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• GCT WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

  Dataset EGAD00001003267

• NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)

  After a 2-4 week assessment/characterization run-in period, 6-14 year-old children who met NAEPP criteria for mild-moderate persistent asthma specifically based on symptom criteria and methacholine PC20 ≤ 12.5 mg/ml and FEV1 ≥ 80% were randomized to one of the three active treatment arms for 12 months. Randomization was stratified according to clinical center, bronchodilator response (< 12% or ≥ 12%), race (Caucasian or non-Caucasian), and methacholine PC20 (< 2 or ≥ 2 mg/ml). The primary outcome variable was the proportion of asthma-free days during the 12-month treatment period. Secondary outcomes included other measures of asthma control (percentage of rescue-free days, albuterol-free days, and episode-free days; the number of asthma exacerbations requiring prednisone therapy and the time to the first asthma exacerbation), forced oscillation and spirometry, reversibility (FEV1 pre- and post 2 puffs of albuterol MDI), methacholine PC20, exhaled nitric oxide, and asthma-related quality of life.

  Study phs001730

• Colon cancer targeted sequencing study contaning WBCs, primary tumor tissue and plasma samples

  In the setting of localized colon cancer (CC), circulating tumor DNA (ctDNA) monitoring in plasma has shown potential for detecting minimal residual disease (MRD) and predicting higher risk of recurrence. With the tumor-only sequencing approach, however, germline variants may be misidentified as somatic variations, precluding the possibility of tracking in up to 11% of patients due to a lack of known somatic mutations. In this study comprising 148 prospectively recruited localized CC patients, a custom 29-gene panel was utilized to sequence both tumor tissue and matched white blood cells (WBCs) to enhance the accuracy of sequencing results. Performing targeted sequencing of paired tumor tissue and WBCs samples detected additional somatic mutations and increased the number of patients eligible for MRD tracking in plasma, although MRD detection sensitivity was not increased. Furthermore, the germline testing approach revealed the presence of pathogenic germline variants, thereby helping identify patients at elevated risk of hereditary cancer syndromes.

  Study EGAS50000000059

• COVID_19_UK_CIC_Spatial

  Understanding the immune response to SARS-CoV-2 is critical to our ability to control the coronavirus pandemic. Spatial transcriptomics will be performed on COVID-19 post-mortem tissues in collaboration with the UK - Coronavirus Immunology Consortium (UK-CIC). UK-CIC encompasses a concerted effort by the UK's world-leading immunology community to deliver a co-ordinated and agile national research programme to increase our understanding of how the immune system interacts with SARS-CoV-2. UK-CIC is led by Professor Paul Moss (University of Birmingham) and brings together 20 UK immunology centres of excellence, with support from the British Society for Immunology.

  Study EGAS00001005817

• AmsterdamUMC Data Access Committee for the MAPS study

  The current data access committee reviews and assesses data requests of researchers that seek to gain access to data acquired from the MAping the Peritoneal immune System (MAPS) project as performed at the AmsterdamUMC, Amsterdam, Netherlands.

  Dac EGAC50000000096

• MB_COMICS_Methylome

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated methylome data for 369 primary MB patient samples.

  Dataset EGAD00010002669

• Whole genome sequencing, single-cell RNA sequencing, and ATAC sequencing of mesothelioma (patient, patient-derived xenograft and cell line)

  Malignant pleural mesothelioma is an aggressive pleural tumor with a poor prognosis, and elucidating its molecular mechanisms is essential for improving diagnosis and treatment. This study investigates key genes and pathways involved in tumor progression, with particular attention to the involvement of neutrophils in the tumor ecosystem of mesothelioma. We performed whole-genome sequencing and single-cell RNA sequencing (scRNA-seq) of one pleural mesothelioma tumor specimen, scRNA-seq of matched patient-derived xenograft tumors, scRNA-seq of mesothelioma-free pleural tissues from three patients, and assay for transposase-accessible chromatin using sequencing (ATAC-seq) of a patient-derived cell line.

  Study JGAS000859

• RNAseq: Acquired non-permissive bone marrow microenvironment impairs hematopoietic stem cell proliferation and maintenance and B-cell development post-HSCT

  Defects in B-cell reconstitution upon hematopoietic stem-cell (HSC) transplantation (HSCT) are a common observation, yet the mechanism remains unexplained. The bone marrow (BM) stroma, including mesenchymal stromal cells (MSCs), guides HSC maintenance and B-lymphopoiesis by secreting crucial cytokines. We report acquired, permanent, selective and complete B-cell deficiency in the context of full donor-chimerism in a patient with X-linked lymphoproliferative disease and aimed to identify the contribution of the BM-microenvironment in disrupted B-cell reconstitution post-HSCT. We studied longitudinal BM samples from the patient and his identical twin, both of whom underwent HSCT with the same donor with opposite outcomes in B-cell reconstitution. In the index patient BM, we observed progressive loss of proliferation of HSCs and a selective block at the pre-BI cell stage. In vitro modeling studies showed limited survival of patient-HSCs and a relative accumulation of pre-B cells. Patient-derived MSCs failed to support survival and proliferation of HSCs and B-cell development of healthy-HSCs which was correlated with reduced CXCL12 levels. Using bulk RNA-sequencing of MSCs and in vitro functional studies, we showed global changes in the patients’ MSCs and a progressive loss of CXCL12 expression. Indeed, survival of patients HSCs improved supplementing in vitro development culture with CXCL12, suggesting a contribution of defective CXCL12 signaling to the phenotype. In summary, our data show that an acquired defect in the BM-stromal microenvironment and exhaustion of HSCs and committed progenitors may cause a permanent non-permissive state for normal B-cell development.

  Study EGAS50000001437

• ATAC-seq: Acquired non-permissive bone marrow microenvironment impairs hematopoietic stem cell proliferation and maintenance and B-cell development post-HSCT

  Defects in B-cell reconstitution upon hematopoietic stem-cell (HSC) transplantation (HSCT) are a common observation, yet the mechanism remains unexplained. The bone marrow (BM) stroma, including mesenchymal stromal cells (MSCs), guides HSC maintenance and B-lymphopoiesis by secreting crucial cytokines. We report acquired, permanent, selective and complete B-cell deficiency in the context of full donor-chimerism in a patient with X-linked lymphoproliferative disease and aimed to identify the contribution of the BM-microenvironment in disrupted B-cell reconstitution post-HSCT. We studied longitudinal BM samples from the patient and his identical twin, both of whom underwent HSCT with the same donor with opposite outcomes in B-cell reconstitution. In the index patient BM, we observed progressive loss of proliferation of HSCs and a selective block at the pre-BI cell stage. In vitro modeling studies showed limited survival of patient-HSCs and a relative accumulation of pre-B cells. Patient-derived MSCs failed to support survival and proliferation of HSCs and B-cell development of healthy-HSCs which was correlated with reduced CXCL12 levels. Using bulk RNA-sequencing of MSCs and in vitro functional studies, we showed global changes in the patients’ MSCs and a progressive loss of CXCL12 expression. Indeed, survival of patients HSCs improved supplementing in vitro development culture with CXCL12, suggesting a contribution of defective CXCL12 signaling to the phenotype. In summary, our data show that an acquired defect in the BM-stromal microenvironment and exhaustion of HSCs and committed progenitors may cause a permanent non-permissive state for normal B-cell development.

  Study EGAS50000001438

• Population_sequencing_phasing

  Whole-genome sequencing of human individuals from Polynesian and Native American populations, as well as 10x Genomics Chromium data from Polynesian, Native American and Aboriginal Australian populations, allowing for experimental phasing of haplotypes. 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/

  Study EGAS00001001852

• Sequencing of Cervical Cancer

  Precision mapping of genetic alterations in cancer can enable better selection of therapies and improved outcomes when combined with new sequencing diagnostics. We describe whole-exome sequences from cervical adenocarcinomas and paired normal samples in Hong Kong Chinese women. These data uncover a heterogeneous genomic landscape but identify commonly aberrant loci including FAT1, ARID1A, ERBB2 and PIK3CA that may provide a focus for the development of individualized targeted therapies for Chinese women with cervical adenocarcinoma.

  Study phs000723

• Raw sequencing data for donor and patient fecal samples

  Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

  Dataset EGAD00001004371

• Atezolizumab Plus Chemotherapy With or Without Bevacizumab in Advanced Biliary Tract Cancer: Clinical and Biomarker Data From the Randomized Phase II IMbrave151 Trial

  PURPOSE Biliary tract cancers (BTCs) harbor an immunosuppressed tumor microenvironment (TME) and respond poorly to PD-1/PD-L1 inhibitors. Bevacizumab (anti-VEGF) plus chemotherapy can promote anticancer immunity, augmenting response to PD-L1 inhibition. PATIENTS AND METHODS This randomized, double-blind, proof-of-concept Phase II study enrolled patients (n=162) with previously untreated advanced BTC (IMbrave151; NCT04677504). Patients were randomized 1:1 to receive 3-weekly cycles of atezolizumab (1200 mg) plus bevacizumab (15 mg/kg) or atezolizumab plus placebo until disease progression or unacceptable toxicity. All patients received cisplatin (25 mg/m2) plus gemcitabine (1000 mg/m2; CisGem) on Days 1 and 8 every 3 weeks for up to 8 cycles. Stratification of patients was by disease status, geographic region, and primary tumor location. The primary endpoint was progression-free survival (PFS). No formal hypothesis testing was performed. Exploratory correlative biomarker analysis was undertaken using transcriptome analysis (n=95) and mutation profiling (n=102) on baseline tumor samples. RESULTS Between February and September 2021, 162 patients were enrolled. Median PFS was 8.3 months in the bevacizumab arm and 7.9 months in the placebo

  Study EGAS50000000387

• Prognostic relevance of microenvironmental factors CD163 and CD8 combined with EZH2 and chromosome 18 gain in a validation cohort of follicular lymphoma patients of the Lunenburg Lymphoma Biomarker Consortium

  Background: In follicular lymphoma (FL), studies addressing the prognostic value of microenvironment-related immunohistochemical (IHC) markers and tumor cell-related genetic markers have yielded conflicting results, precluding implementation in practice. Therefore, the Lunenburg Lymphoma Biomarker Consortium (LLBC) performed a validation study for published markers. Methods: To maximize sensitivity, an end-of-spectrum design was applied for 122 uniformly immunochemotherapy-treated FL patients retrieved from international trials and registries; early failure (EF): progression or lymphoma-related death <2 years versus long remission: response duration of >5 years. IHC staining for T-cells and macrophages was performed on tissue microarrays from initial biopsy and scored with a validated computer-assisted protocol. Shallow whole-genome and deep targeted sequencing was performed on the same samples. Results: 96/122 cases with complete molecular and immunohistochemical data were included in the analysis. EZH2 wild-type (p=0.006), gain of chromosome 18 (p=0.002), low percentages of CD8+ cells (p=0.011) and CD163+ areas (p=0.038) were associated with EF. No significant differences in other markers were observed, thereby refuting previous claims on their prognostic significance. Conclusion: Using an optimized study design, this LLBC study validates wild-type EZH2 status, gain of chromosome 18, low percentages of CD8+ cells and CD163+ area as predictors of EF to immunochemotherapy in FL.

  Study EGAS00001002049

• Genomewide copy number alteration screening of circulating plasma DNA

  Early cancer diagnosis might improve survival rates. As circulating tumor DNA (ctDNA) carries cancer-specific modifications, it has great potential as a noninvasive biomarker for detection of incipient tumors. We collected cell-free DNA (cfDNA) samples of 1002 elderly without a prior malignancy, carried out whole-genome massive parallel sequencing and scrutinized the mapped sequences for the presence of (sub)chromosomal copy number alterations (CNAs) predictive for a malignancy. When imbalances were detected, 6-monthly clinical follow-up was carried out.

  Study EGAS00001006031

• scRNAseq of colonic organoids derived from biopsies taken from healthy human individuals treated with IL22

  scRNAseq dataset of colonic organoids derived from epithelium from biopsies taken from three healthy human individuals. The organoids have either been grown in standard conditions (control) or treated with IL22 (treated). Includes 6 samples in total, one control from each individual (ctrl1, ctrl2, ctrl3) and one treated from each (treat1, treat2, treat3). The samples have been multiplexed using the antibody hashing technique. The 6 samples have been pooled into the one organoids sample. In order to analyse the raw files, they have to be demultiplexed first. Information necessary for demultiplexing, as well as which files belong to which sample, can be found in the map_file.csv, attached to each sample. Dataset includes raw Fastq files and processed csv count matrices. Fastq files are divided into HTO (hashtag) and RNA (transcriptome) files. HTO has one index (I1) and two read (R1, R2) files and RNA has two index (I1, I2) and two read (R1, R2) files. The fastq files are for the pooled (organoids) sample and need to be demultiplexed. Count matrices contain comma-separated values with cell barcodes as column names and gene names as row names. Since count matrices have been created after the demultiplexing step, there’s one matrix for each of the 6 individual samples. scRNA-seq data from human colon organoids was analysed in the same manner as for the Colitis dataset, apart from the following changes. Data was generated with the Cell Hashing technique, which uses oligo-tagged antibodies against surface proteins to barcode single cells. This allows for samples to be multiplexed together and run in a single experiment. The data was demultiplexed using the HTODemux() function from Seurat (Hao et al., 2021).

  Dataset EGAD00001010168

• WES analysis of paired tumor and non-tumoral DNA of 4 patients with non-muscle-invasive bladder cancer

  We performed WES of tumor DNA and non-tumoral DNA (extracted from PBMC) of 4 patients with non-muscle invasive bladder cancer, who after the tumor resection went on to receive BCG treatment as they had high-risk disease. In order to identify tumor-specific mutations that could give rise to patient-specific neo-epitopes, we performed paired WES of tumor and non-tumoral DNA for each patient. For patient UC2, 3 different tumors were resected at the same time and DNA from these 3 tumors were sent separately for WES.

  Study EGAS50000001382

• Bone morphogenetic protein-9 controls pulmonary vascular growth and remodeling

  Pulmonary arterial hypertension (PAH) and hereditary hemorrhagic telangiectasia (HHT) are two distinct vascular diseases linked to impaired signaling through bone morphogenetic protein (BMP) receptor complexes in endothelial cells. Although BMP-9 plays a central role in activating this pathway by binding to ALK1 and BMPR-­II, its precise function in the pulmonary microvasculature has remained unclear. In this study, we uncover a previously unrecognized role for BMP-9 in regulating pulmonary vascular architecture and homeostasis. Our findings demonstrate that BMP-9 signaling intersects with VEGF pathways and contributes to the delicate balance between vascular growth and remodeling in the lungs. We also show that disruption of this pathway can shift vascular responses toward an HHT-­like state, potentially altering disease susceptibility. These insights offer a unique perspective on how BMP-9 and ALK1 shape pulmonary vascular biology and suggest that targeting this axis could inform future strategies for treating complex vascular diseases such as PAH.

  Dataset EGAD50000001496

• Development of actionable molecular targets and/or biomarkers for prognostication and patient stratification in gynecological cancer based on whole-exome sequencing and epigenomic analysis

  We collected 187 samples of normal and primary tumor tissues in 69 cases of endometrial carcinoma. The purpose of this study is to develop actionable molecular targets and/or biomarkers for prognostication and patient stratification.

  Study JGAS000174

• scRNAseq data of human innate lymphoid cells (ILCs) and natural killer (NK) cells from fresh umbilical cord blood

  scRNA-seq was performed on the BD Rhapsody platform. ILCs (ILC1, ILC2, ILC3) and NK cells were bulk sorted from fresh cord bloods of 3 donors. The 4 samples containing ILCs and NK cells from each donor were stained with Sampletag antibodies (12 samples in total) before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted population were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on a Illumina NovaSeq 6000.

  Dataset EGAD50000001713

• Donor InSight III study: Participants typed during UK Biobank version 2 array development phase

  The Donor InSight III study, undertaken by Sanquin research, recruited 3,046 Dutch blood donors between 2015 and 2016. The purpose of the study was to gain more insight into characteristics of donors, their motivations and health. All participants were at the time of recruitment active blood donors. Genotyping data was produced using the Thermo Fisher Scientific Axiom Genotyping platform. The UK Biobank version 2 array design was used, content on this array has been added to allow for accurate DNA based identification of human blood group antigens.

  Dataset EGAD00001005026

• 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

• 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

• Whole genome sequence: cardiomyopathy, 1 HCM patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000704

• Whole genome sequence: cardiomyopathy, 1 ARVC patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000705