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• APOLLO-OV: Applied Proteogenomics of High Grade Serous Ovarian Carcinoma

  APOLLO is a proteogenomic study seeking to describe the major genome, transcriptome, proteome and phosphoproteome alterations, subtypes, and molecular predictors of patient outcomes. This study includes 70 high grade serous ovarian carcinoma tissues from the Gynecologic Cancer Center of Excellence (https://medschool.usuhs.edu/gso/research/gyn-cancer-center-of-excellence). Bulk and laser microdissection enriched tumor tissues were profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and reverse phase protein arrays. Clinical and sample data include survival times, patient features, and tumor characteristics.

  Study phs003488

• FLG LoF Variants are Associated with Atopic Dermatitis in an Early-Life Prospective Cohort

  We performed targeted sequencing of the FLG gene in 438 children with physician-diagnosed Atopic Dermatitis (AD), identified Loss-of-Function (LoF) variants, and tested the association of having one or more of these variants (binary composite) variants with AD-associated outcomes. We found that having a LoF variant was associated with moderate-severe AD compared to mild AD, food allergy at the first visit, and higher transepidermal water loss (TEWL) in both lesional and non-lesional skin in these children.

  Study phs003489

• Childhood Cancer Data Initiative (CCDI): Single-Cell Atlas of NF1 Nerve Sheath Tumors

  The worst outcome of NF1 is the development of the aggressive and highly metastatic malignant peripheral nerve sheath tumors (MPNST), which transform from benign plexiform neurofibroma (PN) and lack effective treatment. In this study, we performed single-cell RNA sequencing of 63 clinically annotated NF1-associated peripheral nerve sheath tumors, including 24 PN, 34 premalignant atypical neurofibromas, and 5 MPNSTs. These results improve the ability of identifying high-risk neurofibromas and provide a unique opportunity for early detection of MPNST.

  Study phs003519

• Genomic and Transcriptomic Sequencing of CAR-T-Treated Patients

  Chimeric Antigen Receptor (CAR)-T cell therapy has revolutionized the treatment of hematologic malignancies. Approximately half of patients with refractory large B-cell lymphomas achieve durable responses from CD19-targeting CAR-T treatment; however, failure mechanisms are identified in only a fraction of cases. Here we use next-generation sequencing technologies to characterize the genomic and transcriptomic features of CAR-T cells and tumors that influence therapeutic responses. Please see our submission to NCBI GEO (GSE273170) for additional data.

  Study phs002922

• Targeted sequencing of genomic regions of interest in depression and obesity

  This study aimed to further explore the genetic relationship between MD and obesity taking advantage of targeted sequencing strategy. Specifically, we searched for genetic risk variants across the entire frequency spectrum in flanking genomic regions and genes previously associated with MD and obesity, assessed the contribution of those variants to the pathophysiology of comorbid MD and obesity, and provided a general overview of the cellular and molecular pathways mapped by those variants when these complex diseases co-occur.

  Study EGAS50000000330

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  Data generated through single nuclei ATAC sequencing on whole ganglionic eminences from 3 human fetuses (two of 16 and one of 17 gestational weeks). Tissue was acquired from the MRC-Wellcome Trust Human Developmental Biology Resource with ethical approval. snATAC-Seq libraries were prepared from ~8,000 nuclei per sample using Chromium Next GEM Single Cell ATAC (v1.1) reagents (10X Genomics). Quality control of libraries was performed using the Agilent 5200 Fragment Analyzer before sequencing on an Illumina NovaSeq 6000 to a depth of at least 617 million read pairs per library. Raw sequencing data were converted into FASTQ files. For a full description of data generation, please see Cameron et al, Schizophrenia Bulletin 2024, https://doi.org/10.1093/schbul/sbae083. Please note that 10X generated BAM files, rather than FASTQ files, have been uploded. FASTQ files can be regenerated using the 10X Genomics bamtofastq tool. https://support.10xgenomics.com/docs/bamtofastq

  Dataset EGAD50000000601

• RNA sequencing from patient-derived intestinal organoids

  RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Study EGAS50000000338

• Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid

  In this study, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the cell-free DNA in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected 20 cerebrospinal fluid samples of pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. For 11 patients in this study we collected matched tumor DNA. This cohort contains fastQ files of cfRRBS data of these samples.

  Study EGAS50000000377

• WES of breast cancer patients and controls

  This study assessed the variant profiles of 408 samples from 126 breast cancer patients with various survival outcomes, including paired uninvolved mammary gland samples collected at proximal distances from primary lesions. As a reference, control samples from 15 mammoplasty individuals without cancer history were studied. Whole exome sequencing was performed to identify post-zygotic and germline variants present in the studied samples. Variant annotation in known databases, interpretation, and statistical analyses followed to discern the clinical relevance of called variants.

  Study EGAS50000000539

• Genomic Data Access Committee for Early and Late Onset Colorectal Cancer Study

  This Data Access Committee (DAC) manages access to genomic data generated from the study "A Clinically and Genomically Annotated Early Onset Colorectal Cancer and Late Onset Colorectal Cancer." The study focuses on identifying the distinct genomic profiles of early-onset colorectal cancer (EOCRC) compared to late-onset colorectal cancer (LOCRC) through whole-genome sequencing (WGS) of both tissue and blood samples. The DAC is responsible for reviewing and approving access requests from researchers who wish to utilize this data for non-commercial, academic purposes related to colorectal cancer research. The committee ensures that all data access is granted in compliance with ethical standards and that the data is used solely for the approved research objectives. Researchers requesting access to this data must provide a detailed research proposal, institutional review board (IRB) approval, and demonstrate relevant expertise in genomic research. All data will be stored in secure, encrypted environments, and any further sharing or use of the data requires additional DAC approval.

  Dac EGAC50000000359

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Study EGAS50000000666

• WGS data for EBiSC iPSC lines

  The European Bank for Induced Pluripotent stem cells (EBiSC) is designed to address the increasing demand by iPSC researchers for quality-controlled, disease-relevant research grade iPSC lines, data and cell services. In this study Whole Genome Sequencing was performed on a selection of lines from the project.

  Study EGAS50000000742

• The Genetic Landscape of Familial Pulmonary Fibrosis

  This dataset was collected from a study that was designed to identify disease-causing rare genetic variants in individuals with Familial Interstitial Pneumonia (FIP). Subjects were identified from our ongoing FIP Registry (IRB #020343), where FIP is defined as idiopathic interstitial lung disease (ILD) in two or more family members with at least one affected individual diagnosed with idiopathic pulmonary fibrosis (IPF). Whole exome sequencing was performed on ~600 affected members from 525 kindreds using genomic DNA isolated from peripheral blood.

  Study phs003750

• Childhood Cancer Data Initiative (CCDI): CCDI Pediatric In Vivo Testing Program - Leukemia

  The goal of this study is to molecularly characterize a large panel of pediatric acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) previously established in immune-deficient mice. These PDXs are utilized as part of the NCI-funded Pediatric Preclinical In vivo Testing (PIVOT) program to identify novel agents and combinations. Biospecimen data include next-generation sequencing (RNAseq, whole exome sequencing, DNA copy number variation), whole-genome analysis of cytogenetic abnormalities, and DNA fingerprint for quality control.

  Study phs003164

• Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL)

  Enteropathy associated T cell lymphoma (EATL) is frequently preceded by a state of refractoriness to the gluten-free diet, called “refractory celiac disease” or RCD. We aim to study which mutations and copy number aberrations are already manifest in RCD and to identify differences between RCD patients that do, and do not, develop EATL. We have applied whole exome sequencing to detect mutations and copy number aberration predictive for progression from RCD to EATL.

  Study EGAS00001006669

• CARE idiopathic subglottic stenosis bulk transcriptomics.

  Idiopathic subglottic stenosis (iSGS) is a severe chronic orphan disease characterised by recurrent scarring of the subglottis, predominantly affecting Caucasian females in their fourth to sixth decade of life. Due to its rarity, understanding the clinical trajectory and molecular factors involved in iSGS disease development and prognosis has been challenging. In this study, we prospectively enrolled patients with iSGS, trauma-induced subglottic stenosis, and controls to investigate the clinical, transcriptional, and genetic features that may be associated with disease pathogenesis and treatment outcomes.

  Study EGAS50000000879

• Kids First: Whole Genome Sequencing Studies of Multiplex Nonsyndromic Cleft Lip/Palate Families

  Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect that affects approximately 135,000 newborns worldwide, and imposes significant medical, psychosocial and financial burdens to affected individuals and their families. Genetic variation in numerous genes has been associated with NSCLP, however the exact mechanisms by which they contribute to the condition remain largely unknown. Here, we will use whole genome sequencing and robust analytical approaches to systematically evaluate the causes of NSCLP in 923 individuals from large multigenerational families.

  Study phs002626

• SweGen genetic variation from the Northern Sweden Population Health Study

  The dataset contains files with single nucleotide variants in VCF format for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

  Dataset EGAD50000001324

• SweGen whole-genome sequencing from the Northern Sweden Population Health Study

  The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

  Dataset EGAD50000001325

• INCLUDE: Human Trisome Project

  The INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project is an NIH-wide collaboration that seeks to improve health and quality-of-life for people with Down syndrome. The INCLUDE Project Data Coordinating Center and partners created the INCLUDE Data Hub, a centralized data resource that allows access to large-scale clinical and multi-omics datasets specific to Down syndrome and supports collaborative, cloud-based analysis to accelerate scientific discoveries related to Down syndrome and its co-occurring conditions.

  Study phs002981

• Longitudinal single-cell transcriptomic study in patient-derived xenografts of pediatric T-ALL

  In this study, we conducted single cell full length total RNA sequencing (VASA-seq) on 13 matched pediatric T-ALL PDX samples at initial diagnosis and relapse, along with 5 non-relapsing PDX samples collected at initial diagnosis. We identified a subpopulation of T-ALL cells with stem-like cell features that expands substantially at relapse indicating resistance to first-line therapy. Chemotherapy resistance was further validated through functional testing: Two samples were subjected to in-vitro drug testing, treated with Cytarabine for three days, followed by single-cell transcriptomic analysis using 10x Genomics. Additionally, in-vivo drug testing was conducted on one sample, involving re-engraftment into mice and treatment with a combination of Vincristine, Doxorubicin, and Dexamethasone. Single-cell transcriptomic analysis using 10x Genomics was performed after 0, 15 and 30 days of treatment.

  Dataset EGAD50000000831

• Genome and transcriptome sequencing of cancer of unknown primary tumours

  Genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA by whole genome sequencing of tissue and cfDNA biopsies, as well as targeted genome sequencing using two panels, including Comprehensive cancer panel (CCP) and TruSight Oncology 500 (TSO500). This study also includes profiling of tumour RNA by whole transcriptome sequencing.

  Study EGAS50000000452

• Spatial heterogeneity, stromal phenotypes, and therapeutic vulnerabilities in colorectal cancer peritoneal metastasis

  Peritoneal metastases (PM) in colorectal cancer (CRC) portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PTs) from PMs and actionable targets facilitating transcoelomic dissemination and progression. We performed multi-omic profiling of 217 samples from 136 patients, including 56 primary tumor (PT) and 120 PMs comprising 25 matched PT-PM pairs. Whole exome, and bulk RNA-seq analysis was conducted to identify underlying genomic aberrations and transcriptomic differences between primary and peritoneal lesions.

  Study EGAS50000000813

• South African Blood Regulatory (SABR) Resource

  Functional genomics resources are critical for interpreting human genetic studies, however they are predominantly from European-ancestry individuals. Here we present the South African Blood Regulatory (SABR) resource, a map of blood regulatory variation that includes three South Eastern Bantu-speaking groups. Using paired whole genome and blood transcriptome data from over 600 individuals, we map the genetic architecture of 40 blood cell traits derived from deconvolution analysis, as well as expression, splice, and cell type interaction quantitative trait loci (QTL).

  Study EGAS50000001008

• Activation-Induced Marker (AIM) Sequencing of Healthy Human T Cells

  T cells from five healthy human donors were stimulated with a peptide pool (CEFX, JPT) and anti-CD28/CD49d co-stimulation. Cells were then sorted based on activation (OX40 and PD-L1 for CD4s, CD137 for CD8s) and labeled with corresponding hashing antibodies prior to sequencing. In total, this dataset encompasses 42,370 cells (12,743 activation-induced marker (AIM)-positive, 15,369 AIM-negative, 14,258 Mock) for CITE-sequencing and TCR-sequencing of sorted activated, unactivated, and mock T cells derived from blood.

  Study phs004043

• Studies of L1-mediated Pseudogene Formation in Human HeLa Cells

  Alu elements mobilize from one genomic location to another by a "copy-and-paste" mechanism known as retrotransposition, which requires the human Long INterspersed Element-1 (LINE-1 or L1) ORF2-encoded protein (ORF2p); however, little is known about other cellular factors required for Alu retrotransposition. Isolates of HeLa cells differ in their ability to support Alu retrotransposition. Here, we generated Illumina whole genome sequencing data derived from four HeLa isolates: HeLa-H1, HeLa-CCL2, HeLa-HA, and HeLa-JVM.

  Study phs003397

• Tumor-associated neutrophil 1 precursors impair homologous DNA repair and promote sensitivity to PARP-inhibition

  Tumor evolution is one of the major mechanisms responsible for acquiring therapy resistant and more aggressive cancer clones. Whether the tumor microenvironment through immune-mediated mechanisms might promote the development of more aggressive cancer types is crucial for the identification of additional therapeutical opportunities. Here, we identify a subset of tumor-associated neutrophils, defined as tumor-associated neutrophil precursors (PreNeu). These PreNeu are enriched in highly proliferative hormone-dependent breast cancers and impair DNA repair capacity

  Study EGAS00001008154

• Observational studies using advanced analytical techniques to understand the biological functions of kidney component cells

  The purpose of this study is to establish a foundation for understanding the functions of kidney component cells and the biology of renal disease. Single cell and spatial transcriptome analyses of human kidney component cells will be performed to analyze the gene expression profiles of those cells and explore their relationship between the gene expression profiles and clinical parameters. The research foundation established here is worthwhile for understanding disease mechanisms in the kidney or discovering novel therapeutic drugs for renal disease.

  Study JGAS000736

• Application of targeted long-read methylation sequencing to dissected lung cancer tissues

  To investigate DNA methylation patterns within the tumor microenvironment, multiple regions were dissected from fresh-frozen sections of two lung adenocarcinoma specimens using the Millisect system. These regions were annotated based on spatial transcriptome data. DNA samples extracted from these regions were subjected to targeted long-read methylation sequencing using t-nanoEM. To establish a control dataset, short-read whole-genome sequencing (WGS) was performed on the tumor and normal parts, and long-read WGS was performed on the tumor part.

  Study JGAS000757

• Transcriptome and epigenomic landscape of cytotrophoblasts from normal and HDP placentas

  Hypertensive isorders of pregnancy (HDP) is a severe pregnancy-related disorder that poses significant risks to both maternal and fetal health. Dysfunctional placental development is one of the major contributors to the onset of HDP. In this study, we investigated the gene expression and epigenomic modifications in cytotrophoblasts from normal and HDP placentas. The information obtained in this study contributes to the growing body of knowledge aimed at improving the diagnosis, management, and treatment of HDP.

  Study JGAS000667

• Genomic analysis of HGSOC using long read sequencing

  High-grade serous ovarian cancer (HGSOC) is characterized by widespread genomic instability, but genomic and epigenomic alterations within repetitive regions remain poorly understood. This study aims to investigate genomic and epigenomic variations in HGSOC using Oxford Nanopore long-read sequencing technology. High-molecular-weight DNA was extracted from cryopreserved, pre-treatment tumor samples and matched blood specimens. The objectives include developing a robust long-read sequencing analysis pipeline, identifying novel genomic and epigenomic variations, and exploring potential applications in future clinical and basic research.

  Study EGAS50000001036

• Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application

  We established hypoimmunogenic human induced pluripotent stem cells (iPSCs) to minimize the immune rejection caused by mismatches of HLA type. Here, we optimized the protocol for good manufacturing practice (GMP)-compatible CRISPR-Cas9 genome editing to deplete the three gene locus (HLA-A, HLA-B, and CIITA genes) simultaneously in HLA homozygous iPSCs. RNA-seq and flow cytometry analyses confirmed the successful depletion of HLAs, and lineage-specific differentiation into cardiomyocytes was verified.

  Study EGAS50000001194

• PEVOsq

  The PEVOData PEVOsq basket trial is an open-label, multi-center, phase II trial investigating the combination of pembrolizumab (an immune checkpoint inhibitor) with vorinostat (a histone deacetylase inhibitor). This trial focuses on treating patients with recurrent or metastatic squamous carcinomas, including cancers of the cervix, head and neck, anus, vulva/vagina, penis, and lung. The aim is to evaluate the efficacy and safety of this combination, with pembrolizumab administered every 3 weeks and vorinostat daily. Outcomes include overall response rate and progression-free survival.

  Study EGAS50000000731

• An Ultrasensitive Method for Detection of Cell-Free RNA

  Our study describes the development of a novel method for cell free RNA (cfRNA) analysis called RARE-Seq (Random priming & Affinity capture of cell-free RNA fragments for Enrichment analysis by Sequencing). We find RARE-Seq improves the limit of detection for tumor-naïve cancer detection while maintaining high specificity. We explore the potential utility of RARE-Seq in diverse clinical applications, including non-invasive ctRNA genotyping, treatment resistance monitoring, and molecular characterization of non-malignant conditions.

  Study phs004091

• Emirati Diploid Single Samples Assemblies

  This study, as part of the Emirati Genome Project, aims to establish a foundational pangenome reference to advance precision medicine in the United Arab Emirates. We are generating single-sample diploid whole genome assemblies for 30 Emirati nationals using deep PacBio HiFi sequencing. This process yielded 60 distinct assemblies representing both the maternal and paternal genomes for each individual. The resulting high-quality reference will capture the unique genetic landscape of the Emirati population, thereby accelerating translational research and genomic discovery.

  Study EGAS50000001233

• Single cell RNA sequencing of mononuclear cells from synovial fluid of patients with rheumatoid arthritis

  Mononuclear cells were collected from synovial fluid of anti-citrullinated positive antibodies (ACPA)-positive rheumatoid arthritis patients (n=8) and ACPA-negative RA patients (n=8). Global cell types (i.e., no enrichment) were obtained from these cryopreserved synovial fluid mononuclear cells (SFMC) samples and immediately fixed and processed using the GEM-X Flex Gene Expression Reagent Kits (10x Genomics) according to protocol. Following Gel Bead-in Emulsion (GEM) generation, samples were processed using the standard manufacturer’s protocol. Once sequencing libraries passed standard quality control metrics, libraries were sequenced on an Illumina NextSeq2000 P4 100 cycle reagent kit with the following read structure: R1: 28, R2: 90, I1: 10, I2: 10. Libraries were sequenced to obtain a read depth greater than 10,000 reads/cell for gene-expression (GEX). FASTQ files are made available. More detailed information can be obtained in Argyriou A. et al, Annals of the Rheumatic Disease, 2025.

  Dataset EGAD50000001801

• Genetic Legacy of Punan Hunter-Gatherer Groups in Indonesian Borneo

  Punan Batu (the “Cave Punan”), the last living nomadic hunter-gatherer (HG) group who still literally live under karst rock shelters in Borneo, is the least-known hunter-gatherer society in Asia. To provide insights on the origin and adaptation of the Cave Punan, here we present the autosomal genome-wide SNPs study of the Cave Punan, including other Punan groups who speak different language from the Cave Punan, which are transitioning into a more sedentary lifestyle.

  Study EGAS00001004471

• genetic analysis of carcinogenesis in GAPPS

  Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal dominant syndrome characterized by polyposis localized in the gastric body and fundus with a strong tendency for adenocarcinoma. The genetic mutations that accumulate during the progression from normal mucosa through fundic gland polyps (FGPs) to carcinoma in GAPPS remain unclear.We investigated the evolutionary process from normal mucosa to FGPs and carcinoma in GAPPS. Through comprehensive mutational and transcriptome analyses, we aimed to provide insights into the biology of this disease.

  Study JGAS000843

• RNAseq of MCL cell lines

  This study provides bulk RNA sequencing data from Mino and Jeko-1 mantle cell lymphoma (MCL) cell lines treated with CDK9 inhibitors, including the novel compound YX0798. CDK9 is a key regulator of RNA polymerase II–mediated transcription, and its inhibition disrupts transcriptional programs critical for tumor survival. The dataset captures transcriptomic changes associated with CDK9 inhibition, including downregulation of oncogenic drivers such as MYC and MCL-1. These data support mechanistic studies of transcriptional reprogramming and therapeutic vulnerability in aggressive MCL.

  Study EGAS50000001089

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

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

  Study EGAS50000001350

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• Targeted exome sequencing identify compound heterozygous TYK2 mutations in patients with primary immunodeficiency who developed EBV-associated lymphoma

  In this study, we evaluated 2 siblings with primary immunodeficiency who developed EBV-associated lymphoma. Immunophenotyping of PBMCs revealed that both patients had significant T cell lymphopenia characterized by low na?ve CD4+ T cell counts. To identify the causative genetic mutations in the patients, we performed targeted exome sequencing using the Illumina MiSeq on the patients and their parents. The results showed a novel compound heterozygous mutations in the gene encoding tyrosine kinase 2 (TYK2) in the patients.

  Study JGAS000098

• Identification of therapeutic target molecules for prostate cancer by using next generation sequencer

  Comprehensive transcriptional characterization of cancer tissues can reveal important molecular signatures associated with the disease progression. Long non-coding RNA (LncRNA) has a diversity of functions such as transcription, epigenetic and gene regulation in cancer cells including prostate cancer cells. Here, we performed directional RNA-sequence (RNA-seq) on clinical samples obtained from prostate cancer (PC) and lethal castration-resistant PC (CRPC) patients to identify novel molecular signatures including protein coding genes and non-coding RNAs induced in CRPC tissues.

  Study JGAS000198

• Single-cell RNA sequencing of human omental tissue in benign and metastatic ovarian cancer

  To elucidate the cellular and molecular mechanisms underlying omental homeostasis and its transformation during ovarian cancer metastasis, a human omental cell atlas was generated encompassing both benign and metastatic conditions. Single-cell RNA sequencing was performed on freshly dissociated omental tissue samples from patients with newly diagnosed benign and malignant disease. Samples collected during diagnostic surgery covered distinct anatomical regions, enabling comparison between non-metastasized omentum and sites along the metastatic gradient, including distant, peritumoral, and tumor core areas.

  Study EGAS50000001465

• WES sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan.

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous mutational profiles with whole exome sequencing for 46 xenografts with known response to irinotecan.

  Study EGAS50000001484

• Bulk RNA sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous expression profiles with bulk RNAseq for 38 xenografts with known response to irinotecan.

  Study EGAS50000001485

• Variability in immune response genes and prediction of severe SARS-CoV-2 infection (INMUNGEN-Cov2 project)

  Genetic factors may contribute to explain the variable clinical response to SARS-CoV-2 infection. To this end we sequenced the DNA of 392 COVID-19 patients from Spain. Whole Exome Sequencing (WES) was performed at two different sequencing centers. Half of the samples were sequenced at a commercial service, NIMGenetics, whereas the other half were sequenced by the EASI-Genomics consortium. Finally, Variant Call Format (VCF) files for each sample was also obtained.

  Study EGAS50000000066

• ERDERA Diagnostic Research Workstream - WES reanalysis (distributed approach)

  The ERDERA Diagnostic Research Workstream – WES reanalysis (distributed approach) aims to improve diagnostic yield by systematically reanalyzing existing whole exome sequencing (WES) data from rare disease cases. The goal is to apply updated bioinformatics pipelines, novel variant interpretation tools, and the latest reference databases to detect clinically relevant variants that may have been missed in earlier analyses. By using a distributed approach across multiple expert groups, the project fosters collaborative interpretation and knowledge sharing to enhance diagnostic outcomes for patients.

  Study EGAS50000001514

• Immune activation in the tumor microenvironment of renal cell carcinoma

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

  Study EGAS50000001349

• Access to "A Spatially Resolved Single-Cell Atlas of the Human Fetal Olfactory System"

  The human nasal region arises from neural crest and placodal lineages, yet its early development remains poorly understood owing to limited fetal tissue access and structural complexity. Here we present an integrated single-nucleus and spatial transcriptomic atlas of the human fetal nasal region, generated from 10 fetuses (males and females) between 7 and 12 post-conceptional weeks. Single-nucleus RNA sequencing resolved 32 distinct cell types, while integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) enabled spatial and temporal mapping of gene expression dynamics across the olfactory epithelium (OE) and adjacent tissues. We identify novel markers of olfactory sensory neuron differentiation and pathways governing epithelial patterning and OE morphogenesis. Notably, spatially organized expression of 169 olfactory receptor genes reveals molecular evidence for the “one neuron-one receptor” principle during the first trimester. Together, this work establishes the first molecular and spatial framework of early human olfactory development and provides a foundational resource for studies of sensory neurogenesis and congenital disorders.

  Dac EGAC50000000688

• Insights into Adult Gut Microbiota Composition Using the Estonian Cohort

  This study explores the gut microbiota of 1,826 adult individuals, predominantly from the Estonian population. The cohort includes 16S rRNA gene V4 region amplicon sequencing data along with metadata, such as age, sex, health status, anthropometric parameters, and stool consistency. The research aims to characterise the microbial community structure, identify distinct enterotypes, and examine their associations with host characteristics. The dataset provides a valuable reference for understanding gut microbiota composition and supports research in personalised nutrition and lifestyle-related health strategies.

  Study EGAS50000001611

• Tools

  EGA Tools This page provides details of the applications available at the EGA. Submission Tool Description EgaCryptor Encrypt and create md5sum values. Crypt4gh Encrypt, decrypt or re-encrypt files. INBOX Upload your files once encrypted. FTP Upload your files once encrypted. Submitter Portal Submit and manage your submission metadata online (SEQUENCING AND PHENOTYPE ONLY) Submitter Portal API Submit and manage your submission metadata programmatically. Webin Submit and manage your submission metadata online (array data) Webin API Submit metadata using XML files. Aimed to array-based submissions. Star2xml Format conversion tool to transform tabular formats (e.g. spreadsheets) into EGA's XMLs. Used for large programmatic submissions. Data Access Tool Description DAC Portal Manage and control data access request. Download Tool Description PyEGA3 Download and decrypt datasets requested through your EGA web account. Live Outbox Download and decrypt datasets requested through your EGA web account. Fuse Client A quick and convenient way to browse through EGA files without the need for complete downloads. EGA QuickView A quick and convenient way to browse through EGA files without the need for complete downloads.

  Documentation tools

• Khoe-San Genome Project

  The dataset contains BAM files of whole genome sequencing data of African Khoe-San population (n=169, 30X coverage) recruited from South Africa and Namibia. The population captured the true extent of human genetic diversity as represent the earliest diverged human population. The project described a detailed divergence of human population and identified positive selections associated forager lifestyles in Khoe-San population. These findings emphasise an inclusive catalogue with better representation of the earliest human genomic diversity to better advance biomedical research.

  Study EGAS50000001408

• RNA sequencing of CD8 T cells from melanoma patients prior to and during checkpoint immunotherapy and untreated healthy controls

  We are interested in inter-individual variation in transcriptional response to immune checkpoint blockade. We have analysed poly A purified RNA expression from CD8 T cells (297 transcriptomes in total) isolated from metastatic melanoma patients (n=106) prior to and during treatment with either single agent (Pembrolizumab) or combination (Ipilimumab/ Nivolumab) immune checkpoint blockade. We compare expression at different stages of treatment and additionally contrast this with that from healthy controls (n=68).

  Study EGAS00001004081

• Genomic, transcriptomic and epigenomic profiling of GCTB

  Giant cell tumor of bone is a rare bone neoplasm driven by oncogenic hotspot G34W/L/V mutations in the non-canonical histone variant H3.3. This study provides primary data of genomic (WGS), transcriptomic (RNA-seq) and epigenomic (histone mark ChIP-seq, WGBS, ATAC-seq) profiling of primary GCTB samples from several cohorts in Germany and Korea. We confirm the H3.3-G34 mutations as sole genetic drivers of GCTB, and describe the epigenetic alterations in mutant GCTB stromal cells.

  Study EGAS00001003730

• cfDNAme allows early prediction of PE

  Preeclampsia (PE) is a leading cause for peripartal morbidity, especially if developing early in gestation. To enable prophylaxis to prevent PE, it is essential that pregnancies at risk of PE are identified early, in the first trimester. To identify patients at risk, we profiled methylomes of plasma-derived cell-free DNA (cfDNA) from pregnant women. We detected DNA methylation differences between control and PE pregnancies that enable risk stratification of patients, at PE diagnosis but also presymptomatically, around 12 weeks of gestation.

  Study EGAS00001007071

• Investigating genetic susceptibility to rheumatic heart disease in Oceania

  This case-control study investigated susceptibility to rheumatic heart disease in over 3,000 individuals recruited across eight Oceanian countries. Cases were patients with rheumatic heart disease and controls were members of the general population. In addition to the Illumina HumanCore-24 BeadChip genotyping, a subset of 128 samples were analysed using the higher density Illumina HumanOmniExpressExome BeadChip of which 64 were also analysed using low coverage sequencing with the Illumina HiSeq 4000 platform.

  Study EGAS00001001881

• H3Africa - Consortium WGS

  To address gaps in sequence data for some of the African populations being studied in H3Africa projects, additional sequencing has been carried out through various projects and the data are being made available. The first dataset includes a high coverage whole genome sequence dataset generated at the Baylor College of Medicine with samples provided by H3Africa PIs and collaborators, funded by the National Institutes of Health. The sequence data files are accompanied by minimal metadata, including country, ethnic group (where available) and sex.

  Study EGAS00001005972

• Exome_sequencing_of_Congenital_Heart_Disease_families_Leuven

  This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).

  Study EGAS00001000185

• Barcelona_kids_with_melanoma

  This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma.

  Study EGAS00001000733

• Mutational spectrum of highly differentiated, fusion-negative rhabdomyosarcoma (set 1).

  Pediatric PAX-FOXO1 fusion-negative rhabdomyosarcoma represents a diverse spectrum of tumors. In this study, the mutational spectrum of 22 fusion-negative rhabdomyosarcomas with high, rhabdomyoma-like levels of differentiation was evaluated using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 cancer-relevant genes. Corresponding normal tissue was not available. Discarded normal human skeletal muscle, obtained from 7 donors without tumor history, were also included in the sequencing run.

  Study EGAS00001002630

• AML_targeted_resequencing_study

  Genomic libraries will be generated from whole genome amplified genomic DNA derived from 3,000 myeloid neoplasms. Targeted capture will be performed by multiplexing 16 barcoded samples in each library. Pools of 96 DNA samples will be subjected to 1-2 lanes of HiSeq 75bp sequencing. Reads will be mapped to the current build of the human reference genome to facilitate the generation of a comprehensive catalog of somatic mutations associated with 116 known myeloid and cancer driver genes.

  Study EGAS00001000275

• Identification_of_low_frequency_variants_associated_with_ulcerative_colitis_using_whole_genome_sequencing

  2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD.

  Study EGAS00001000329

• Convergent evolution drives therapy resistance in DNA repair-deficient mCRPC

  These are FASTQ files obtained from RNA-sequencing and DNA-sequencing of tumor biopsies obtained from metastatic castration-resistant prostate tumors. Patients were treated with multiple lines of therapy with samples obtained at the time of rapid autopsy following the CASCADE protocol. Multiple biopsies were obtained from each patient under guidance of pathology. DNA were analyzed by high-depth whole genome, exome, and targeted sequencing. RNA were analyzed using a Nugen amplification protocol as described in Quigley Cell 2018.

  Study EGAS00001007147

• MeDALL epigenetics study

  MeDALL- (Mechanisms of the Development of ALLergy) is a collaborative project supported by the European Union under the Health Cooperation Work Programme of the 7th Framework programme (grant agreement number 261357).MeDALL epigenetics study includes illumina 450k methylation measurements from 4 cohorts: Infancia y Medio Ambiente (INMA), Etudes des Déterminants pré et postnatals précoces du développement et de la santé de l’ENfant (EDEN), Children’s Allergy Environment Stockholm Epidemiology study(BAMSE), and Prevention and Incidence of Asthma and Mite Allergy (PIAMA)

  Study EGAS00001002169

• Next generation sequencing of sporadic schwannomatosis samples

  Schwannomatosis (MIM #162091) is characterized by the development of multiple schwannomas without vestibular nerve involvement (which is a characteristic of neurofibromatosis type 2 - NF2). In an effort to detect novel genetic alterations predisposing to schwannomatosis, we sequenced eight tumor-blood DNA pairs from de novo schwannomatosis patients. The results of our study are present in the paper "Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants" published in Acta Neuropathologica (PMID:25008767)

  Study EGAS00001000767

• Genetic landscape of relapsed DLBCL

  Diffuse large B-cell lymphoma is a heterogenous malignancy that can arise de novo or can result from histologic transformation from indolent lymphomas. Considerable sequencing effort has been placed on determining the mutations that are common at the time of diagnosis in DLBCL but little is known about the nature of relapsed disease. We have sequenced tumour and matched normal exomes of 38 rrDLBCL patients including 25 de novo DLBCLs and 13 transformed lymphomas to identify somatic mutations and copy number alterations associated with relapse.

  Study EGAS00001001553

• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.

  Study EGAS00001001479

• Comprehensive investigation of genome architecture of gastric adenocarcinoma with whole-genome sequencing in the Chinese population.

  In this study, we performed whole-genome sequencing (WGS) of 214 paired GC tumors and adjacent normal tissues to identify novel potential biomarkers. We extracted mutational signatures which induce somatic mutations and classified GC tumors into four groups with significantly different prognosis. Moreover, we observed copy number changes and structural variations frequently occurring in some cancer related genes. Our study covers a comprehensive genetic framework that can be used in clinical trials and treatment modalities in GC.

  Study EGAS00001002404

• Hip OA Functional Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001002483

• WGS of breast cancer diagnosed during pregnancy and matched control

  The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology.

  Study EGAS00001002685

• Colorectal adenomas and carcinomas NKI-AvL TGO series Gut2009

  Colorectal cancer (CRC) develops from normal epithelium, through a benign precursor lesion called adenoma, by accumulation of genetic alterations affecting oncogenes and tumour suppressor genes. These CRC-related genomic alterations often result in specific RNA-expression patterns. RNA isolated from fresh frozen specimen of 32 adenomas and 29 CRCs was obtained from the previously published study (Carvalho et al. 2009) and RNA-sequencing was performed with the aim to examine RNA expression changes in colorectal adenoma-to-carcinoma progression.

  Study EGAS00001002758

• Mutational spectrum of highly differentiated, fusion-negative rhabdomyosarcoma (set 2).

  Pediatric PAX-FOXO1 fusion-negative rhabdomyosarcoma represents a diverse spectrum of tumors. In this study, the mutational spectrum of 22 fusion-negative rhabdomyosarcomas with high, rhabdomyoma-like levels of differentiation was evaluated using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 cancer-relevant genes. Corresponding normal tissue was not available. Discarded normal human skeletal muscle, obtained from 7 donors without tumor history, were also included in the sequencing run.

  Study EGAS00001002771

• Genomic profiling of matched well differentiated and de-differentiated liposarcoma.

  Well-differentiated (WD) and de-differentiated (DD) liposarcoma, subtypes of adipocytic sarcomas, are pathologically and clinically dissimilar, but are poorly distinguishable at the molecular level. These tumors harbor neochromosomes formed from amplifications and rearrangements of chr12q. Nineteen selected patients with matched WD and DD tumors underwent extensive exomic and transcriptomic profiling to distinguish genomic features between the two subtypes. Shared point mutations suggest a common tumor origin and de-differentiated tumors have higher burdens of deletions.

  Study EGAS00001002807

• Genetic_background_for_the_major_psychiatric_disorders_in_the_general_Finnish_population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers.

  Study EGAS00001000162

• Genomic profiling of paediatric glioma cell lines

  Although paediatric gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular profiling of paediatric glioma cell lines KNS42, SF188, UW479, RES259 and RES186.

  Study EGAS00001003006

• Single cell sequencing of endoscopic biopsies from Barrett's oesophagus and proximal tissue from the normal GI tract

  Barrett’s oesophagus is a precursor of oesophageal adenocarcinoma. In this common condition, squamous epithelium in the oesophagus is replaced by columnar epithelium in response to acid reflux. Barrett’s oesophagus is highly heterogeneous and its relationships to normal tissues are unclear. We investigated the cellular complexity of Barrett’s oesophagus and the upper gastrointestinal tract using RNA-sequencing of single cells from multiple biopsies from six patients with Barrett’s oesophagus and two patients without oesophageal pathology.

  Study EGAS00001003144

• SNP arrays for chemotherapy response project

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). Illumina SNP arrays (760k markers) were performed using DNA from 49 tumors and associated germline DNA (49x median coverage). Data provided here consist of 98 files.

  Study EGAS00001004519

• Neuromics / RD-Connect - Huntington's disease

  This study contains omics datasets from the Neuromics project (www.rd-neuromics.eu) on rare neuromuscular and neurodegenerative disorders. Data includes BAM and VCF files from whole-exome sequencing and standardised phenotypic data mapped to the human phenotype ontology (HPO). In some cases proteomic, transcriptomic and metabolomic data may also be available. This study groups together datasets from individuals with a Huntington's disease phenotype and also includes some unaffected family members. Search under the Neuromics name to find related studies for other neuromuscular and neurodegenerative disorders.

  Study EGAS00001000698

• Genomic_landscape_of_liver_cirrhosis

  We are interested in the genomic landscape of liver cirrhosis and its potential manifestations for liver physiology and risk for hepatocellular carcinoma. Previous work in CASM has shown that there is a strong element of clonality within cirrhotic nodules and that some recurring mutations have been identified. However how this relates to the overall liver is not known and therefore by taking geographically disparate biospies, we aim to correlate our findings and make conclusions as to the characteristics of the overall genomic landscape.

  Study EGAS00001004329

• Bulk RNAseq gene expression of baseline tumors from metastatic urothelial bladder cancer patients (IMvigor210) and metastatic renal cell carcinoma (IMmotion150)

  We examined tumors from a large cohort of patients with metastatic urothelial bladder cancer (mUC) and metastatic renal cell carcinoma (mRCC) treated with an anti-PD-L1 agent (atezolizumab) and found that high tumor IL8 gene expression was associated with worse overall survival (OS). We further identified the tumoral immune presence based on Teff signature. We found that high tumor IL8 expression continued to be associated with worse OS even in inflamed tumors in mUC and mRCC.

  Study EGAS00001004386

• Multi-omics analysis of primary glioblastoma cell-lines shows recapitulation of pivotal molecular features of parental tumors

  Glioblastoma (GBM) is the deadliest primary brain cancer in adults. Emerging innovative therapies hold promise for personalized cancer treatment. Improving therapeutic options depends on research relying on relevant preclinical models. In this line we have established in the setting of the GlioTeX project (GBM and experimental therapeutics), a GBM-patient derived cell line library (GBM-PDCL). Multi-OMIC approach was used to determine the molecular landscape of PDCL and the extent to which they represent GBM tumors.

  Study EGAS00001001871

• Genetic ancestry contributes to somatic mutations in lung cancers from admixed Latin American populations

  Inherited lung cancer risk, particularly in non-smokers, is poorly understood. Genomic and ancestry analysis of 1,153 lung cancers from Latin America revealed striking associations between Native American ancestry and their somatic landscape, including tumor mutational burden (TMB), and specific driver mutations in EGFR, KRAS, and STK11. A local Native American ancestry risk score predicted EGFR and KRAS mutation frequency more strongly than global ancestry, suggesting that germline genetics (rather than environmental exposure) underlie these disparities.

  Study EGAS00001004752

• Whole genome sequencing of primary and metastatic Melanoma cases in an Australian cohort.

  Melanoma is the fourth most common cancer in Australia and the leading cause of cancer death in young adults. The Australian Melanoma Genome Project (AMGP) is analysing whole genomes from melanomas. We include the results of whole genome sequencing (WGS) for a number of datasets that include cutaneous, acral and mucosal melanoma subtypes.

  Study EGAS00001001552

• Mutations conferring differential treatment response in breast cancer

  Poor prognosis primary breast cancer patients usually receive cytotoxic chemotherapy as a component of treatment, but despite this aggressive therapy recurrences remain common. Improved understanding of chemoresistance pathways would allow better stratification of chemotherapy using predictive markers, and may allow therapeutic inhibition of resistance mechanisms in order to chemosensitise tumours. We aimed to identify molecular pathways that define chemoresponse using the novel approach of examining the selection exerted by neoadjuvant chemotherapy on sub-clonal somatic mutational profiles of cancer cells.

  Study EGAS00001003626

• Paired exome analysis in urothelial carcinoma

  In this study we characterized genomic alterations in two to five metachronous tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth), Ultra deep targeted sequencing (~6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor.

  Study EGAS00001001686

• Reconstruction of human phylogenetic trees using single-cell genome sequencing

  The trillions of cells that constitute the human body are developed from a fertilized egg through embryogenesis. However, cellular dynamics and developmental outcomes of embryonic cells remain to be largely unknown due to the technical and ethical challenges. Here we sequenced whole-genomes single-cell-derived clones and various bulk tissues dissected from entire human bodies. Using the discovered somatic mutations as an intrinsic barcode, we reconstructed cellular phylogenetic trees that provide novel insights into early human embryogenesis.

  Study EGAS00001004824

• Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer

  Brain metastasis (BM) of colorectal cancer (CRC) is rare but lethal, and lacks effective therapies or a good understanding of its genomic landscapes. We conduct an analysis of whole-exome sequencing (WES) and whole-genome sequencing (WGS) data on 19 trios of patient-matched BMs, primary CRC tumors, and adjacent normal tissue to (1) document genomic signatures during the evolution of CRC BM; (2) identify clinically actionable targets for the BM treatment; and (3) identify potential drivers in CRC BM.

  Study EGAS00001003659

• Knee_OA_Functional_Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of knee osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001001899

• Targeted panel data for newly diagnosed myeloma patients.

  Genomic abnormalities in MM are common and can affect a patients outcome. Here we have performed targeted sequencing on xx patient tumor samples and matched control DNA. The targeted panel consists of ~160 genes and copy number regions, as well as key regions of chromosomal translocation including IGH, IGK, IGL and MYC. Using mutation, copy number, and translocation information we have been able to identify abnormalities that affect prognosis including bi-allelic inactivation of TP53 and rearrangements involving MYC.

  Study EGAS00001002859

• RNA sequencing in blood samples of cluster headache patients

  Cluster headache is a relatively rare headache disorder, typically characterized by multiple daily, short-lasting attacks of excruciating, unilateral (peri-)orbital or temporal pain associated with autonomic symptoms and restlessness. To better understand the pathophysiology of cluster headache, we used RNA sequencing to identify differentially expressed genes and pathways in whole blood of patients with episodic (n = 19) or chronic (n = 20) cluster headache in comparison with headache-free controls (n = 20). Blood samples were subjected to globin reduction before sequencing.

  Study EGAS00001001918

• Discovering genetic causes of optic atrophy syndromes through whole exome sequencing

  The genetic defects leading to optic atrophy range from mitochondrial DNA (mtDNA) point mutations in Leber’s hereditary optic neuropathy (LHON), to dominant and recessive mutations affecting a cluster of nuclear genes implicated in mitochondrial dynamics. We performed WES in patients with an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions, to identify the genetic causes of this syndrome.

  Study EGAS00001003850

• High-grade serous ovarian cancer refined with single-cell RNA-sequencing

  We performed single-cell RNA-sequencing of 18,403 cells unbiasedly collected from 7 treatment-naive HGSOC tumours. For each phenotypic cluster of tumour or stromal cells, we identified specific transcriptomic markers. Next, we explored which phenotypic clusters correlate with overall survival based on expression of these transcriptomic markers in 1467 bulk RNA-seq tumours. By evaluating molecular subtype signatures in single cells, we assessed to what extent a phenotypic cluster of tumour or stromal cells contributes to each molecular subtype.

  Study EGAS00001004987

• Relapse series of two Pediatric ALL patients

  In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. In patient 1, who experienced two relapses, the analysis unraveled a continuous interplay of aberrant AID/APOBEC-associated activities. Patient 2 had three relapses. We identified episodic mutational processes at diagnosis and first relapse leading to mutations resembling UV light-driven DNA damage, and thiopurine-associated damage at first relapse.

  Study EGAS00001005001

• The_British_Autozygosity_Populations_BioResource

  This data set contains whole exome sequences of 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. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002742

• Comprehensive molecular profiling of high-grade serous ovarian cancer

  The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC) is not well understood. Here, we performed comprehensive molecular analysis, including high-pass whole genome sequencing, targeted deep sequencing, RNA sequencing, reverse phase protein arrays and immune assessment, on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent or poor response.

  Study EGAS00001003804

• Solve-RD Solving the Unsolved Rare Dieseases

  Solve-RD – solving the unsolved rare diseases is a research project funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257 from 1 January 2018 to 31 March 2024. Six European Reference Networks (ERNs; ERN-RND, -ITHACA, -EuroNMD, -GENTURIS, -RITA and -EpiCare) contributed data and samples to one or more of the four cohorts for data re-analysis and novel omics. For more information see https://solve-rd.eu/results/solve-rd-data/.

  Study EGAS00001003851

• Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples

  Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no comprehensive and direct accuracy evaluations of these tools is published. Here, we evaluate and determine the precision of five commonly used computational NIPT aneuploidy analysis tools, considering diverse sequencing depth (coverage), arbitrary sequencing read placement, and fetal DNA fraction on clinically validated NIPT samples.

  Study EGAS00001005323

• COVID_19_Challenge_Project_Single_Cell_Profiling

  Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection

  Study EGAS00001005696

• The distinct DNA methylome of acute lymphoblastic leukemia

  Here, using whole genome bisulfite sequencing (WGBS) data of over one hundred patients from multiple subtypes of acute lymphoblastic leukemia (ALL), controls samples and ALL cell lines, we show that in contrast to the prevailing paradigm, ALL samples exhibit CpG island hypermethylation but little to no global loss of methylation. The subtype-specific CpG island hypermethylation levels in T cell ALL span a broad range of methylation levels rather than previous binary classifications and are influenced by multiple factors, including TET2 expression.

  Study EGAS00001005203