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• 2014_Lung_sq_WES

  Purpose Lung squamous cell carcinoma (SqCC) is the second most prevalent type of lung cancer. Currently, no targeted-therapeutics are approved for treatment of this cancer, largely due to lack of systematic understanding of the molecular parthenogenesis of the disease. To identify therapeutic targets and comparatively analyze them in lung SqCC, we probed somatic alterations of Korean lung SqCC. Patients and Methods We performed massively parallel whole-exome sequencing of 104 Korean lung SqCC patients’ samples with matched normal samples. In addition, copy number analysis and transcriptome analysis were conducted for a subset of these samples. Clinical association with cancer-specific somatic alterations was investigated.

  Study EGAS00001002844

• Genomic and ecologic characteristics of the airway microbial-mucosal complex

  Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide. Microbial communities at the airway mucosal barrier are conserved and highly ordered, reflecting symbiosis and co-evolution with human host factors. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species. We match the gene content of bacterial isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

  Study EGAS00001006689

• Linked-read based analysis of Medulloblastomas

  Medulloblastoma (MB) is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases of medulloblastomas. The molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants (SVs) in recurrently affected gene typically requires the application of long-read technologies. Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements.

  Study EGAS00001007064

• Molecular Characterization of ETMRs

  ETMRs are poorly characterized embryonal brain tumors with a dismal outcome. We collected tumors from 184 ETMR patients and 23 matched recurrences to investigate the genomic landscape of this distinct entity. Tumors without C19MC amplification, the proposed driver, harbor other miRNA related aberrations like DICER1 mutations and amplifications of the MIR17-92 miRNA cluster. All tumors behave molecularly similar and no subgrouping was observed. Whole-genome sequencing revealed an overall low recurrence of SNVs, but highly prevalent R-loop associated genomic instability. Finally, we show that targeting R-loops with TOP1 and PARP inhibitors might be an effective treatment strategy for this deadly disease.

  Study EGAS00001003256

• PAGE: Prenatal Assessment of Genomes and Exomes

  The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth.

  Study EGAS00001001713

• Sequencing data of multiple sarcoma samples for personalized medicine and endotype identification

  Sequencing data derived from multiple patient samples was used to guide multiple patient-specific experiments and identify potential therapeutic options. These diseases are rare and high-risk (undifferentiated pleomorphic sarcoma, rhabdomyosarcoma) and thus have few available validated clinical options. This leaves the population of patients with few options if, and when, standard therapy fails to cure or control disease. An aspect of the personalize therapy design included the identification of broader disease endotypes (a combination of genetic and clinical data describing patient status) to identify subgroups of the individual disease that could better define treatments and could segment patient populations for deeper preclinical research.

  Study EGAS00001003981

• Mapping_regulatory_variation_in_sensory_neurons_using_IPS_lines_from_the_HIPSCI_project

  Sensory neurons are nerve cells that are activated by sensory input such as heat, light and convey information to the brain. Although a key cell type in complex organisms, human sensory neurons are challenging to study because they are impossible to obtain from living donors. We have collaborated with the Neucentis Pharmaceutical Research Unit to differentiate sensory neuron like cells from human induced pluripotent stem cells derived as part of the Human Induced Pluripotent Stem Cells Initiative. We will sequence RNA from 100 IPS lines derived from healthy individuals and perform RNA-seq on the differentiated cells to identify noncoding variants that alter gene expression in human sensory neurons.

  Study EGAS00001001149

• Reconstruction of complex rearrangement patterns causing the initiation of clear cell renal cell carcinoma.

  The genomic hallmark of clear cell renal cell carcinoma is the loss of the short arm of chromosome three. This appears to be the earliest genomic event in the formation of these cancers. Often chromosome 3 is lost at the same time as part of chromosome 5 is duplicated via an unbalanced translocation, often with features consistent with focal chromothripsis. In this study, we sought to reconstruct the chromothriptic event that underlies the initiation of kidney cancer. We used long read sequencing (promethION, Oxford Nanopore Technologies) of patient tumour-derived DNA to elucidate how a single cell division error can generate cancer genome complexity.

  Study EGAS00001004015

• Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese Samples

  Affymetrix 6.0, Illumina OMNIExpress, and llumina Immunochip genotype data for Han Chinese population including rheumatoid arthritis cases and controls. Data is in PLINK binary format. Illumina genotype clustering was performed using Illumina’s BeadStudio software. SNPs were reclustered using the study samples, low quality subjects were removed, and a subset of clustering results were manually inspected and verified. All SNPs with GenCall scores less than 0.15 were excluded. For Affymetrix chips, clustering was performed using the program Birdseed version 2, as implemented using Affymetrix Genotyper Console v4.0, using the default quality control (QC) thresholds.

  Study EGAS00000000131

• Genome Wide Association Study:GR@ACE Stage I

  The Genome Research program at Fundacio ACE (GR@ACE, Barcelona, Spain), represents a new effort to study Alzheimer's Disease susceptibility. The GR@ACE study comprises 7,409 unrelated individuals. 4,120 AD cases were diagnosed at Fundació ACE Memory Clinic (Barcelona, Spain). 3,289 Controls were obtained from three collections (Fundació ACE, Barcelona; DNA National Biobank, Salamanca and HU Valme, Seville). Genotyping was carried out using the 815K Axiom Spain Biobank array (Affymetrix.) in the Spanish national center for genotyping (CEGEN, Santiago de Compostela, Spain). After genotyping, an extensive quality control was conducted, including re-sampling, gender match, stratification, relatedness, heterozygosity, differential missingness and HWD analyses.

  Study EGAS00001003424

• Evolution of GBM through therapy

  Primary glioblastoma (GBM) tumours recur following treatment. This is likely due to intratumour heterogeneity (ITH), which reduces the effectiveness of cancer therapies by enabling therapy-driven tumour evolution: Darwinian selection of genotypically and/or phenotypically distinct cells (subclones) that resist treatment to seed regrowth of an even less treatable recurrence. To investigate this we sequenced a pilot cohort of nine paired primary and locally recurrent GBM tumours, alongside matched blood samples, in order to begin characterising therapy resistant cells and thereby infer the mechanisms by which they evaded treatment. These data were included in the first data release from the Glioma Longitudinal AnalySiS (GLASS) consortium.

  Study EGAS00001003546

• Raw multi-omics dataset from the lungNENomics cohort of lung neuroendocrine tumours

  This study contains raw multi-omics data generated as part of the lungNENomics project, a multi-omics study aimed at deep molecular profiling of lung neuroendocrine tumours, including typical carcinoids (grade 1) and atypical carcinoids (grade 2). The study includes whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and Infinium MethylationEPIC array data from samples in the lungNENomics cohort. These raw data complement the associated processed molecular data released on Zenodo (10.5281/zenodo.19366762) and the corresponding whole-slide pathology images deposited in the EBI BioImage Archive (10.6019/S-BIAD3143). See Sexton-Oates et al medrxiv 2025 (https://www.medrxiv.org/content/10.1101/2025.07.18.25331556v1) for details.

  Study EGAS00001005979

• CONSERTING: integrating copy number analysis with structural variation detection

  We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection to achieve high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. This study contains all data for "CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data", which was previously split between EGAS00001001202 and EGAS00001001050.

  Study EGAS00001001202

• Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

  The human placenta is a dynamic and cellular heterogeneous organ, which is critical in fetomaternal homeostasis and the development of preeclampsia. Previous work has shown that placenta-derived cell-free RNA increases during pregnancy. We applied large-scale microfluidic single-cell transcriptomic technology to comprehensively characterize cellular heterogeneity of the human placentas and identified multiple placental cell-type–specific gene signatures. Analysis of the cellular signature expression in maternal plasma enabled noninvasive delineation of the cellular dynamics of the placenta during pregnancy and the elucidation of extravillous trophoblastic dysfunction in early preeclampsia.

  Study EGAS00001002449

• Whole genome sequencing data of pediatric hypodiploid acute lymphoblastic leukemia

  Hypodiploid acute lymphoblastic leukemia (ALL) is a rare subtype of B-cell ALL characterized by chromosome number < 45 , encompassing near-haploid (24–29 chromosomes) and low-hypodiploid (30–39 chromosomes) subgroups. These subgroups display distinct genetic landscapes, including Ras and receptor tyrosine kinase pathway alterations in near-haploid ALL, and frequent IKZF2, RB1, and germline TP53 alterations in low-hypodiploid ALL. Clinically, hypodiploid ALL is associated with dismal prognosis, with 5-year overall survival rates often between 50-70% in children and markedly worse in adults. Despite advances in risk stratification and MRD-guided therapy, allogeneic stem cell transplantation remains the current standard recommendation for affected patients.

  Study EGAS50000001305

• Combination Therapies for Personalised Cancer Medicine in 11-18

  This study involves mutagenizing 11-18 with ENU to identify those mutations which engender resistance to targeted treatment. In the last decade we have begun to move towards the use of targeted therapeutics in the clinic, often resulting in dramatic response rates in cancer patients. However, clinical experience has demonstrated time and time again that such responses are invariably followed by the development of drug resistance. Identification of the underlying mechanisms may enable us to reverse such resistance. Traditional methods of modelling this resistance in vitro can lead to a plethora of potential resistance mechanisms that can be difficult to decipher.

  Study EGAS00001002579

• Whole Genomes Define Concordance in Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer

  Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis of any common solid epithelial tumour. Multiple failed clinical trials necessitate newer approaches to understand the molecular etiology of this disease. Patient-derived xenografts (PDX) and patient-derived organoids (PDO) may serve as pre-clinical disease models; however, characterization remains largely unaddressed at the whole genome level. We conducted a comprehensive assessment of the genetic landscape of tumours and matched PDX and PDO from patients with PDAC. Our data show that PDX and PDO recapitulate PDAC tumourigenesis with respect to simple somatic mutations and copy number changes, and capture major structural variation events.

  Study EGAS00001002597

• Exome array analysis of adverse reactions to fluoropyrimidine-based therapy for gastrointestinal cancer

  Fluoropyrimidines, including 5-fluororacil (5FU) and its pro-drug Capecitabine, are the common treatment for colorectal, breast, neck and head cancers – either as monotherapy or in combination therapy. Adverse reactions (ADRs) to the treatment are common and often result in treatment discontinuation or dose reduction. Factors contributing to ADRs, including genetic variation, are poorly characterized. We performed exome array analysis to identify genetic variants that contribute to adverse reactions.Our final dataset consisted of 504 European ancestry individuals undergoing fluoropyrimidine-based therapy for gastrointestinal cancer. A subset of 254 of these were treated with Capecitabine. All individuals were genotyped on the Illumina HumanExome Array.

  Study EGAS00001002763

• Genome Landscape of Primary Pancreatic Ductal Adenocarcinoma

  The purpose of the Australian ICGC Pancreatic Cancer Genome Sequencing Initiativestudy is to identify the common driving mutations underlying the initiation anddevelopment of Pancreatic Adenocarcinoma in a large cohort of pancreatic cancerpatients (n=350). Matched genome sequences will be generated from normal tissue(duodenum) and resected primary tumour tissue in each patient using exome andwhole genome sequencing. The complete repertoire of somatic mutations will bedetermined (substitutions, indels, copy number changes and structural changes).Where possible, matched transcriptome sequencing will also be carried out todetermine locus activity, which mutations are actively expressed and whichrearrangements give rise to gene-fusion transcripts.

  Study EGAS00001000154

• Single-cell atlas of penile cancer reveals TP53 mutations as driver for an aggressive phenotype, irrespective of HPV status, and provides clues for treatment personalization

  Our aim was to identify molecular differences in the microenvironment of penile squamous cell carcinoma (PSCC) stratified by TP53 loss-of-function (TP53LOF) mutations and HPV-status. Hence, we present a first single-cell transcriptomic atlas of PSCC. Stratification based on TP53 and HPV-status uncovered differences in CSS and underlying molecular pathways. Our data indicate that TP53LOF tumors are characterized by worse biological behavior regardless of HPV-status. These findings and further research are essential for trial design in PSCC, allowing us to move away from the current one-size-fits-all approach.

  Study EGAS50000000217

• DNTR sequencing data of paediatric acute lymphoblastic leukemia

  This study used the DNTR-seq method in leukaemia samples to profile the whole-genome and mRNA jointly in single cells. Direct tagmentation is used in a collection of single-cell whole genome sequencing (scWGS) methods, including DNTR-seq, which provide high quality data at ultra-low to low coverage. The overall goal was to characterize the genetic and transcriptional heterogeneity of cancer samples. To infer clonal structure and evolutionary history, copy number analysis based workflows were implemented. Bone marrow mononuclear cells from pediatric acute lymphoblastic leukemia samples were FACS sorted into 384 plates to generate the DNA and RNA profiles.

  Study EGAS50000001247

• Bulk RNAseq - Calprotectin in vitro effects on human early hematopoiesis

  To explore the effects of calprotectin (CAL) on early hematopoiesis, we incubated CD34+ cells from four healthy donors for 7 days in the presence of stem cell factor (SCF), FLT3-ligand and thrombopoietin (TPO) without and with CAL, interleukin-6 (IL6) and the IL6_CAL combination before collecting cells. We performed the same experiment with CD34+ cells collected from three patients with JAK2-V617F-mediated myelofibrosis (MF). A total of 135,545 cells from healthy donors and 111,725 cells from myelofibrosis patients were analyzed by single-cell RNA sequencing (scRNA-seq) using the 10X Chromium droplet-based platform. Bulk RNAseq 4 conditons : -Control - Calprotectin - IL-6 - Calprotectin+IL-6

  Study EGAS50000000454

• The landscape of Usher syndrome-associated transcript isoforms in the human neural retina

  Usher syndrome is an autosomal recessively inherited disorder characterized by the combination of progressive loss of visual function due to retinitis pigmentosa, sensorineural hearing loss and vestibular dysfunction in a subset of cases. Usher syndrome is clinically and genetically heterogeneous. To date, eleven genes have been identified that are associated with Usher syndrome. It is known that these genes express multiple isoforms, however, for most of the known isoforms their relative importance in the human retina is unknown. To fill this gap, using PacBio long-read mRNA sequencing we aimed to provide an overview of the Usher syndrome transcripts in the human retina.

  Study EGAS50000000504

• PTPN22 SNPs and outcome after lung transplantation

  Obstructive chronic lung allograft dysfunction (BOS) is the major limiting factor for lung transplantation (LTx) outcome. PTPN22 is described as the hallmark autoimmunity gene, and one specific single nucleotide polymorphism (SNP), rs2476601, is associated with multiple autoimmune diseases, impaired T cell regulation and autoantibody formation. Taking into consideration the contribution of autoimmunity to LTx outcome, we hypothesized that polymorphisms in the PTPN22 gene could be associated with BOS incidence. We selected six SNPs within PTPN22 and analyzed both patient and donor genotypes on BOS development post-LTx. A total of 144 patients and matched donors were included, and individual SNPs and haplotype configurations were analyzed.

  Study EGAS00001003380

• Dynamics of tumor ecosystems and microbiome in response to neoadjuvant atezolizumab, bevacizumab, and FOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis

  This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes. The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospective cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was done for stool samples from cohort B.

  Study EGAS50000000677