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• A98234A

  Whole genome sequencing for single cells for library A98234A 1240 cells; filetype=bam

  Dataset EGAD00001007626

• A98244A

  Whole genome sequencing for single cells for library A98244A 1271 cells; filetype=bam

  Dataset EGAD00001007628

• A98253A

  Whole genome sequencing for single cells for library A98253A 1250 cells; filetype=bam

  Dataset EGAD00001007629

• A98253B

  Whole genome sequencing for single cells for library A98253B 1388 cells; filetype=bam

  Dataset EGAD00001007630

• A98254A

  Whole genome sequencing for single cells for library A98254A 1490 cells; filetype=bam

  Dataset EGAD00001007631

• A98255B

  Whole genome sequencing for single cells for library A98255B 1394 cells; filetype=bam

  Dataset EGAD00001007632

• A98271A

  Whole genome sequencing for single cells for library A98271A 1190 cells; filetype=bam

  Dataset EGAD00001007633

• A98289A

  Whole genome sequencing for single cells for library A98289A 1066 cells; filetype=bam

  Dataset EGAD00001007634

• A98290B

  Whole genome sequencing for single cells for library A98290B 869 cells; filetype=bam

  Dataset EGAD00001007635

• A98305A

  Whole genome sequencing for single cells for library A98305A 986 cells; filetype=bam

  Dataset EGAD00001007637

• A108732A

  Whole genome sequencing for single cells for library A108732A 1139 cells; filetype=bam

  Dataset EGAD00001007592

• A108833B

  Whole genome sequencing for single cells for library A108833B 866 cells; filetype=bam

  Dataset EGAD00001007594

• A108842A

  Whole genome sequencing for single cells for library A108842A 1477 cells; filetype=bam

  Dataset EGAD00001007595

• A108863A

  Whole genome sequencing for single cells for library A108863A 1301 cells; filetype=bam

  Dataset EGAD00001007597

• A110618A

  Whole genome sequencing for single cells for library A110618A 1184 cells; filetype=bam

  Dataset EGAD00001007599

• Genomic landscape of Neutrophilic Leukemias of Ambiguous Diagnosis

  Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and unclassified myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN-U) are a group of rare, heterogeneous myeloid disorders. There is strong morphologic resemblance amongst these distinct diagnostic entities as well as lack of specific molecular markers and limited understanding of disease pathogenesis, which has made their diagnosis challenging. Treatment has remained empirical, resulting in dismal outcomes. We, therefore, performed whole exome and RNA-sequencing on a cohort of over 100 cases of these rare hematologic malignancies and present the most complete survey of the genomic landscape of these diseases to date. [Abstract from manuscript currently under review so copyright not yet determined]

  Study phs001799

• Neutralizing Antibodies against West Nile Virus Identified Directly from Human B Cells by Single-Cell Analysis and Next Generation Sequencing

  West Nile virus (WNV) infection is a mosquito-borne disease that can cause severe neurological illness. We analyzed the humoral response to WNV of subjects infected with WNV at different stages of the infection and at different levels of detail, from single cells to the repertoire level. We integrated single-cell analysis by microengraving with next-generation sequencing and identified four novel WNV neutralizing antibodies with potential use as therapeutics against WNV infection. The results indicate persistence of WNV-specific memory B cells and antibody-secreting cells in post-convalescent subjects and suggest that the antibody response itself does not predict the clinical severity of the disease.

  Study phs001200

• Integrated Single-Nucleus and Spatial Transcriptomics Elucidate Heterogeneity and Hypoxia-Driven Organization of Supratentorial Ependymoma

  Supratentorial ependymomas are often life-threatening brain tumours that are characterised by significant molecular heterogeneity. In this study, single-nucleus (n = 63) and spatial transcriptomics (n = 30) was performed to delineate the cellular and spatial landscape of supratentorial ependymoma. This study characterises the transcriptional consensus programs of this entity and connects them to clinical outcome. Two previously undescribed programs – associated with the remodelling of the extracellular matrix and the ZFTA fusion identity – are shown to be related to highly unfavourable outcome and to be exclusive to ZFTA fusion-positive tumours. Also, Hypoxia is proposed as the potential driver of spatial organisation, which may affect treatment success.

  Study EGAS50000001318

• Transcriptomic profiles of early and late passage metastatic colorectal cancer (mCRC) tumoroids

  The breadth and depth at which cancer models are interrogated contribute to successful translation of drug discovery efforts to the clinic. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, the setting where experimental therapies are typically tested. XENTURION is a unique open-science resource that combines a platform of 129 PDX models and a sister platform of 129 matched PDX-derived tumoroids (PDXTs) from patients with metastatic CRC, with accompanying multidimensional molecular and therapeutic characterization. This specific dataset is focused on a comparison of early and late passage tumoroids transcriptomes.

  Study EGAS50000000108

• The genetic footprint of the European Roma diaspora: Evidence from the Balkans to the Iberian Peninsula

  Our genomic approach focuses on: (i) the internal genetic structure of Roma and its correlation with geography; (ii) the relationships between Iberian Roma and other non-Roma populations to explore possible contacts during the period of population upheaval following the Roma’s arrival on the Iberian Peninsula; (iii) estimation of the admixture events in the Iberian Roma before and after their arrival to the Iberian Peninsula; and (iv) the assessment of endogamy patterns and assortative mating of the European Roma. Our study provides a detailed analysis of the intricate population history of the Iberian Roma, offering insights from both micro-geographical and large-scale perspectives on the population history of European Roma.

  Study EGAS50000000746

• Exome sequencing to identify predisposition to Wilms tumour

  To identify new Wilms tumor predisposition genes, we performed whole-exome paired-end sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families in which known causes had been excluded.We prepared DNA libraries from 1.5 mg blood-derived genomic DNA using the Paired-End DNA Sample Preparation Kit (Ilumina). DNAwas fragmented using Covaris technology and the libraries were prepared without gel size selection. We performed target enrichment using the TruSeq Exome Enrichment Kit (Illumina) by targeting 62 mb of the human genome. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers.Sequencing was performed with an Illumina HiSeq2000 generating 2?101 bp reads.

  Study EGAS00001000904

• STREP GENE: Genetics and Severe Streptococcal Infections

  This study investigated host genetic susceptibility to invasive group A streptococcal disease in the UK. Cases were either survivors recruited retrospectively through a patient group or identified from the a tissue bank at Imperial College London. Those recruited through the patient group had survived an episode of invasive GAS disease at a UK hospital since 1980 with microbiological confirmation obtained either through Public Health England or from the treating hospital. Those identified from the tissue bank had been diagnosed with invasive GAS disease at the Hammersmith Hospital, London, UK, since 2006. All cases aged less than 65 years without long-term medical conditions genome-wide genotyped using either the Illumina HumanCore or the Global Screening Array platform.

  Study EGAS00001003421

• Whole genome sequencing of 25 South African individuals with myasthenia gravis

  This study investigated the genetic basis of an ophthalmoplegic subphenotype of MG (OP-MG) which occurs in a proportion of myasthenics with juvenile symptom onset and African genetic ancestry. This OP-MG subphenotype is characterised by treatment resistant weakness of the extraocular muscles (EOMs) and the pathogenetic mechanism(s) underlying its development is unknown. The aim of this study was to use a hypothesis-generating genome-wide case-control analysis to identify candidate OP-MG susceptibility genes and pathways. Whole genome sequencing (WGS) was performed on 25 AChR-antibody positive myasthenic individuals of African genetic ancestry sampled from the phenotypic extremes: 15 with OP-MG (cases) and 10 individuals with control MG (EOM treatment-responsive).

  Study EGAS00001003462

• ALS-FTD brain motor cortex single-nucleus RNA-seq of NeuN+ nuclei sorted for TDP-43 low vs. high

  A dataset of single-nucleus RNA-seq data of nuclei from the post-mortem human primary motor cortex from patients with ALS-FTD. The nuclei were sorted by flow cytomotetry into NeuN+ (neuronal) TDP-43 low vs. TDP-43 high fractions.

  Dataset EGAD50000002243

• Single-cell DNA sequencing dataset of aplastic anemia and RCC (31 samples)

  This dataset contains raw single-cell DNA sequencing data generated from 31 patients with aplastic anemia using the Mission Bio Tapestri platform. Libraries were prepared with a targeted DNA amplicon panel and sequenced on an Illumina platform. These raw data capture single-cell variant profiles and clonal architecture and serve as the basis for downstream analysis of somatic mutations and clonal hematopoiesis.

  Dataset EGAD50000002189

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Total RNAseq data from 8 patients with muscle invasive bladder cancer

  For this dataset we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The data consists of 8 sets of paired fastq files with accompanying UMI fastq files. Sequenced on the Illumina NoveSeq6000 platform using S2 flow cells (v1.5,2x150 cycles), with a mean yield of 313 million reads.

  Dataset EGAD50000001380

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

  This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001098

• Dataset for Multiple Myeloma RNA data

  This dataset contains 371 case and control RNA sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X, HiSeq 4000 and HiSeq 2000 using TruSeq Stranded RNA and TruSeq Stranded total mRNA Kits. The sequencing was always paired.

  Dataset EGAD50000000683

• mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines

  mRNA-Sequencing of 73 primary multiple myeloma (MM) samples and human MM cell lines before and after siRNA-mediated knockdown of ADAM8 (n=5 cell lines), ADAM9 (n=7 cell lines) and ADAM15 (n=5 cell lines). Paired-end sequencing was performed on a NovaSeq (Illumina). Fastq and bam files are provided for each sample.

  Dataset EGAD50000000575

• Dataset for desmoplastic small round cell tumor - RNA

  This dataset contains 32 RNA sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq RNA and TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000912

• Suspected Lynch syndrome dataset

  This dataset comprises a genomic and a phenotypic excel sheet displaying 137 cases classified as suspected Lynch syndrome. Included are genotypic data such as tumour mutational burden, tumour mutational signatures and germline/somatic variant calls for each colorectal, endometrial or sebaceous skin tumour screened. Genomic data is derived from targeted multigene panel sequencing including ~300 hereditary cancer genes.

  Dataset EGAD50000000031

• H3Africa AWIGEN Pilot MetaboChip

  Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.

  Dataset EGAD00010001258

• Sequencing data for oesophageal and related samples - BOs release 5 (RNA)

  Dataset EGAD00001005385

• WGS - germline - oral squamous cell carcinoma

  We conducted a retrospective, single-center Canadian cohort study of patients who underwent primary surgery for OSCC between 2010 and 2024. Nucleic acid quality was assessed using the 4150 TapeStation System (Agilent) prior to library preparation. WGS was performed on germline DNA, following Genome Analysis Toolkit’s (GATK) Best Practices and procedures, with a target of 30X deduplicated coverage per sample, using an Illumina NovaSeq 6000 instrument.

  Dataset EGAD50000002608

• Whole genome DNA sequencing for two long-lived humans.

  Two long-lived human samples were sequenced to a mean 20x coverage genome wide. Sequencing was done using the Illumina hi-seq platform, alignment to GRCh37/hg19 reference genome was done using the BWA alignment tool.

  Study EGAS00001000877

• NIHR BioResource Rare Diseases WGS project - Hypertrophic Cardiomyopathy (HCM) Rare Disease domain (VCF data)

  Short read whole genome sequencing (WGS) VCF files for the NIHR BioResource Rare Diseases WGS project – Participants from the Hypertrophic Cardiomyopathy (HCM) Rare Disease domain

  Dataset EGAD00001007885

• Epigenome of sorted human muscle stem cell

  This dataset contain RNA-seq, ChIP-seq, WGBS and ATAC-seq of 1 human muscle stem cell sample. NCAM+ITGB1+ CD31−CD45−CD34− were used as the sorting strategy for the sample. H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K36me3 and H3K9me3 are the targets of ChIP-seq.

  Dataset EGAD00001008686

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• Genomic data of acute myeloid leukemia cases for integration with metabolomic analyses

  Whole exome sequencing (WES) data of paired (germline and leukemic) samples of 100 adult patients affected by acute myeloid leukemia. Targeted sequencing data of myeloid-related genes of 21 leukemia (not paired) samples from adult patients affected by acute myeloid leukemia.

  Dataset EGAD00001007941

• ctDNA whole exome genome sequencing dataset

  Dataset contains all available exome sequencing paired-end fastq files from our study "A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes"

  Dataset EGAD00001010069

• Dataset_for_linked_WES_and_WGS_data_from_EGAS00001004813 which belong also to EGAS00001005537 for germline controls of rare cancers

  WES/WGS sequencing data of 37 germline runs, which were uploaded to umbrella studies. The sequencing was always paired. The WGS sequencing was on HiSeq X Ten using the Illumina TruSeq DNA Nano Kit. The WES Sequencing was on HiSeq4000 with Agilent Sureselect V5+UTR.

  Dataset EGAD00001010046

• MSC_busulfan_small_intestine_organoids

  This dataset represent the RNA-seq, which was done on untreated small intestinal organoids; small intestinal organoids treated with chemotherapeutic, busulfan; untreated small intestinal organoids co-cultured wth mesenchymak stromal/stem cells (MSCs; busulfan treated small intestinal organoids co-cultured with MSCs. The same set of samples was done for 3 different primary bone marrow MSC donors.

  Dataset EGAD00001011176

• WGS dataset for Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with Constitutional Mismatch Repair Deficiency

  Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.

  Dataset EGAD00001015157

• Genome Denmark Phase II - alignments

  Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).

  Dataset EGAD00001003157

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: PACA-AU.

  Dataset EGAD00001003410

• ICGC PCAWG Dataset: PACA-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: PACA-AU.

  Dataset EGAD00001003411

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: OV-AU.

  Dataset EGAD00001003415

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: OV-AU.

  Dataset EGAD00001003416

• Radiotherapy induced Sarcoma exome (2017-05-17)

  Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations This dataset contains all the data available for this study on 2017-05-17.

  Dataset EGAD00001003339