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• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006796

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who underwent mastectomies due to a breast cancer diagnosis. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005924

• Transcriptome profiling of three giant cell tumour of bone (GCTB) cell lines

  This dataset contains RNA-seq data of giant cell tumour of bone (GCTB) cell lines (n=3). Cell lines consist of neoplastic "stromal" cells harboring a heterozygous H3F3A p.G34W mutation. RNA-seq was performed on the BGISEQ-500 platform (PE100) and uploaded data contains fastq files, vcf files, and gene expression values (TPM). Cell lines, data generation, and data analysis are described in the following publication: Venneker et al., Histone deacetylase inhibitors as a therapeutic strategy to eliminate neoplastic “stromal” cells from giant cell tumors of bone, 2022.

  Dataset EGAD00001009074

• Whole-genome plasma DNA sequencing in CRC patients under anti-EGFR therapy

  In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy.

  Dataset EGAD00001000748

• H3K27ac/H3K27me3 landscape of medulloblastoma

  We profiled 111 patient medulloblastoma primary tumor samples by bulk RNA-seq (19 samples), 27ac (98 samples) / 27me3 (61 samples) ChIP-Seq, WGS (4 samples) and 27ac hichip (8 samples). Submitted data consists of data generated from previously unpublished tumors as well as complementary data for data sets already published for identical medulloblastoma tumors (ex: 27me3 ChIP-Seq and RNA-Seq data submitted for a tumor with publicly available WGS data). The raw fastqs and hg19 aligned RNA-Seq bams are provided.

  Dataset EGAD00001009709

• MutWP5: CRUK Mutographs of Cancer: Breast: BRCA Carriers (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Targeted data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005920

• Single cell atlas of neuroblastoma and the human fetal adrenal gland

  Using the chromium 3' expression assay, we generated an atlas of neuroblastoma and the human fetal adrenal gland. These data were complemented with whole genome sequencing of normal and tumour DNA from the neuroblastoma samples.

  Dataset EGAD00001008345

• Adeno-associated virus in the liver: natural history and consequences in tumor development

  Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterize the natural history of AAV infection in the liver and its consequence in tumor development. In silico analyses using viral capture data explored viral variants and new clonal insertions. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus.

  Dataset EGAD00001004484

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006797

• Sequencing data for Maturity-Onset Diabetes of the Young (MODY) patients in south India

  We performed whole genome, whole or targeted exome sequencing for 289 individuals from India. This included 152 clinically diagnosed MODY and 137 control samples. Whole genome libraries were constructed using TruSeqNano DNA Library Preparation Kit (Illumina, CA) and sequenced on Illumina HiSeq2500 (Illumina, CA). The whole exome analysis was performed using Agilent SureSelect (Santa Clara, CA) Human All Exome kit v5 (50 Mb). Exome capture libraries were sequenced on HiSeq 2500 (Illumina, CA). Targeted exome sequencing was performed using custom probes corresponding to 1965 genes implicated in pancreatic cell biology and/or diabetes.

  Dataset EGAD00001003919

• 4 subjects, 12 brain regions, UKBEC

  Brain samples for this dataset were provided by the Medical Research Council Sudden Death Brain and Tissue Bank (Edinburgh, UK). All four individuals sampled were of European descent, neurologically normal during life and confirmed to be neuropathologically normal by a consultant neuropathologist using histology performed on sections prepared from paraffin-embedded tissue blocks. Twelve regions of the central nervous system were sampled from each individual. The regions studied were: cerebellar cortex, frontal cortex, temporal cortex, occipital cortex, hippocampus, the inferior olivary nucleus (sub-dissected from the medulla), putamen, substantia nigra, thalamus, hypothalamus, intralobular white matter and cervical spinal cord.

  Dataset EGAD00001001274

• Aligned reads from specific genomic locations derived from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 3,001 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these bam files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001003513

• Clonal expansion of mutated cell population in bladder urothelium (2018-08-03)

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference. . This dataset contains all the data available for this study on 2018-08-03.

  Dataset EGAD00001004274

• Cardiogenics_Custom_Pools - Agilent SureSelect

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000397

• Targeted NGS panel

  The mutational status of 121 genes recurrently altered in B-cell lymphoma was examined in 55 of 56 diagnostic and 10 of 12 relapse samples using a custom targeted NGS panel. Libraries were generated from 150 ng of DNA using molecular-barcoded library adapters (ThruPLEX Tag- seq kit; Takara) coupled with a custom hybridization capture-based method (SureSelectXT Target Enrichment System Capture strategy, Agilent Technologies). The quality of the libraries was determined using the Bioanalyzer high sensitivity DNA kit (Agilent) and quantified by PCR using the KAPA library quantification kit (KAPA Biosystems). Finally, the libraries were pooled and sequenced in the MiSeq instrument (Illumina).

  Dataset EGAD00001010842

• Exome sequencing of Congenital Heart Disease families Royal Brompton

  This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected at the Royal, Brompton Hospital in collaboration with Stuart Cook and Piers Daubeney. Ethic approval has been sought for in the UK 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).

  Dataset EGAD00001000797

• Nimblegen

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000398

• CCA WGS data (16 CCA with matched normal, 4 cell-line)

  Fastq files for WGS for 16 CCAs (with matched normal tissues), and 4 cell lines in an AA-treatment experiment (0, 10, 20, 40ug AA treatment after 180 days; 2 runs each for 10ug and 40ug experiments). Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen). Sequencing libraries were prepared from DNA extracted using the SureSelect XT2 Target Enrichment System for the Illumina Multiplexed Sequencing platform (Illumina) according to the manufacturer’s instructions. Whole genome sequencing was performed on Illumina HiSeq4000 sequencer with paired-end sequencing.

  Dataset EGAD00001012100

• Chracterising cellur pathways underlying CD3/CD28 activation of human CD4+ cells

  We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Isolated memory and naïve T cells were activated using anti-CD3, anti-CD28 or both in combination. As a control we cultured cells in the same conditions but without the stimuli. We carried Chipmentation using the H3K27ac antibody on 200,000 cross-linked cells. 1) 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 please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001006611

• Long-read and short-read isoform sequencing in breast cancer

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Study EGAS00001004819

• Amplicon based NGS of human CD4 and CD8 T cells

  Panel-based next-generation sequencing data of 211 human CD4 T cells, CD8 T cells and genomic DNA. The panel was designed to capture 260 SNVs in high linkage disequilibrium with multiple sclerosis susceptibility SNVs. NGS was carried out using PE300 reads on the Illumina MiSeq (Illumina Inc., San Diego, CA, United States).

  Study EGAS00001004139

• Finding structural variation and functional consequences from the primary leukemia cells (AML) at the single-cell level

  In this study, we aimed to identify somatic structural variation of acute myeloid leukemia (AML) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 32 year old male donor.

  Study EGAS00001004903

• Whole genome sequencing of AVM endothelial and non-endothelial cell fractions

  We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing, which were enhanced in AVM endothelial cell fractions. We have now performed whole genome sequencing on AVM endothelial and non-endothelial cell fractions, as well as paired blood samples, in order to identify further somatic mutations.

  Study EGAS00001006719

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• Variant calling 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 whole exome sequencing data from tumor samples processed with the Vegan pipeline. In the absence of matching germline samples, variant calling is performed using two panel of normals (one for female and one for male). It includes SNP and CNV calling.

  Dataset EGAD50000002235