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• Accelerating Medicines Partnership-Rheumatoid Arthritis (AMP-RA/SLE)

  This project is analyzing tissue and blood samples from people with RA and lupus to pinpoint genes, proteins, chemical pathways, and networks involved at a single cell level. This type of modular, molecular analysis will allow comparisons across the diseases and will provide insights into key aspects of the disease process. The project will identify differences between those RA patients who respond to therapies and those who do not, as well as provide a better systems level understanding of disease mechanisms in both RA and lupus. This knowledge is essential for the development of targeted therapies and for the application of existing and future therapies to appropriate patient populations. Additional datasets can be accessed through ImmPort (http://www.immport.org/immport-open/public/home/studySearch), accession: SDY998, SDY999.

  Study phs001457

• Genome_Diversity_in_Africa_Project___ancient_samples___standard_libraries

  Given the central importance of Africa to studies of human origins, genetic diversity and disease susceptibility, large-scale and representative characterisation of genetic diversity in Africa is needed. Analyses of ancient DNA from Africa would complement sequencing of modern African populations and provide unique opportunities to transform our understanding of the pre-history of the region. This approach would greatly refine our understanding of population structure and gene flow in Africa and globally, including genetic signatures of ancient admixture. This low coverage sequencing experiment will allow us to test and refine our pipeline for ancient DNA sequencing.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 EGAS00001001182

• Molecular and Clinical Analyses of PHF6 Mutant Myeloid Neoplasia Provide Clues as to Their Pathogenesis and Therapeutic Targeting

  PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Our comprehensive genomic analyses yielded three main findings. Firstly, we revealed a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 were co-mutated with PHF6. In contrast, female cases revealed co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis revealed a direct interaction between PHF6 and the pioneer transcription factor RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrated a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival were additive as PHF6MT cases with RUNX1 mutations had worse outcomes when compared to cases carrying single mutation or wild-type.

  Study phs003303

• Ductal keratin 15+ luminal progenitors in normal breast exhibit a basal-like breast cancer transcriptomic signature

  Normal breast luminal epithelial progenitors have been implicated as cell of origin in basal-like breast cancer, but their anatomical localization remains understudied. Here, we combine micro-collection of uncultured organoids and single cell mRNA sequencing (scRNA-seq) of FACS-sorted luminal epithelial cells with multicolor imaging to profile ducts and terminal ductal lobular units (TDLUs) and compare them with breast cancer subtypes. Unsupervised clustering reveals eleven distinct clusters and a differentiation trajectory starting with keratin 15+ (K15+) progenitors enriched in ducts. Spatial mapping of luminal progenitors is confirmed at the protein level by staining with critical duct markers. Comparison of the gene expression profiles of normal luminal cells with those of breast cancer subtypes reveals a strong correlation between normal breast K15+ ductal progenitors and basal-like breast cancer. We propose that K15+ basal-like breast cancers originate in ductal progenitors, which emphasizes the importance of not only lineages but also cellular position within the ductal-lobular tree.

  Study EGAS00001005963

• Download Metadata

  Metadata Distribution Welcome to the realm of Metadata Distribution within the EGA ecosystem! Our Metadata REST API empowers you to effortlessly retrieve metadata from the expansive landscape of EGA. By utilising this API, you gain access to publicly available insights across various EGA domains, including studies, samples, experiments, runs, analyses, policies, DACs, and datasets. Furthermore, this API facilitates cross-referencing of objects, enabling you to gather, for example, all the datasets associated with a specific DAC, seamlessly. In addition, we have added the ability to query private data using the metadata API. If you possess the necessary permissions, you can access behind-the-login private data for a specified list of datasets. Metadata Distribution Index Identifiers Dataset Mappings Website Download Metadata API - Private Identifiers At the core of EGA's organisational structure are unique accessions that serve as essential tags for our diverse objects. Here's a quick overview of the accessions and their corresponding object types: EGA Accession ID EGA Object description EGAS EGA Study Accession ID EGAC EGA DAC Accession ID EGAP EGA Policy Accession ID EGAN EGA Sample Accession ID EGAR EGA Run Accession ID EGAX EGA Experiment ID EGAZ EGA Analysis Accession ID EGAD EGA Dataset Accession ID EGAB EGA Submission ID EGAF EGA File Unique Accession ID For further information check our metadata schema documentation. Dataset Mappings For authorised datasets, comprehensive mappings reveal meaningful connections: Sample_file: This file presents information about the linkage between samples and files available in the dataset. Study_experiment_run_sample: This file presents information about the linkage between studies, experiments, runs, and samples within the dataset. Study_analysis_sample: This file presents information about the linkage between studies, analyses, and samples contained within the dataset. Run_sample: This file presents information about the linkage between runs and samples within the dataset. Analysis_sample: This file presents information about the linkage between analyses and samples within the dataset. An empty file indicates the absence of corresponding information. Website Download Our website serves as your gateway to downloading metadata. Simply navigate to the dataset page, and you'll find a blue Metadata button. Once authenticated, you can click this button for authorised datasets. If you lack permissions for a particular dataset, request access by clicking the 'Request Access' button. For authorised datasets, choose your preferred metadata format: CSV, TSV, or JSON. Metadata API - Private Leverage the power of programmatic metadata downloads! Start by authenticating yourself with your credentials to obtain an access token. With this token, programmatically query private information. Queries mirror the structure of the Public Metadata API. However, behind the login, you can delve into specific mapping information (as mentioned above in dataset mappings) alongside object-level exploration. Authentication An active session is required to work with the API. Each time you log in with your credentials a new session is started, which is identified by an access_token. Below an example on how to obtain one using curl: curl https://idp.ega-archive.org/realms/EGA/protocol/openid-connect/token \ -d 'client_id=metadata-api' \ -d 'username=...' \ --data-urlencode 'password=...' \ -d 'grant_type=password' All responses from the API are in JSON format. A successful response should include a new token to be used for the session: {"access_token":"eyJhbGciOiJSUzI1NiIsInR5cCIgOiA...TNw", "expires_in":300, "refresh_expires_in":1800, "refresh_token":"eyJhbGciOiJIUzI1NiIsInR5cCIgOiA...pTX10", "token_type":"Bearer", ... } Save the access_token value and include it in the API call headers. Example query usage Below you can find some example of queries available behing authentication and authorisation. Querying study-experiment-run-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/study_experiment_run_sample \ -H 'Authorization: Bearer access_token' Querying run-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/run_sample \ -H 'Authorization: Bearer access_token' Querying study-analysis-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/study_analysis_sample \ -H 'Authorization: Bearer access_token' Querying analysis-sample mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/analysis_sample \ -H 'Authorization: Bearer access_token' Querying sample-file mappings: curl https://metadata.ega-archive.org/datasets/{datasetID}/mappings/sample_file \ -H 'Authorization: Bearer access_token' You can get a different output format by adding one of these options to the curl command: -H 'Accept: text/tsv' -H 'Accept: application/json' -H 'Accept: text/csv' For more detailed information, refer to the Metadata API Specification.

  Documentation access/download/metadata

• Role_of_Epigenetic_Memory_in_Human_Induced_Pluripotent_Stem_Cells_Pilot

  Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. 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 EGAS00001000742

• Validation of a Haloplex platform for targeted re-sequencing of the exons of 25 genes

  We recently used the Agilent SureSelect platform to re-sequence a set of genes known to be mutated in human AML. The results from 10 AML DNA samples were very satisfactory, but the effort required was significant. Thus, we decided to re-sequence the same genes using the Haloplax system for target enrichment in 48 AML samples. We planned to do this using MiSeq and have data from a pilot of 3 samples. The data is promising but coverage appears pathcy so far. However, in order to get a better understanding of the data we will need deeper sequencing. We will need two lanes of HiSeq to get the same degree coverage as Sureselect. his 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/

  Dataset EGAD00001000603

• Genetics of Inherited Muscle Disease

  The samples are drawn from a collection of patients with a heterogeneous set of neuromuscular disorders, including congenital muscular dystrophy, congenital myopathy, limb-girdle muscular dystrophy, Emery-Dreifuss muscular dystrophy, and arthrogryposis, along with unaffected parents and siblings in some cases. The samples were collected by the following clinicians affiliated with the associated institutes: Kathryn North and Nigel Clarke (Institute for Neuroscience and Muscle Research, Children's Hospital at Westmead, Australia) Hanns Lochmuller and Kate Bushby (The Newcastle Muscle Centre, Newcastle University, UK) Peter Kang (Boston Children's Hospital) Carsten Bonnemann (National Institutes of Health, Bethesda, MD, USA) Nigel Laing (University of Western Australia) All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 or Illumina's Rapid Capture Exome enrichment kit and sequencing was performed on an Illumina HiSeq 2000. In addition some samples were whole genome sequenced on Illumina HiSeq X Ten.

  Study phs000655

• Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

  Whole Exome Sequencing was performed in a dilution series containing known amounts of human and mouse DNA, 3x 100% human 0% mouse, 2x 90/10, 3x 50/50, 2x 25/75 and 3x 0/100. A set of breast cancer clinical samples, matched normal tissue and matched PDTXs (total number = 14) were also analysed. Paired-end 75bp sequences for the dilution series and paired-end 125bp for the clinical samples were obtained on Illumina HiSeq2500; fastq files are provided. A triplicate analysis of the transcriptome using RNA-seq was also performed for the Universal Human RNA Reference and the Universal Mouse RNA Reference samples. Paired-end 150bp fastq files obtained on Illumina HiSeq4000 are provided.

  Dataset EGAD00001003800

• Kidney_transplant_nephrectomy_scRNAseq

  Single cell transcriptomics study of tissue from human kidney transplant nephrectomies Tissue is acquired from kidney transplant nephrectomies, homogenised and disaggregated to a single cell suspension prior to droplet encapsulation single cell RNAseq (10X protocol) or plate based single cell RNAseq (SS2 protocol). Human tissues, including the kidney are seeded with a tissue resident immune cell network throughout life. These cells may self renew in situ or be replaced by circulating precursors which enter the tissue in response to tissue specific niche and inflammatory signals. We are using single cell RNA sequencing of kidney transplant nephrectomy tissue to 1) understand the immune cell populations which are resident within the human kidney 2) identify which of these populations is donor or recipient derived. 3) Uncover the temporal dynamics of donor/recipient chimerism in the the human kidney following transplantation. 4) Understand transcriptional differences between organs removed for a variety of reasons (infection, chronic rejection, vascular emergencies) 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 EGAS00001003935

• Bulk-tissue RNA-sequencing of anterior cingulate cortex samples derived from Lewy body disease patients

  Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular “window” of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.

  Study EGAS00001005305

• Characterization of copy number quiet oral cancer

  Copy number quiet head and neck squamous cell carcinoma are a distinct subset with relatively good prognosis. Previous work has indicated this subset is most commonly found in the oral cavity and is highly enriched for HRAS and CASP8 mutations. TP53 mutations are much less common than in CNA-quiet oral cancers. In this study we corroborate the validity of CNA-quiet tumors as a distinct subset in a large OSCC cohort and further chart clinical, genomic, and immunological characteristics of this subset.

  Study EGAS50000000558

• Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis

  This dataset contains raw sequencing files associated with the paper "Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis" (https://doi.org/10.1038/s41590-023-01490-5). It is composed of two experiments, which are as follows: 1. Single-cell profiling of whole blood leukocytes: This experiment comprises sequencing files generated using the BD Rhapsody single-cell multi-omics profiling (RNA + protein) platform. This platform was used to profile the whole blood leukocyte population in a cohort of sepsis patients, cardiac surgery controls and healthy controls. There are 48 samples and four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the protein profiling (ADT-based AbSeq) library. 2. Single-cell profiling of circulating HSPCs: This experiment comprises sequencing files generated using the 10X single-cell multi-omics (RNA-seq + ATAC-seq) profiling platform. This platform was used to profile circulating HSPCs in a cohort of sepsis patients and healthy controls. There are 5 samples (or plexes), each of which consists of a pool of individuals for whom cells were multiplexed and sequenced as a single sample. There are four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the ATAC-seq library. Because these samples consists of multiplexed pools, index files are also provided. These can be used for sample deconvolution using the Cell Ranger pipeline. NOTE: Due to EGA's constrains in the number of files permitted per sample, index files (I1 and I2) for the HSPC data set are provided as a separate experiment named "FASTQ index files (I1 and I2) for deconvolution of 10X single-cell multiomics libraries".

  Dataset EGAD00001010927

• dbGaP Collection: Psychiatric Genomics Consortium (PGC) dbGaP Datasets

  This dbGaP Collection includes cases and controls used in the GWAS meta-analysis of neuropsychiatric phenotypes studied by investigators in the Psychiatric Genomics Consortium including major depression, bipolar disorder, attention deficit and hyperactivity disorder, schizophrenia, Tourette Syndrome, and obsessive-compulsive disorder. The consent type for data sets includes general research use as well as phenotype-specific restricted usage. This dbGaP collection was created to facilitate identification of datasets used in PGC analyses in order to expedite the application and ascertainment process for PGC members wishing to access data within the consortium. Non-PGC members may also apply for this dbGaP collection.

  Study phs001254

• UK10K NEURO ASD BIONED

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. The BioNED (Biomarkers for Childhood onset neuropsychiatric disorders) study has been carrying out detailed phenotypic assessments evaluating children with an autism spectrum disorder. These assessments included ADI-R, ADOS, neuropsychology, EEG etc. There are 56 DNA samples from this study (25 extracted from blood). For further information with regard to this cohort please contact Patrick Bolton (patrick.bolton@kcl.ac.uk).

  Study EGAS00001000111

• RNA-seq analysis of metastatic prostate cancer solid tumor biopsies

  The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)–targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival.

  Study EGAS00001006369

• Dataset of 5 RNAseq from 3 non-muscle-invasive bladder cancer patients

  RNAseq (FASTQ files) of 5 tumor from 3 non-muscle-invasive bladder cancer patients. For patient UC2, RNA from 3 different synchronous tumors was extracted. Relating to the other datasets from the project : no RNA was available from patient UC4. NB : patients aliases are the following : ROXY : UC1, OMAD : UC2, MAKI : UC3, HAPE : UC4

  Dataset EGAD50000002009

• Exome sequencing data

  Exome sequencing fastq files from 6 mutation carriers and 5 non-carriers from 2 families. One µg DNA was used for library preparation using the TruSeq DNA LT Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina). Hybridization was performed using Nimblegen SeqCap EZ Exome v3 (Roche) and Paired-end Sequencing (2x100 bp) on the Illumina HiSeq 2000 with TruSeq v3 chemistry (Illumina).

  Dataset EGAD00001003745

• 10x genomics RNAseq of an isogenic human iPSC model of SMA

  10x genomics single-cell RNAseq of an isogenic human iPSC model for SMA and control. The transcriptomic analysis was performed at 3 timepoints, day 4, day 20 and day 40. The analysis of this dataset was reported in the manuscript "An isogenic human iPSC model unravels neurodevelopmental abnormalities in SMA" from Grass et al.:

  Dataset EGAD00001011259

• Bulk and RIP-seq transcriptome datasets from skin fibroblasts in PTBP1- and PTBP2-related disorders

  PTBP1- and PTBP2-related disorders are rare human conditions that cause variable neurodevelopmental phenotypes, including intellectual disability and behavioral problems such as autism spectrum disorder, anxiety, aggressiveness, and attention disorders, with or without hyperactivity. PTBP1-related disorder is also associated with skeletal dysplasia. In this study, we generated bulk RNA sequencing and RNA immunoprecipitation sequencing (RIP-seq) data from skin fibroblasts obtained from patients and healthy controls.

  Study EGAS50000001210

• Whole genome study of Hurthle cell thyroid carcinoma

  Oncocytic thyroid carcinoma, also known as Hürthle cell thyroid carcinoma, accounts for only a small percentage of all thyroid cancers. However, this malignancy often presents at an advanced stage and poses unique challenges to patients and clinicians. Surgical resection of the tumor accompanied in some cases by radioactive iodine treatment, radiation and chemotherapy are the established modes of therapy. Knowledge of the perturbed oncogenic pathways can provide better understanding of the mechanism of disease and thus opportunities for more effective clinical management. Initially, two oncocytic thyroid carcinomas and their matched normal tissues were profiled using whole genome sequencing. Subsequently, 72 oncocytic thyroid carcinomas, one cell line and 5 Hürthle cell adenomas were examined by targeted sequencing for the presence of mutations in multiple endocrine neoplasia I (MEN1) gene. We report the identification of MEN1 loss-of-function mutations in approximately 7% of patients diagnosed with oncocytic thyroid carcinoma. Whole genome sequence data also revealed large regions of copy number variation encompassing nearly the entire genomes of these tumours. Menin, a ubiquitously expressed nuclear protein, is a well-characterized tumor suppressor whose loss is the cause of multiple endocrine neoplasia type 1 syndrome. Menin is involved in several major cellular pathways such as regulation of transcription, control of cell cycle, apoptosis and DNA damage repair pathways. Mutations of this gene in a subset of Hürthle cell tumors point to a potential role for this protein and its associated pathways in thyroid tumorigenesis.

  Study EGAS00001000940

• Gut metagenome/FR 2002

  The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

  Study EGAS00001005038

• WGS and Avenio Surveillance Panel data to previously submitted data under study number EGAS00001004276 of ALK-rearranged lung cancer

  Some data was previously submitted data under study number EGAS00001004276. In this new dataset we provide additional WGS and Avenio Surveillance Panel data. We utilized 43 ALK+ NSCLC patients receiving targeted ALK therapy to evaluate ctDNA levels based on matched panel-based targeted next generation sequencing (tNGS) and untargeted shallow whole genome sequencing (sWGS). For the Avenio panel the sequencing was done on Illumina NextSeq 550 paired end 150 bp, for WGS the sequencing was done on Illumina HiSeq 4000, partly with KAPA_Hyper_Prep_Kit. In this dataset there are 132 WGS tumor samples and 134 panel sequencing data of plasma.

  Dataset EGAD00001007818

• Assessment of Health-related Quality of Life in Rare Kidney Stones

  The purpose of this study is to learn about Health-related Quality Of Life (HRQoL) in patients enrolled in the Rare Kidney Stone Consortium (RKSC) registries. Quality of life studies look at different aspects of both physical and mental components of people's lives. HRQoL data for people affected by kidney stones are not currently available for people followed over time. All participants enrolled in the RKSC registries will be invited, via email or postal mail, to participate in this study. Health-related quality of life in people with rare kidney stones enrolled in the RKSC registries will be measured. Instruments used in this study are the SF-10 for pediatric participants and SF-36v2 for adult participants. The surveys will be completed online. Participants without a computer or internet access will participate using a paper version of the survey. These surveys will be done at enrollment and annually thereafter. The SF-36v2 includes 36 questions and is estimated to take 15 minutes for its completion, while the SF-10 includes 10 questions and could be completed in 5 minutes. The research questions are: Assessment of HRQoL in patients with rare kidney stones. Comparison of HRQoL results between rare kidney stone formers, general population and other populations with relevant chronic diseases. Comparison of HRQoL results in the same populations affected by different stones and analyzed with attention to the effects of various factors included in the disease registry, such as stone activity, burden of urologic interventions, medication and other treatments. Evaluation of HRQoL and its trends over time in patients undergoing treatment for rare kidney stones. About this study: The plan is to have 400 participants from all four registries take part in this multi-center study. The assessment of your HRQoL will be done annually for 5 years.

  Study phs001770

• Epigenetics/genetics of the patient-derived xenografts of pediatric T-cell leukemia

  We compared 12 pediatric T cell acute lymphoblastic leukemias collected at initial diagnosis and relapse with their corresponding PDX models. The analysis was performed on genomic level (whole genome sequencing (WGS), whole exome sequencing (WES), multiplex ligation probe amplification (MLPA), targeted sequencing) and the epigenetic level (DNA methylation, Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq)). In sum, this study underlines the remarkable genomic stability, and for the first time documents the preservation of the epigenomic landscape in T-ALL-derived PDX models.

  Study EGAS00001003248

• Genomic Data Archive From the Network for Pancreatic Organ Donors With Diabetes

  The Network for Pancreatic Organ Donors with Diabetes (nPOD) is the largest biorepository of human pancreata from organ donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, and islet autoantibody positive (AAb+)/pre-T1D. The mission of the nPOD is to distribute biospecimens and associated de-identified data/metadata to an international researcher network, and to promote the development of new treatments for these diabetes conditions. Here, we describe the release of high-parameter genotyping data for the nPOD cohort. Specifically, 372 subjects were genotyped using a customized precision medicine single nucleotide polymorphism (SNP) microarray (UFDIchip). These data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 subjects were queried for rare known and novel coding region variants via whole exome sequencing (WES). These data are now publicly available, enabling genotype-selected sample requests and the study of novel genotype : phenotype associations, ultimately to explain diabetes heterogeneity and inform precision medicine strategies to interrupt diabetes pathogenesis.

  Study phs002861

• Molecular profiling of an AML case following treatment with a BCL2 inhibitor

  Molecular profiling of a single AML case. Exome sequencing was performed at diagnosis and after treatment with conventional chemotherapy and BCL2i. Some samples required whole genome amplification. Data will be made available to researchers upon completion of a data transfer agreement; use is restricted to ethically approved research focused on haematological malignancy, and precludes germline analysis.

  Study EGAS00001004841

• Pancreatic Cancer Case Control Association Study

  Pancreatic cancer is the fourth leading cause of cancer death in the United States. This is in large part due to the rapidly fatal course of this disease, as the vast majority of patients die within months of diagnosis and the five-year survival rate is less than 5. We have brought together over 8000 participants from 9 studies of pancreatic cancer, to conduct a GWAS of pancreatic cancer. The studies were drawn from the Pancreatic Cancer Case-Control consortium and include case-control studies from the United States, Europe and Australia. Sites include: Johns Hopkins National Familial Pancreas Tumor Registry, Mayo Clinic Biospecimen Resource for Pancreas Research, Ontario Pancreas Cancer Study (OPCS), Yale University, MD Anderson Case Control Study, Queensland Pancreatic Cancer Study, University of California San Francisco Molecular Epidemiology of Pancreatic Cancer Study, International Agency of Cancer Research and Memorial Sloan Kettering Cancer Center.

  Study phs000648

• Host genotyping data from Dutch adult bacterial meningitis patients and linked bacterial genome sequences

  Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. This study includes 1146 samples of host genotyping data (genotyped and imputed) from Illumina Omni arrays. Samples were collected from adults (>16 yrs) patients with CSF confirmed bacterial meningitis in the Netherlands between 2006 and 2015. Metadata includes patient outcome, species of bacteria, and for 467 samples a link to an ENA run with the associated bacterial genome (S. pneumoniae only).

  Study EGAS00001005993

• Charles R. Bronfman Institute for Personalized Medicine (IPM) BioBank Genome Wide Association Study of Cardiovascular, Renal and Metabolic Phenotypes

  The Institute for Personalized Medicine (IPM) Biobank Project is a consented, EMR-linked medical care setting biorepository of the Mount Sinai Medical Center (MSMC) drawing from a population of over 70,000 inpatients and 800,000 outpatient visits annually. MSMC serves diverse local communities of upper Manhattan, including Central Harlem (86% African American), East Harlem (88% Hispanic Latino), and Upper East Side (88% Caucasian/white) with broad health disparities. IPM Biobank populations include 28% African American (AA), 38% Hispanic Latino (HL) predominantly of Caribbean origin, 23% Caucasian/White (CW). IPM Biobank disease burden is reflective of health disparities with broad public health impact: average body mass index of 28.9 and frequencies of hypertension (55%), hypercholesterolemia (32%), diabetes (30%), coronary artery disease (25%), chronic kidney disease (23%), among others. Biobank operations are fully integrated in clinical care processes, including direct recruitment from clinical sites, waiting areas and phlebotomy stations by dedicated Biobank recruiters independent of clinical care providers, prior to or following a clinician standard of care visit. Recruitment currently occurs at a broad spectrum of over 30 clinical care sites. Minorities are strikingly underrepresented in GWAS, including Coronary Artery Disease (CAD) and Chronic Kidney Disease; multigenic genetic risk scores for CAD have been recently validated in European ancestry populations, but not in AA or HL populations. Several important opportunities exist for extending additional GWAS to minority populations with a shared risk spectrum of CAD and CKD. For example, progressive CKD is a major and independent risk factor for CVD with an inverse relationship between estimated GFR (eGFR), and risk for mortality and cardiovascular events. This increased risk is only partially explained by the prevalence of cardiovascular risk factors among these patients. We conducted a GWAS of CAD and CKD related phenotypes in IPM Biobank with the primary objective to explore the genetics of overlapping CAD and CKD predominantly in minority populations characterized by increased risk.

  Study phs000388

• Evaluation of novel therapies using primary cultured gynecological cancer cells and search for predictors of efficacy

  The objective of this study is to establish an optimal method to evaluate the anti-tumor efficacy and biological activity of the novel therapies under investigation in our department using cancer tissues and cells derived from patients with gynecological malignancies in vitro and to evaluate them in practice. This research will contribute to the development of new treatments for gynecological cancer.

  Study JGAS000809

• The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

  Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find novel patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a novel genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.

  Dataset EGAD00001012101

• Microbiome-Host Interactions in Oral Squamous Cell Carcinoma: a Metatranscriptomic Exploratory Study

  Oral cancer (predominantly squamous cell carcinoma; OSCC) is the 14th most prevalent malignancy worldwide, accounting for more than 300,000 new cases and 145,000 deaths annually. Despite advances in cancer treatment modalities, OSCC continues to have poor prognosis with 5-year survival rates less than 50%. Although use of tobacco and alcohol consumption constitute the major risk factors, there is emerging evidence for the role of the microbiome in OSCC. However, studies on the association between the microbiome and OSCC has so far focused on compositional analysis and has been largely limited to the bacterial component of the microbiome. The aim of this study is to characterize the transcriptional activity (function) as well as composition of the multi-kingdom microbiome associated with OSCC and correlate it with the gene expression of the host using ultra-deep metatranscriptome sequencing, which will provide new insight into the role of the microbiome in OSCC and the possible mechanisms by which the tumor’s microbial community may influence on its behavior. This project comprises RNA-Seq data from twenty OSCC tumor/normal tissue pairs and twenty tongue scraping samples from healthy controls. However, due to consent constraints, the human sequences from the control data are filtered out.

  Study phs002678

• ProstOmics - Spatial Transcriptomics

  Spatial transcriptomics data (ST) from 32 human prostate tissue samples originating from 8 prostate cancer patients (5 patients with post-surgery relapse). The ST data was acquired using the Visium Spatial Gene Expression kit which resulted in over 20 000 spatially defined spots for the 32 tissue samples. The raw transcriptomics data is RNA-seq. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Each ST spot has metadata such as sample origin, histology class (stroma, normal epithelium, cancer of various grading etc), number of cells and estimated cell type fractions. Patient metadata include information of age at surgery, time (months) until reported relapse, total follow-up time, pre-surgery PSA, post-surgery T-stage and metastasis status.

  Dataset EGAD50000000603

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four B-other ALL patients (ALLT-314, ALLT-319, ALLT-327, ALLT-334), and from relapse sample of one B-other ALL patient (ALLT-316) . NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002598

• Dataset for identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

  WGS (tumor and germline samples) was performed to identify structural variants in the UBTF/CDX2 subgroup. RNA-seq was performed to detect gene fusion in the UBTF/CDX2 subgroup. HiChIP was performed to investigate 3D chromatin architecture and enhancer landscapes of representative patient samples and cell lines harboring Type I and II FLT3-PAN3 deletions and amplifications.

  Dataset EGAD00001008416

• Single-cell expression of Hodgkin and Reed-Sternberg (HRS) cell

  Hybrid capture sequencing was performed to 3 purified Hodgkin and Reed-Sternberg (HRS) cell samples. In brief, Probes for 177 genes were designed and synthesized by Twist Bioscience. Hybridization capture of DNA libraries was performed using Twist Hybridization and Wash Kit (Twist Bioscience). The captured library was measured using Agilent Bioanalyzer High Sensitivity chip and Qubit dsDNA HS Assay Kit and run on Illumina Nextseq550. The BAM files were generated from the raw sequencing data using Cell Ranger (v6.0.2) mkfastq and count commands

  Dataset EGAD00001010892

• Chromatin profiling of baseline and Notch inhibitor treated HCC PDX model

  We generated chromatin accessibility profiles for anti-Notch2 (n=3) and anti-gD (n=3) treated LIV78 tumors. Tumors were isolated, snap frozen in liquid nitrogen and stored at -80C. Tumor tissue was pulverized using a Covaris CP02 CryoPrep Pulverizer. Flash frozen pulverized tumor samples were sent to Active Motif to perform the ATAC-seq assay. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina) to produce FASTQ sequencing files.

  Dataset EGAD50000000735

• Single cell sequencing of human normal breast myoepithelial cells

  The dataset includes 6 FASTQ files with single cell transcriptome sequencing data of normal breast myoepithelial cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3’ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the Illumina® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA.

  Dataset EGAD00001008468

• sQTL summary statistics

  This dataset contains the sQTL summary statistics (nominal pass, significant sQTLs). sQTL mapping was performed with QTLtools. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005042

• Patient-tailored design for selective co-inhibition of leukemic cell subpopulations

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells of 2 acute myeloid leukemia patients at refractory stage. The profiling was performed using 10x Genomics Chromium Single Cell 3ʹ Gene Expression platform. The raw data are available as fastq files.

  Dataset EGAD00001006360

• Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post- therapy medulloblastoma

  Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post- therapy medulloblastoma (2 samples). One sequencing was done on GridION, the other one on a P2 Solo. In both cases the SQK LSK-109 Kit was used for preparation.

  Dataset EGAD00001009490

• Epigenetic Biomarkers of Aging

  The aim of the study was to discover new epigenetic biomarkers of aging. We used a genome-wide screen for genetic loci showing consistent changes of DNA methylation with progressive aging. Blood DNA samples from 19 apparently healthy individuals aged 22-80 years obtained from the NINDS repositories were analyzed for DNA methylation using Reduced Representation Bisulfite Sequencing. We followed the New England Biolabs (NEB) protocol for methylated adaptors as described previously. Briefly, 1 microgram of genomic DNA was spiked with 100 picograms of lambda phage DNA as the unmethylated standard and digested with MspI endonuclease at C’CGG sites. Ends of restriction fragments were filled in, 3’-dA tailed and methylated adaptors were ligated to the ends of restriction fragments. Bisulfite treatment using the Epitect kit (Qiagen) followed. Bisulfite-converted libraries were amplified using EpiMark Taq DNA polymerase (NEB) and primers with dual barcode indices. The libraries were pooled and sequenced on Illumina HiSeqX instrument using paired end reads of 150 bases. We used Bismark v0.23.1 to align the sequences to hg19 human genome assembly. We used methylKit v1.22.0 to analyze differential methylation in individuals of different ages.

  Study phs003046

• Whole genome sequencing of adult glioblastoma nuclei

  Nuclei were extracted from three primary adult glioblastoma samples and processed for scATAC-seq, and residual nuclei left over from these same samples were used to extract DNA and processed and sequenced for WGS. This WGS data was then used to cross-validate assessment of large-scale copy number alterations with scATAC-seq using the Copy-scAT tool.

  Study EGAS00001005256

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  COG-N-519 primary neuroblastoma cells were innoculated by subcutaneous injection into NSG mice. When tumours reached a size of 100-200mm3 miRNAs conjugated to nanoparticles were injected intratumourally every 2 days for 1 week. 24 hr after the last injection, snap frozen tumour tissue was harvested for RNA extraction and RNA-seq analysis.

  Study EGAS00001005581

• Transcriptomics for LUNG-NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.

  Dataset EGAD50000002236

• The Genomic Landscape of Childhood and Adolescent Melanoma

  Despite remarkable advances in the genomic characterization of adult melanoma, the molecular pathogenesis of pediatric melanoma remains largely unknown. We analyzed 15 conventional melanomas (CM), 3 melanomas arising in congenital nevi (CNM), and 5 spitzoid melanomas (SM), using various platforms, including whole genome or exome sequencing, molecular inversion probe assay, and/or targeted sequencing. CM demonstrated a high burden of somatic single nucleotide variations (SNV), with each case containing a TERT promoter (TERT-p) mutation, 13/15 containing an activating BRAF V600 mutation, and >80% of the identified SNV consistent with UV damage. By contrast, the 3 CNM contained an activating NRAS Q61 mutation and no TERT-p mutations. SM were characterized by chromosomal rearrangements resulting in activated kinase signaling in 40%, and an absence of TERT-p mutations except for the one SM that succumbed to hematogenous metastasis. We conclude that pediatric CM has a very similar UV-induced mutational spectrum to that found in the adult counterpart, emphasizing the need to promote sun protection practices in early life and to improve access to therapeutic agents being explored in adults in young patients. By contrast, the pathogenesis of CNM appears to be distinct. TERT-p mutations may identify the rare subset of spitzoid melanocytic lesions prone to disseminate.

  Study EGAS00001000901

• The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer

  One key barrier for improving efficacy of cancer immunotherapy remains patient stratification. While patients with CD3+CD8+ T cell inflamed ‘hot’ tumors typically show better response to immune checkpoint inhibitors, it is still unknown if the repertoire of HLA bound peptides (HLAp) presented in ‘hot’ and ‘cold’ tumors is substantially different. We surveyed 61 tumor regions and adjacent non-malignant lung tissues from eight lung cancer patients and performed deep antigen discovery combining immunopeptidomics, genomics, bulk and spatial transcriptomics and explored the heterogenic expression and presentation of tumor (neo)antigens. We associated diverse immune cell populations with the immunopeptidome in CD3+CD8+ T cell excluded, infiltrated, hot and cold tumors and found evidence for lack of immune-editing and higher presentation efficiency of tumor antigens in cold and CD3+CD8+ T cell excluded tumors. This could have implications for the choice of combination therapies tailored to the patient’s mutanome and microenvironment.

  Study EGAS00001006298

• Comprehensive genomic characterization of early stage bladder cancer - whole exome sequencing data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed WES data from 438 patients. The dataset is composed of 876 BAM files: 438 tumor samples and 438 paired blood samples.

  Study EGAS50000000511

• Panel-based next-generation sequencing study of human liver samples.

  Panel-based next-generation sequencing study of 150 human surgical liver samples from Caucasian donors with detailed medical documentation. The overall purpose of the study was to identify expression quantitative trait loci (eQTL) in human liver for genes involved in absorption, distribution, metabolism and excretion of drugs, other xenobiotics, and endogenous substances.

  Study EGAS00001003426