the primary driver of progression in the localized CC setting, facilitated by a functional mutational burden at relapse. This suggests that immunotherapy could extend its efficacy to patients with microsatellite stability, broadening treatment options. Moreover, organoid modeling affirms the promising potential of targeted therapy to surpass conventional treatments in eradicating MRD.

  Study EGAS50000000204

• Cell fate mapping of human glioblastoma reveals an invariant stem cell hierarchy pre- and post-treatment

  Human glioblastomas (GBMs) are thought to harbour a subpopulation of glioblastoma stem cells (GSCs) that initiate tumour formation and regrowth following treatment. However, the origin of their proliferative heterogeneity during tumour growth pre- and post-treatment remains poorly understood. Here we study the clonal evolution of DNA barcoded GBMs following their serial propagation in xenograft mouse models to define the fate behaviour of individual GBM cells. Through quantitative analysis of clone sizes scored across multiple passages, we show that the growth of GBM clones in vivo are consistent with a remarkably neutral process resulting from a conserved proliferative hierarchy. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, that in turn generates short-lived cells that lack proliferative ability. We also identify rare "outlier" clones that deviate from these dynamics, and further show that chemotherapy reproducibly facilitates the selective expansion of pre-existing drug-resistant GBM lineages. Finally, we show that coexisting, functionally distinct GSCs may be targeted separately with epigenetic compounds. These findings show that, independent of an evolving mutational signature, the clonal dynamics of human GBM can be surprisingly robust, with intratumoural heterogeneity derived primarily from the defined stochastic fate behaviour of tumour cells within a conserved proliferative hierarchy.

  Study EGAS00001002424

• Homozygous loss-of-function variants in European cosmopolitan and isolate populations

  Homozygous loss of function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown-as are the phenotypic effects of losing function for most human genes. Here, we make use of 1432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation.

  Study EGAS00001001606

• Epigenetic profiling of human CD4+ memory T cells reveals their proliferative history and argues in favor of a progressive differentiation model driven by epigenetically controlled master regulators.

  A key element of adaptive immunity is the development of long-lived memory cells, which protect against recurring infection by providing a highly enriched pool of antigen-specific cells ready to react to the pathogen. Different classes of memory T cells occur upon primary activation of naive T cells, however, their detailed differentiation pathway is not entirely clear. As part of the IHEC consortium, we generated genome-wide epigenetic maps of a number of CD4+ T cell memory (Tmem) stages including rare subsets such as terminally differentiated (TEMRA) and bone marrow-resident Tmem. We found that CD4+ T cells show progressive global DNA demethylation with differentiation into memory stages, which reflects their proliferative history and likely indicates their decline in differentiation and proliferation potential. Furthermore, transcriptomic profiling combined with co-regulation network analyses arranged different Tmem subsets into a successive differentiation pathway. In addition, we identified a number of epigenetically controlled candidate master regulators for Tmem formation, of which we functionally validated a new methylation-sensitive promoter for the known 'naive-keeper' transcription factor Foxp1. Our study highlights the power of epigenomic datasets in the elucidation of the cellular history but also of the functional potential of T cell populations including the identification of epigenetically controlled master regulators.

  Study EGAS00001001624

• Walter and Eliza Hall Institute Research Data Access Committee

  Dac EGAC00001002877

• Carcinosarcoma Cohort from NHS Greater Glasgow, Clyde Biorepository, and Imperial College London

  Dac EGAC00001003299

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001003220

• Data Access Commitee for single-cell analysis of multiple myeloma and precursors

  Dac EGAC00001002920

• Longitudinal DNA methylation in the Lothian Birth Cohorts of 1921 and 1936

  Dac EGAC00001000218

• Associations between APOE and cognitive ability in Generation Scotland.

  Dac EGAC00001000332

• Peter Mac Translational Breast Cancer Genomics and Therapeutics Lab Data Access Committee

  Dac EGAC00001000837

• DAC: Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Dac EGAC00001000847

• The APL DAC comprises a clinician and biologist who conducted the study.

  Dac EGAC00001000865

• DAC for Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

  Dac EGAC00001001101

• Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles

  Dac EGAC00001001591

• Human MPN RNA-seq and DNA methylation data requests committee

  Dac EGAC00001001688

• University of Helsinki Systems Biology and Turku University Hospital Data Access Committee

  Dac EGAC00001001978

• Data access committee for Gut microbiome of BA patients and normal controls

  Dac EGAC00001002146

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002205

• Variation and transmission of the human gut microbiota across generations - 16S data

  Dac EGAC00001002344

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Dac EGAC00001002355

• "DAC for RNAseq from regions of insitu and invasive human mammary ductal disease"

  Dac EGAC00001002538

• DAC - U1085 Team Physiology and Physiopathology of the urogenital tract (INSERM / IRSET)

  Dac EGAC00001002830

• DAC - Liquid biopsy with matched tumor tissue and saliva: CRC + controls

  Dac EGAC00001002835

• Single-cell sequencing of adipose-derived mesenchymal stromal cells and dermal fibroblasts.

  Dac EGAC00001003062

• Mitochondrial DNA (mtDNA) analyses in patients with schizophrenia and healthy control individuals

  Study EGAS00001003269

• DAC for Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

  Dac EGAC00001003522

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  Dac EGAC50000000583

• ATAC-Seq and CTCF ChIP-Seq on the OCIAML-2 cell line

  Study EGAS00001004741

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Study EGAS00001006395

• Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer

  Study EGAS00001004328

• Array-based methylation analysis of SDHB-deficient pheochromocytoma and paraganglioma

  Study EGAS00001007844

• Population Genomics of Native Americans from Andes and Amazon

  Study EGAS00001004639

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

  Study EGAS00001005296

• Human gut microbiome in babies with biliary atresia and normal controls

  Study EGAS00001005350

• RNAseq from regions of insitu and invasive human mammary ductal disease

  Study EGAS00001005370

• Optimisation of CITE-seq on liquid and solid tissues

  Study EGAS00001005849

• Oesophageal adenocarcinoma whole exome and RNA-seq raw sequencing data

  Study EGAS00001005957

• Treated and control Patient Derived Xenografts of colorectal cancer (CRC) samples

  Study EGAS00001006973

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  Study EGAS00001007491

• EGAD00010000704

  610k genotyping imputed on Hapmap 3 and 1000G Phase 1 CEU

  Dataset EGAD00010000704

• saudi_qc_data

  Genotyped case and control sampes using HumanExome Beadchip

  Dataset EGAD00010000872

• Advanced Genomic Techniques in Sequencing of Colorectal Cancer

  We developed a method that uses allelic imbalance information in combination with phased genomic sequencing to generate mega-haplotypes that can encompass entire chromosome arms. We applied this technique to characterize aneuploidy and chromosomal alterations in colorectal cancers.

  Study phs001400

• Large Cancer Fingerprint Screening for Detection of Minimal Residual Disease.

  We describe an approach for large cancer fingerprint screening and its application to cell-free DNA from patients with cancer. Our approach involves tracking somatic mutations identified from patients' tumor biopsies, in the cell-free DNA from a blood draw.

  Study phs001977

• Molecular Characterization of Germ Cell Tumors

  We performed comprehensive molecular profiling of germ cell tumors, including whole exome sequencing and transcriptome sequencing, derived from patient samples. This project additionally explores mechanisms of chemosensivity in these patients, as well as mechanisms of tumor evolution in the context of treatment.

  Study phs000923

• Understanding the Progression of Metastatic Colorectal Cancer

  This study is to understand (1) the clonal evolution of metastatic colorectal cancer using DNA sequencing and (2) long non-coding RNAs associated with metastatic colon cancer using RNA sequencing. Our goal is to better understand the progression of aggressive colorectal cancer.

  Study phs001722

• DAC for "Longitudinal copy number variation analysis from plasma DNA of head and neck cancer patients under re-radiotherapy"

  This is the DAC for "Longitudinal copy number variation analysis from plasma DNA of head and neck cancer patients under re-radiotherapy" with Florian Janke f.janke@dkfz-heidelberg.de German Cancer Research Center, Division of Cancer Genome Research Holger Sültmann h.sueltmann@dkfz-heidelberg.de German Cancer Research Center, Division of Cancer Genome Research Magdalena Görtz magdalena.goertz@dkfz-heidelberg.de German Cancer Research Center, Multiparametric Methods for Early Detection of Prostate Cancer

  Dac EGAC50000000114

• MOSAIC Window - Bladder dataset

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 15 Muscle-invasive Bladder Cancer patients, treated with upfront cystectomy. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000000967

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• Transcriptome analysis of Familial dysautonomia patient cells treated with splice-regulating compounds

  In order to investigate familial dysautonomia patient fibroblasts in response to splice-regulating compounds, cells were treated with RECTAS or TG003 and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000170

• exploration of biomarkers in colorectal cancer

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

  Study JGAS000489

• DNA methylation array analysis of pediatric T-cell acute lymphoblastic leukemia

  Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate epigenetic profiles of pediatric T-ALL, we performed DNA methylation array analysis in 79 cases of pediatric T-ALL.

  Study JGAS000138

• Transcriptome analysis of Fabry disease iPSC-derived cardiomyocytes treated with splice-regulating compound; RECTAS

  In order to investigate transcriptome profiles in response to splice-regulating compounds, iPSC-derived cardyomyocytes were treated with RECTAS and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000225

• Genome-wide integrative analysis of pediatric pancreatoblastoma

  Pancreatoblastoma is the most common pancreatic malignancy of young children, but its molecular pathogenesis remains poorly understood. To understand the molecular pathogenesis of pancreatoblastoma, we comprehensively analysed the whole exome sequencing, RNA sequencing, SNP array, and methylation array data of pancreatoblastoma.

  Study JGAS000088

• WTCCC case-control study for Coronary Artery Disease - Combined Controls

  WTCCC genome-wide case-control association study for Coronary Artery Disease (CAD) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000004

• WTCCC case-control study for Type 1 Diabetes - Combined Controls

  WTCCC genome-wide case-control association study for Type 1 Diabetes (T1D) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000015

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Effects of KSP inhibitor filanesib in aggressive hepatoblastoma PDX cells

  Aim of this RNA sequencing dataset has been to asses effects caused by the KSP inhibitor filanesib in aggressive hepatoblastoma PDX cells. Two cell lines (HB-279 and HB-284) were utilised. DMSO-treated cells were used as controls.

  Study EGAS50000000899

• smallRNA-seq of isolated pancreatic islets

  In this study we performed smallRNA-sequencing, a sequencing method designed for small noncoding RNAs, to investigate the miRNA expression profile of human islets isolated from pancreata of donors without diabetes mellitus (n=3) and donors with type 2 diabetes (n=3).

  Study EGAS50000000865

• WTCCC case-control study for Type 2 Diabetes - Combined Controls

  WTCCC genome-wide case-control association study for Type 2 Diabetes (T2D) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000017

• WGS_skin_punches

  We wish to understand the degree of copy number alterations in normal human sun exposed skin. We have collected small punches of epithelia and using a bait set design have shown the these span a clone. WGS will provide copy number information on these.

  Study EGAS00001004465

• WES data from primary CRCs tissues in ctDNA positive patients

  Whole exome data from primary colorectal cancer tissue samples were analysed in patients where mutations where found in circulating tumour DNA. DNA was extracted from FFPE blocks and exome libraries were prepared using the KAPA HyperPlus Kit (Roche diagnostics)

  Study EGAS50000000650

• Whole-genome sequencing study of uveal melanoma

  Uveal melanoma is the most common primary intraocular cancer, characterized by metastasis-related mortality. Here, we explored whole-genome sequences from 40 primary uveal melanomas to illustrate the landscape of genomic mutations and investigate their association with prognosis.

  Study EGAS50000001603

• Bulk RNASeq of metastatic colorectal cancer organoids with ATOH1 knockout

  Bulk RNA sequencing was performed on mCRC organoids subjected to cetuximab treatment, comparing ATOH1 knockout and control conditions. The dataset is intended to elucidate the contribution of ATOH1-regulated secretory cell population to cetuximab persistence mechanisms.

  Study EGAS50000001421

• Idiopathic Collapsing Glomerulopathy in Brazilian patients

  Collapsing glomerulopathy is a severe kidney disease that often leads to chronic dialysis or kidney transplantation. To expand its understanding, we performed a broad clinical and genetic analysis of a highly admixed patient population with idiopathic collapsing glomerulopathy.

  Study EGAS50000000064

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• Clinical data of liver cancer patients from EuCanImage - Use case 1 Synthetic

  This study is part of EuCanImage project. It contains the standardized clinical information following FHIR model. The data was collected together with MRI of patients diagnosed with liver cancer (HCC) and controls (non-HCC). All data is synthetic.

  Study EGAS50000001444

• 3' mRNA- sequencing bams

  This project stores bam files from 3'RNA-seq from oesophageal adenocarcinoma at different timepoints during neoadjuvant treatment (prior, during, post treatment), which were used to analyse evolutionary and phenotype dynamics in oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Study EGAS50000000242

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell RNA-sequencing (CITE-seq) and single-nucleus RNA-sequencing data were generated from neuroblastoma patient tumors to uncover transcriptional heterogeneity at a single-cell resolution. In addition, we used the data to validate our findings of the NBAtlas.

  Study EGAS50000000223

• Analysis of T cells in follicular lymphoma

  This study aimed to identify new heterogeneities in human T cells of follicular lymphoma. To do so, we performed scRNA-seq of human lymph node and follicular lymphoma samples. We identified minor T cell subsets expanding in follicular lymphoma.

  Study EGAS50000000778

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

  Dataset EGAD50000002026

• Bulk RNASeq of metastatic colorectal cancer organoids treated with crenigacestat alone or in combination with cetuximab

  Bulk RNA sequencing was performed on mCRC organoids cultured under untreated conditions or treated with crenigacestat alone or in combination with cetuximab. This dataset was generated to investigate the transcriptional changes associated with combination therapy and to compare these profiles with the adaptive responses observed following cetuximab monotherapy in the corresponding ATOH1 wild-type and knockout organoid models.

  Dataset EGAD50000002061

• TenK10K Phase 1: scRNA-seq AnnData objects

  Single cell RNA-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (1925 individuals post-QC). Libraries were prepared using the 10x Genomics 3’ Chromium Next GEM Single Cell HT V3.1 kit and sequenced on the NovaSeq 6000 platform. Reads were mapped to the GRCh38 reference genome with Cellranger, and count matrices were preprocessed using Scanpy.

  Dataset EGAD50000002379

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 18-19)

  The dataset contains RNA sequencing data of 66 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 155 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000002370

• 10X single-cell Multiome (RNA+ATAC) of bone marrow-derived HSPC

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries, sequenced on an Illumina NovaSeq 6000 platform. BAM files are provided. Samples from 6 donors were sequenced after sorting for primitive HSPCs in 5 libraries; each library comprises a single donor, except one with cells from 1 male and 1 female donor.

  Dataset EGAD50000002326

• WGS data from PASS-01 trial

  WGS data for pancreatic cancer samples (PASS-01 Trial; Knox et al., Journal of Clinical Oncology, 2025).  The dataset includes tumour and normal cram files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=127 tumour/normal pairs)

  Dataset EGAD50000002309

• RNA-Seq for SF3B1 splicing signature

  This dataset includes exome-captured RNA-Seq made with exome v8 (Agilent) - library preparation on a MAGNIS XT-HS2 starting from 100ng of RNA. RNA has been extracted from lymphocytes cultures from 2 probands with SF3B1 mutations and 14 controls. All 16 RNA-Seq were sequenced on a single HighOutput flowcell 2x75bp (NextSeq550). Raw fastq files have between 20 and 30M paired-reads.

  Dataset EGAD50000002121