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• Dataset with genome-wide array data from Algerian Amazigh (Chaoui and Mozabite) and non-Amazigh individuals

  In this study we perform a genetic characterization of different Amazigh populations in Algeria and assess the impact of recent demography on their genomes.

  Study EGAS00001007235

• Targeted_NanoSeq___TwinsUK_Blood

  Utilising Targeted NanoSeq, we hope to explore the driver landscape in unprecedented detail in donors from TwinsUK. These donors have paired buccal swabs and data from this will help contextualise that work.

  Study EGAS00001007595

• RNA dataset of ALK study

  Here we sequenced biopsies from a patient with ALK-positive NSCLC progressing on first-line lorlatinib. This dataset contains one mRNA-seq and one Total-RNAseq. This aims to investigate the impact of the K1150dup mutation on lorlatinib progression and to explore potential therapeutic strategies to overcome resistance.

  Dataset EGAD50000002553

• Molecular characterization of Barrett’s esophagus at single cell resolution

  Backgrounds & Aims: Patient with Barrett’s esophagus (BE) have an increased risk to develop esophageal adenocarcinoma and are under periodical endoscopic surveillance for malignant transformation. Pathologists distinguish between different BE stages to identify high-risk patients, but this process remains difficult as stage-specific markers are still missing. We established BE organoid cultures, applied single cell sequencing approaches to identify differences in gene expression and genomic alterations, and validated candidate genes for their predictive value on histological sections. Methods: We collected 43 epithelial biopsies from 21 patients, established organoids for the clonal expansion of matching healthy and diseased tissue from two patients to identify genomic alterations by whole genome sequencing (WGS). We performed single cell DNA-sequencing (scDNAseq) to analyse DNA alterations within biopsies from 8 patients and single cell RNA-sequencing (scRNAseq) to identify gene expression differences between BE stages from 19 patients. Candidate marker genes were then validated by RNA in situ hybridization experiments on histological resection specimen. Results: Most BE biopsies were chromosomal stable (CS) and their single base substitution (SBS) signatures were indistinguishable from the healthy control tissues. Dysplastic BE cells contained areas of chromosomal instabilities (CIN), which differed by the presence of the SBS17 signatures from biopsy-matching CS cells or patient-matching healthy control cells. Such CIN areas affected efficient clustering of the scRNAseq data. We identified two sets of marker genes (SLC5A5, PSCA, LIPF and ANPEP, CEACAM6, REG4), which distinguish columnar BE epithelium from non-dysplastic/dysplastic stages. CLDN2 allowed the distinction between dysplastic and more advanced stages as its expression level increased and spread in dysplastic BE glands. Conclusions: Molecular characterization of BE samples identified a correlation between the presence of CIN and COSMIC signature 17, and we report seven marker genes that help in distinguishing different BE stages.

  Study EGAS00001005221

• Neuroblastoma sequencing data

  This dataset contains tumor and normal whole exome DNA sequence data for a patient with neuroblastoma

  Dataset EGAD00001008120

• Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data

  Juvenile Pilocytic Astrocytoma (JPAs) are highly vascular tumors and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. In some instances, this results in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. Overall, we demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution.

  Study EGAS00001006388

• Data from Shea et al Can Research 2025

  This dataset contains single cell RNA sequencing (192 fastq files for 59 samples), whole exome sequencing (20 BAM files -hg38- for 20 samples) and bulk RNA sequencing (138 paired-end fastq files and 17 single-end fastq files for 8 samples)

  Dataset EGAD50000001334

• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• Demultiplexed FASTQs for each volunteer

  This submission consists of 15 volunteer FASTQs, split by chemistry: Chemistry v1.1: 7 FASTQ sets, one set for each volunteer (RA1-7) Chemistry v2: 16 FASTQ sets, two for each volunteer (RA8-15; FASTQ set 1: Gene Expression (GEX); FASTQ set 2: TCR enrichment (VDJ))

  Dataset EGAD00001007586

• This agreement governs the terms on which access will be granted to the data generated by the United Kingdom Brain Expression Consortium.

  Dac EGAC00001001408

• Longitudinal Multi'omics of the Human Microbiome in Inflammatory Bowel Disease (IBDMDB)

  Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of individuals worldwide. The Integrative Human Microbiome Project (HMP2) characterized a total of 132 CD, UC and non-IBD patients across a year to generate longitudinal molecular profiles of host and microbial activity during this time frame. A total of 2,965 stool, biopsy and blood specimens were produced and analyzed from this cohort. A comprehensive view of the gut microbiome's functional dysbiosis during IBD activity was derived from analyzed samples each providing a different window into disease activity. The study's resources, results and data are available through the Inflammatory Bowel Disease Multi'omics Database (IBDMDB) provide the most comprehensive description of host and microbial activities in IBD to date.

  Study phs001626

• Acquired Copy Number Alterations in Adult Acute Myeloid Leukemia Genomes

  We performed genome-wide copy number analysis with paired normal and tumor DNA obtained from 86 adult patients with de novo AML using the Affymetrix Genome-Wide Human SNP array 6.0 containing 1.85 million features. Acquired copy number alterations (CNA) were confirmed using an independent, higher resolution, custom array comparative genomic hybridization platform. A total of 201 somatic CNA were found in the 86 AML genomes (mean 2.34 CNA/genome), with FAB M6 and M7 AML genomes containing the most changes (10-29 CNA/genome). Twenty-four percent of AML patients with normal cytogenetics had CNA, while 40% of patients with an abnormal karyotype had additional CNA detected by SNP array, and several regions contained CNA in multiple AML genomes. The mRNA expression levels of 57 genes were significantly altered in 27 of 50 recurrent CNA regions <5 megabases in size. Array data are available online at http://www.ncbi.nlm.nih.gov/geo/ as GEO accession #GSE10358. A total of 8 uniparental disomy (UPD) segments were identified in the 86 genomes and 6/8 UPD regions occurred in samples with a normal karyotype. Collectively, 40% of AML genomes contained alterations not found with cytogenetics, and 96% of these regions contained known or novel AML associated genes. 43/86 AML genomes had no CNA or UPD at this level of resolution. The number of CNA per genome was not associated with overall survival, independent of cytogenetic classification. In this study of 86 adult AML genomes, subcytogenetic CNAs or UPD did not add prognostic information to standard cytogenetics. However, arrays identified many somatically mutated oncogenes and tumor suppressor genes, and also genes not previously implicated in AML that may be relevant for pathogenesis. AML CNA segments from 86 adult AML patients are available through dbVar at ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/nstd11_Walter_et_al_2009.

  Study phs000201

• Single Cell Sequencing of Medulloblastoma Samples

  This dataset contains the results of sequencing 9 samples (7 human/PDX, 2 cell lines) of medulloblastoma tumours (or 2 Neural Stem Cell lines). The data was collected to characterize the intratumour heterogeneity of chromothripsis in this tumour type. The 7 tumour samples underwent single cell DNA and RNA sequencing using the 10x CNVkit and 10xRNA protocols, and 1 of the tumour samples as well as the Neural Stem Cell lines underwent StrandSeq sequencing. All experiments were sequenced on Illumina sequencers. The provided files are paired-end fastq files from the sequencing experiments.

  Dataset EGAD50000000909

• OncoArray: Follow-up of Ovarian Cancer Genetic Association and Interaction Studies (FOCI)

  The Follow-up of Ovarian Cancer Genetic Association and Interaction Studies (FOCI) was one of five projects funded in 2010 as part of the NCI's Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative (http://epi.grants.cancer.gov/gameon/). FOCI represents a collective effort that builds upon the strengths and history of collaboration inherent in the Ovarian Cancer Association Consortium (OCAC), a multidisciplinary group comprised of epidemiologists, genetic epidemiologists, statistical geneticists, molecular and cell biologists and clinicians that was formed in 2005. The other four funded GAME-ON projects were: the ColoRectal TransdisciplinaryStudy (CORECT), Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE), Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE), and Transdisciplinary Research in Cancer of the Lung (TRICL). As part of our aim to discover, expand, and replicate ovarian cancer susceptibility loci, the GAME-ON projects and other consortia formed the OncoArray network (http://epi.grants.cancer.gov/oncoarray/) to develop and genotype a new custom genotyping array in large numbers of cancer cases and controls (over 400,000 samples) across multiple cancer types. The FOCI data includes over 50,000 ovarian cancer cases and controls genotyped with the Oncoarray at the Center for Inherited Disease Research (CIDR). Genotype calling and quality control procedures were performed under a standardized protocol across the Oncoarray consortium, and over 490,000 SNPs passed QC and are included under this dbGaP submission.

  Study phs001882

• Molecular determinants of response to PD-L1 blockade across tumor types

  Immune checkpoint inhibitors targeting the PD-1/PD-L1 axis lead to durable clinical responses in subsets of cancer patients across multiple indications, including non-small cell lung cancer (NSCLC), urothelial carcinoma (UC) and renal cell carcinoma (RCC). Herein, we complement PD-L1 immunohistochemistry (IHC) and tumor mutation burden (TMB) with RNA-seq in 366 patients to identify unifying and indication-specific molecular profiles that can predict response to checkpoint blockade across these tumor types. Multiple machine learning approaches failed to identify a baseline transcriptional signature highly predictive of response across these indications. Signatures described previously for immune checkpoint inhibitors also failed to validate. At the pathway level, significant heterogeneity was observed between indications, in particular within the PD-L1+ tumors. mUC and NSCLC were molecularly aligned, with cell cycle and DNA damage repair genes associated with response in PD-L1- tumors. At the gene level, the CDK4/6 inhibitor CDKN2A was identified as a significant transcriptional correlate of response, highlighting the association of non-immune pathways to the outcome of checkpoint blockade. This cross-indication analysis revealed molecular heterogeneity between mUC, NSCLC and RCC tumors, suggesting that indication-specific molecular approaches should be prioritized to formulate treatment strategies.

  Study EGAS00001004343

• Genomic analysis of seminomas

  This study looks at the genomic landscape of seminomas, based on exome sequencing data and SNP array data. Eight seminoma tumors and their matched normal DNAs were exome sequenced on Illumina platforms. The same samples were also processed on Affymetrix SNP 6.0 arrays.

  Study EGAS00001000943

• Genomic and transcriptomic profiling of colorectal cancer patient-derived organoids

  This study describes controlled-access human sequencing data generated from colorectal cancer patient-derived organoids established using the CTOS method. Whole-exome sequencing (WES) and RNA sequencing (RNA-seq) were performed to characterize genomic alterations and transcriptomic profiles of the organoids.

  Study EGAS50000001669

• Breast_cancer_sequential_sampling_study

  This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Study EGAS00001000300

• Clonal_architecture_of_pre_malignant_and_malignant_tumours

  Single cells have been isolated from normal and pre-invasive lung cancer lesions from one patient. These have been grown into colonies that will then be whole genome sequenced. This will reveal the mutational burden in normal and premalignant tissues, and the heterogeneity between different cells.

  Study EGAS00001001676

• Myeloproliferative_Neoplasms__MPN__Targeted_Gene_Screen

  Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool.

  Study EGAS00001000406

• RNA-seq on bronchial brushings collected in controlled human exposure to diesel exhaust

  COPA study examined the impact of short-term exposure on airway epithelium transcriptome. It was a randomized, double-blind, controlled human exposure study to diesel exhaust with a crossover design. This human study was registered on clinicaltrials.gov with the identifier NCT02236039.

  Study EGAS00001006966

• Visium Spatial tramscriptomics data set

  This data set contains raw FASTQ files and processed files of spatial transcriptomics of 6 EMD samples collected from MM patients. The processed files contain the h5 expression matrices, the Image of the Visium slide, and a TSV of spatial coordinates. Patients included in this data set are PT01A, PT01B, PT02, PT03, PT07, PT08, PT09, PT10, and PT11.

  Dataset EGAD50000000336

• MCL NGS data

  We have performed a comprehensive and integrative genomic study of mantle cell lymphoma (MCL) to elucidate the features that may determine the different clinical and biological behavior of the two molecular subtypes of this lymphoma, conventional (cMCL) and leukemic non-nodal MCL (nnMCL). This data integrated with epigenomics and transcriptomics has allowed to uncover novel molecular mechanisms in the origin and development of these tumors and provide relevant information to stratify patients in different risk groups.

  Dataset EGAD00001006025

• Altered chromosomal topology drives oncogenic programs in gastrointestinal stromal tumors

  Metabolic lesions with pleiotropic effects on epigenetic regulation and other cellular processes are widely implicated in cancer, yet their oncogenic mechanisms remain poorly understood. Succinate dehydrogenase (SDH) deficiency causes a subset of gastrointestinal stromal tumors (GISTs) with DNA hyper-methylation. Here we associate this hyper-methylation with changes in chromosome topology that activate oncogenic programs. To investigate epigenetic alterations in this disease, we systematically mapped DNA methylation, CTCF insulators, enhancers and chromosome topology in KIT-mutant, PDGFRA-mutant and SDH-deficient GISTs. Although these respective subtypes share similar enhancer landscapes, we identified hundreds of putative insulators where DNA methylation replaced CTCF binding in SDH-deficient GISTs. We focused on disrupted insulators that partitions super-enhancers from FGF3, FGF4 and the KIT oncogene. Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs, allowing aberrant physical interaction between enhancers and oncogenes. CRISPR-mediated excision of the corresponding CTCF motif in an SDH-intact model disrupted the boundary and up-regulated FGFs and KIT expression. Our findings reveal how a metabolic lesion destabilizes chromatin structure to facilitate the initiation and selection of epigenetic alterations that drive oncogenic programs in the absence of canonical mutations.

  Study phs001906

• Transcriptome of CD4+ T cells and CD8+ T cells in glioblastoma multiforme

  Patients included in this study were over 18 years of age and had a histology-confirmed diagnosis of glioblastoma multiforme (GBM). Exclusion criteria were the previous administration of any anti-tumor therapy including radiation therapy. All patients gave written informed consent. The study was approved by the local ethics committee (TUM Medical school) and conducted following the Declaration of Helsinki. During resection of the tumors, tumor tissue and tissue from normal appearing brain within the operative channel was collected. Blood was drawn during the surgical procedure. Single cell suspensions were prepared from the tumor tissue, the normal appearing brain, and the blood. CD4+ T cells and CD8+ T cells were sorted by flow cytometry. Only patients with a complete set of specimens (CD4+ tumor infiltrating lymphocytes (TIL), CD8+ TIL, CD4+ T cells from normal appearing brain, CD8+ T cells from normal appearing brain, blood-derived CD4+ and CD8+ T cells) containing a minimum of 1000 cells in each sorted sample were further analyzed (n=9). Total RNA was isolated from sorted cell populations using the RNAeasy Plus micro kit (Qiagen, 74034). Quality and integrity of total RNA was controlled on a Bioanalyzer 2100 (Agilent Technologies). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (ThermoFisher Scientific, EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated and 3'-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read 1 and barcodes and UMIs in read 2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 59 cycles for the cDNA in read 1 and 16 cycles for the barcodes and UMIs in read 2. Data were processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to the Genecode Annotation Version 35.

  Study EGAS50000000156

• Highlighted samples from the BCH CRDC

  These exomes are from some of the patients and family members detailed in our forthcoming publication, Children’s Rare Disease Cohorts: an integrative research and clinical genomics initiative. While this paper details an institutional collection of exomes, the samples here were specifically highlighted as having significant findings.

  Study EGAS00001004436

• Genetic dysregulation of gene expression and splicing during a ten-year period of human aging in the PIVUS study

  We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging.

  Study EGAS00001003583

• Comprehensive molecular portrait reveals genetic diversity and distinct molecular subtypes of small intestinal neuroendocrine tumors

  This study aims to characterize neuroendocrine tumors of the small intestine (siNETs) from genomic, transcriptomic, epigenomic, and clinical perspectives. Involving 122 patients and 219 samples, we generated whole-genome sequencing data, RNA sequencing data, genotyping arrays, and methylation arrays to conduct an integrative analysis of this rare tumor type. Our findings identify distinct molecular subtypes that correlate with siNET clinical features.

  Study EGAS50000000642

• RNA sequencing, ATACseq, and TCR-seq of Tfh cells and CXCR5- CD4+ T cells in HIV infected lymph nodes

  The high dimensional analyses of CD4+ T cells in human lymph nodes are case-based analyses of the TCR repertoire, transcriptome, and epigenetic signatures of various CD4+ T cells in human lymph nodes. The study aims to determine clonal overlap between phenotypically distinct CD4+ T cells and the similarities between these populations on transcriptional and epigenetic levels. This study performs TCR repertoire sequencing using Molecular Identifier Clustering-based Immune Repertoire Sequencing (MIDCIRS). We found clonal overlap between a population of CXCR5- T cells and follicular helper T (Tfh) cells. We also show epigenetic and transcriptional similarities between CXCR5-PD-1+ T cells and Tfh cells. This study shares an overlapping set of donors with phs001548.

  Study phs001849

• Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research

  In glioblastoma (GBM) the intricate interplay between tumor cells and the surrounding microenvironment plays a crucial role in tumor progression, invasion, and therapeutic resistance. So far, studying these interactions in a controlled and representative model system has been challenging. Here, we report the development of hGliCS, a human glioma-cortical spheroid model that allows the elucidation of the biology of GBM cells and their interactions with a human-specific brain-like microenvironment and neurons. GBM cells efficiently invade the cortical spheroids, forming a well-connected network of communicating cells. The heterogeneous cellular states of the GBM cells within this model closely resembled findings previously observed in glioblastoma patients and in mouse xenografts. We observed a transition from predominantly mesenchymal-like cells to heterotopic states with a high diversity. In contrast to the substantial changes observed in the tumor cell population, the impact of the GBM cells on the neurons was minimal. We further demonstrate the suitability of hGliCS to test compounds targeting tumor-specific neurobiological features.

  Study EGAS50000000757

• Guardians of the genome: protecting DNA from endogenous sources of damage

  Mutational signatures are imprints of cell-intrinsic and extrinsic pathophysiological processes that have occurred through tumorigenesis. Experimental efforts to explore signature etiologies have produced a compendium of signatures of exogenous mutagens previously. Here, we unearth major sources of endogenous DNA damage and the genes that are critical to mitigating this innate stream of DNA damage under normal, physiological circumstances. We performed whole genome sequencing of 173 subclones of CRISPR-Cas9 knockouts of 43 genes in a human induced pluripotent stem cell system, in the absence of any added DNA damage. We reveal substitution and indel signatures that arise from those genes which are essential guardians of the genome. By detailed dissection and comparisons to cancer-derived signatures, we demonstrate interminable sources of constitutive DNA damage, and some mechanistic knowledge into how guardian genes preserve the genome. Based on these experimental insights, we develop and benchmark a tool for clinical classification of tumor samples.

  Dataset EGAD00001006055

• RNA-seq dataset for two NUP98-Rearranged Acute Myeloid Leukemia PDX samples

  This dataset includes RNA-seq of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.

  Dataset EGAD50000001564

• CBD-RAW-REPERTOIRE-T: T cell bulk repertoire sequence files

  fastq and filtered fasta files for T-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007961

• Sequencing_melanoma_germlines

  In this project we performed targeted sequencing of around 50 candidate melanoma genes in the germline of melanoma patients and matched controls. Our aim was to identify variants that contribute to melanoma susceptibility.

  Study EGAS00001002081

• GWAS of SJS/TEN in Thai population

  This study looks at the Phenytoin-Induced SJS/TEN development based on SNP genotyping data of 1965 individuals from Thailand. Their normal DNAs were genotyped on Illumina HumanOmniExpressExome-8 v1.2 array.

  Study EGAS00001008316

• Small RNA sequencing of human oocytes and early embryos

  This study looks at small RNA expression in human oocytes (n=12), zygotes (n=5), and embryos (n=10). The sample preparation and sequencing were done in two batches.

  Study EGAS50000000157

• DNA methylation and Metabolic data from type 2 diabetes adolescents

  This data contains DNA methylation data obtained from the PBMCs obtained from type 2 diabetes adolescents and controls. There are 21 diabetic samples and 10 controls. This dataset also contains metabolic data obtained from the serum of 155 samples. There are 113 diabetic and 42 control samples.

  Dataset EGAD00001005271

• Somatic Mutational Analysis by Exome Sequencing Late-Stage Endometrioid Endometrial Carcinoma

  The purpose of this study was to identify somatic (tumor-specific) mutations in advanced stage endometrioid endometrial carcinoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 19 de-identified primary tumor DNAs, from advanced stage tumors, and matched non-tumor DNAs.

  Study phs001153

• Prevalence of rare pathogenic variants in cancer-predisposing genes among Japanese advanced prostate cancer patients.

  The prevalence of rare pathogenic variants in cancer-predisposing genes including those associated with DNA repair remains unknown among Japanese patients with advanced prostate cancer. This study was designed to elucidate the prevalence of pathogenic variants in 27 known cancer-predisposing genes and to explore the prognostic significance of the variants identified.

  Study JGAS000509

• Immune Landscape of Cervical Lymph Nodes in Multiple Sclerosis

  This study aimed to investigate the cellular compartment of deep cervical lymph nodes (dcLNs) during early MS before the influence of immunosuppressive treatments. We used ultrasound-guided FNAs followed by scRNA-seq,CITE-seq, TCR and BCR seq to characterize the immune landscape in MS patients compared to controls within the dcLNs.

  Study EGAS50000000843

• Whole exome DNA sequence profiling of spatial biopsies of high grade serous epithelial ovarian cancer

  The study aims at dissecting the heterogeneity across multiple biopsies of high grade serous epithelial ovarian cancer (HGS-EOC) through a comprehensive characterization of variants and structural changes at the whole exome level. To this aim, the study uses samples from multiple bioptic sites taken from eight HGS-EOC patients.

  Study EGAS00001003048

• RNAseq for 208 patients with medulloblastoma cancer (MB_COMICS cohort)

  This dataset contains 208 paired fastq files sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000000600

• Taste Receptor Genotypes_Centenarians and Young

  This dataset includes targeted genotyping data for six BMI-associated polymorphisms across four candidate genes in young and centenarian individuals.

  Dataset EGAD00010002829

• Analysis of ATL progression by CD30 signaling and its biomarkers (2)

  Adult T-cell leukemia/lymphoma (ATL) develops via stepwise accumulation of gene mutations and chromosome aberrations. However, the molecular mechanisms underlying this tumorigenic process are poorly understood. We aim to elucidate the mechanism of the tumorigenic process involving genomic aberrations by CD30 signaling in HTLV-1���infected T-cells.

  Study JGAS000537

• Oncogenic gene fusions in primary colon cancers

  This study represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. The project goal was to identify novel oncogenic gene fusions in these data. In addition, we studied the detected gene fusions at the molecular level and defined their effects on downstream pathways.

  Study EGAS00001002197

• The_British_Autozygosity_Populations_BioResource

  This data set contains whole exome sequences of 500 individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.

  Study EGAS00001001565

• Somatic_mutation_and_clonal_evolution_in_the_human_testes

  In this study we aim to characterise the landscape of Pathogenic variants and clonal dynamics in normal and cancerous testes and their role in cancer predisposition. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from testes. The range of patients studied will include healthy individuals, and patients with testicular cancer.

  Study EGAS00001003021

• Somatic_mutation_and_clonal_evolution_in_the_human_testes___WES

  In this study we aim to characterise the landscape of Pathogenic variants and clonal dynamics in normal and cancerous testes and their role in cancer predisposition. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from testes. The range of patients studied will include healthy individuals, and patients with testicular cancer.

  Study EGAS00001003023

• WGS data from both single-cell and bulk samples

  This dataset contains the raw BAM/CRAM files used in the manuscript "Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma" Steemers et al. (2026). This includes: - 332 PTA-based single-cell WGS samples (~15X depth) - 7 bulk tumour samples (~30X depth) with matched germline samples (~30X depth) - 14 bulk tumour samples seqeunced by the Princess Maxima Centre diagnostics department (~105X depth) with matched germline samples (~35X depth)

  Dataset EGAD50000002411

• Transcriptome profiling of head and neck squamous cell carcinomas with paired patient-derived xenografts

  This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.

  Dataset EGAD50000000995