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• DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells

  Clonal haematopoiesis (CH) arises from the expansion of hematopoietic stem cells (HSCs) carrying leukaemia-associated somatic mutations. CH is linked to pathological immune dysregulation and a greater risk of age-related inflammatory diseases. Yet, how CH mutations impact HSC differentiation into immune effector cells remains understudied. Here, we report a single-cell resolution functional and multi-omic investigation of HSC clonal and differentiation dynamics in individuals with DNMT3A-R882 CH. DNMT3A-R882 reshapes the clonal architecture of haematopoiesis towards an aged phylogenetic structure. Functionally, DNMT3A-R882 HSCs produce decreased monocytic output but more abundant and mature neutrophil progeny compared to WT HSCs in the same individual. Whereas DNMT3A-R882 myeloid progenitors display attenuated inflammatory transcriptional programmes, DNMT3A-R882 mature neutrophils acquire proinflammatory and immunomodulatory features typical of maladaptive immunity and CH co-morbidities. Our findings, validated in humanised mice, identify aberrant DNMT3A-R882 HSC-driven neutropoiesis as a key link between CH, immune dysregulation and risk of inflammatory disease.

  Dataset EGAD00001015750

• Targeted Myeloid DNA-Panelsequencing, DKFZ

  Targeted myeloid DNA-Panelsequencing from purified bone marrow blasts of 104 treatment naive AML patients from the discovery cohort. For more details, we refere to Jayavelu, Wolf, Buettner et al. Libraries were prepared from 40 ng DNA using the QIASeq Human Myeloid Neoplasms Panel (Qiagen) according to the manufacturer’s protocol. Samples were tagged with the QIAseq 96-Unique Dual Index Set A for Illumina platforms (Qiagen) to yield unique combinations of i5 and i7 barcodes for each sample. Sample fragment size distribution and concentration was estimated using the Agilent High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent). Samples were pooled in an equimolar fashion, denatured, and diluted to 1.5 pM according to Illumina’s recommendations. The diluted library was sequenced on a NextSeq 500 benchtop sequencer (Illumina) using NextSeq High Output cartridges. Demultiplexing was performed using the BaseSpace cloud platform (Illumina).

  Dataset EGAD00001008501

• NEOPREDICT-Lung: longitudinal whole exome sequencing of non-small cell lung cancers under immunotherapy

  In 43 patients pretreatment tumor biopsies, resected tumors and normal tissue of sufficient quality and quantity were obtained to longitudinally explore the mutational profiles of a comprehensive set of cancer-related genes. For tumor samples, one to four FFPE sections (10 µm thickness, number depending on sample size) were lysed for genomic DNA isolation. Isolation was performed semi-automatically on the Maxwell purification system (Maxwell RSC DNA FFPE Kit, AS1450, Promega) as specified by the manufacturer. DNA was eluted in 50 µl RNase-free water and quantified fluorescently for library preparation using a Qubit 2.0 fluorometer (Life Technology) with its appertaining DNA broad-range assay. Corresponding normal DNA was isolated from blood or PBMCs using routinely available QIAGEN technology. DNA was stored at -20°C before use. Whole-exome sequencing (WES) was performed using the Twist Human Core + RefSeq + Mitochondrial Panel (Twist Bioscience), and 2 x 100 bp fragment sizes were sequenced using a NovaSeq6000 (Illumina). Demultiplexing of sequenced reads was achieved using bcl2fastq (version 2.2).

  Dataset EGAD00001015362

• The effect of freezing delay of cell-type specific transcriptome responses in human brain via snRNA-seq

  In other analysis in the current manuscript, we find a similar gene signature (to dissociation based artifacts in mouse and human tissue) is present in post-mortem microglia and astrocytes, across all snRNA-seq datasets analyzed, although it is highly variable between subjects. ​ Using acutely-resected neurosurgical tissue, we performed single-nucleus RNA-seq and reveal that a similar signature can be detected in microglia following prolonged exposure to room temperature. Tissue handling and methods details, as well as sequencing and analysis details) can be found in the methods section of related manuscript (Marsh et al., 2022). Together, these results suggest that the presence of this signature in post-mortem brain samples may be the result of a combination of acute pre-mortem (agonal state, cause of death, comorbidities, etc.) and post-mortem (post-mortem interval (PMI), storage time, RNA quality, etc.) variables and may not represent normally present cell state.

  Dataset EGAD00001008541

• DERMATLAS: Hidradenoma papilliferum_RNAseq

  Virtually no other tumour type is associated with so many different forms as skin cancer. Histologically, tumours of the skin may arise from epithelium, including epidermis, hair follicle, sebaceous or sweat gland, melanocytes, dermal-associated mesenchymal structures or tissue resident immune cells, making for a diversity of clinical presentations. Importantly, many skin tumour types have an extremely poor prognosis. Many skin tumour subtypes have never undergone molecular profiling, or if they have, targeted sequencing has been used and the number of cases analyzed has been so limited that deriving firm conclusions about the profile of driver genes, DNA mutational signatures and germline alleles has not been possible.For 70 key skin tumour subtypes defined by the World Health Organization, that have not undergone extensive genetic analysis previously, we propose to perform whole exome and transcriptome sequencing, from a range of body sites, to build a genomic atlas of dermatological tumours, including detailed maps of SNVs, copy number alterations, genome-wide methylation and expression profiles.

  Dataset EGAD00001015480

• Distinct embryonic phylogenies and driver events of infant Wilms tumor - RNA

  Cancers of adults typically arise through progressive rounds of clonal diversification and intratumoral selective sweeps which generate a long mutational trunk with shorter subclonal branches. Here, we investigated whether tumors of young children exhibit the same phylogenetic configuration. We studied three infants, including two newborns, with the childhood kidney cancer, Wilms tumour, through whole genome sequencing of bulk tissues, of single cell derived organoids, and of microdissections. All three cancers exhibited unusual driver events, with tumours of newborns harbouring FOXR2 rearrangements, delineating a distinct variant of Wilms tumour. Phylogenetic analyses suggest that tumors were seeded in an early, possibly confined window of development. Unusually, following seeding there was extensive polyclonal diversification with little evidence of clonal sweeps, leading to a distinct phylogenetic configuration more reminiscent of normal tissues rather than of adult cancers. These findings indicate that some childhood cancers may diversify via unorthodox phylogenetic pathways.

  Dataset EGAD00001009813

• Transcriptional consequences of SETBP1 variants in developmental disorders and malignancies

  The SETBP1 gene encodes a DNA-binding nuclear protein that regulates gene expression across multiple tissues. Precise control of SETBP1 dosage is essential for normal cellular function, as both loss- and gain-of-function variants of SETBP1 can lead to severe phenotypic consequences. De novo germline gain-of-function point mutations that prolong SETBP1 half-life result in Schinzel-Giedion syndrome (SGS), an ultra-rare and severe congenital disorder associated with extensive developmental abnormalities and health complications. These SGS-associated variants cluster within a hotspot in the SKI-homology domain of SETBP1, overlapping with somatic mutations recurrently observed in myeloid leukaemia with poor prognosis. Thus far, the precise mechanisms by which these SETBP1 mutations drive disease remain largely unclear. Here, through single-cell and single-nucleus mRNA sequencing of a rare collection of primary patient samples with SGS and myeloid leukaemia, we examined the transcriptional consequences of SETBP1 gain-of-function variants in haematopoietic cells, comparing their impacts when acquired in the germline and somatically in malignancies.

  Dataset EGAD00001015482

• Genomic variants in 121 genes associated with ovarian cancer in cancer tissue and derived organoids

  High-grade serous ovarian cancer (HGSOC) likely originates from the fallopian tube (FT) epithelium, but advanced stages are mostly found outside the FT. We used ex-vivo cultures of HGSOC and knock-out of tumor suppressors in FT organoids to study changes in epithelial cells and niche requirements for normal and transformed FT cells. We found that transformed cells require BMP signaling and are growth arrested in Wnt rich medium. A SureSelectXT Automation Custom Capture Library (Agilent) target enrichment panel was designed. The enrichment panel comprised all coding exons of 121 genes associated with ovarian cancer. Capture was performed according to the manufacturer’s instructions using an NGS Workstation Option B (Agilent) for automated library preparation starting with 3 μg DNA per sample. Sequencing was performed on a Illumina Hiseq 2500 system gnerating 2x100bp paired end reads and a target coverage of >200 per sample. Sequence reads were mapped to the haploid human reference genome (hg19) using BWA. Variants where called with FreeBayes v1.1.

  Dataset EGAD00001005279

• The mutational landscape of normal human endometrial epithelium

  All normal somatic cells are thought to acquire mutations. However, characterisation of the patterns and consequences of somatic mutation in normal tissues is limited. Uterine endometrium is a dynamic tissue undergoing cyclical shedding and reconstitution lined by a gland-forming epithelium. Whole genome sequencing of normal endometrial glands showed that most are clonal cell populations derived from a recent common ancestor, with mutation burdens differing from other normal cell types and many fold lower than endometrial cancers. Mutational signatures found ubiquitously account for most mutations. Many, in some women all, endometrial glands are colonised by cell clones carrying driver mutations in cancer genes, often with multiple drivers. Total and driver mutation burdens increase with age, but are also influenced by other factors, including body mass index and parity, and clones with drivers often originate during early decades of life. The somatic mutational landscapes of normal cells differ between cell types and are revealing the procession of neoplastic change leading to cancer.

  Dataset EGAD00001004547

• DERMATLAS: Hidradenoma papilliferum_WES

  Virtually no other tumour type is associated with so many different forms as skin cancer. Histologically, tumours of the skin may arise from epithelium, including epidermis, hair follicle, sebaceous or sweat gland, melanocytes, dermal-associated mesenchymal structures or tissue resident immune cells, making for a diversity of clinical presentations. Importantly, many skin tumour types have an extremely poor prognosis. Many skin tumour subtypes have never undergone molecular profiling, or if they have, targeted sequencing has been used and the number of cases analyzed has been so limited that deriving firm conclusions about the profile of driver genes, DNA mutational signatures and germline alleles has not been possible.For 70 key skin tumour subtypes defined by the World Health Organization, that have not undergone extensive genetic analysis previously, we propose to perform whole exome and transcriptome sequencing, from a range of body sites, to build a genomic atlas of dermatological tumours, including detailed maps of SNVs, copy number alterations, genome-wide methylation and expression profiles.

  Dataset EGAD00001015481

• A New CA19-9 Cut-Off Value Identifies Lewis Antigen Status and Refines Prognostic Stratification in PDAC

  This study investigates the clinical utility of serum CA19-9 levels in pancreatic ductal adenocarcinoma (PDAC), with a focus on identifying patients with Lewis antigen–negative status due to germline FUT3 variants. Using data from multicenter prospective cohorts in Taiwan, we analyzed CA19-9 classification, FUT2/FUT3 genotypes, and clinicopathological annotations. The goal of this study is to refine prognostic stratification and reduce false-negative interpretation of CA19-9 in PDAC patients. All participants provided informed consent, and the study was approved by the relevant institutional review boards.

  Study EGAS50000001575

• The DIRECT study: A roadmap for ctDNA-based risk prediction, molecular profiling and MRD detection in Diffuse Large B Cell Lymphoma

  DIRECT was a prospective, multisite study assessing the feasibility and utility of circulating tumor DNA (ctDNA) in 188 patients with aggressive B-cell non-Hodgkin lymphoma using capture panel sequencing and an open-source computational pipeline. The aims of the study were 1)baseline risk stratification, 2)genetic profiling and 3)ultrasensitive minimal residual disease (MRD) assessment. This study highlighted the considerable potential, but also the caveats and limitations, of ctDNA technology when applied to aggressive B-cell lymphoma.

  Study EGAS50000000968

• T cell repertorie analysis fom a Spanish cohort of mild and severe cases of COVID-19 recovered patients

  The cohort included 98 mild and 75 severe cases with a median age of 53 years. We amplified and sequenced the T Cell Receptor (TCR β) chain complementary determining region 3 (CDR3b) and performed bioinformatic analyses to assess repertoire diversity, clonality, allelic usage, and epitope affinity CDR3b clustering. CDR3b sequences were amplified by multiplex PCR and sequenced by Illumina. The resulting raw files were processed for clonotype assembly, filtering for coding clonotypes, removal of non-TRB alleles, and downsampling.

  Study EGAS50000000331

• ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19

  In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

  Study EGAS00001004571

• RNA-sequencing of gluten-reactive and non-reactive T-cells from blood samples of treated CeD patients during a gluten-challenge

  Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Here we aimed to characterize such cells in blood of treated CeD patients during gluten challenge with comparison to similar cells of untreated disease. Treated CeD patients underwent a 3-day gluten-challenge with blood sampling at baseline and day 6 (d6). Blood cells were stained with HLA-DQ:gluten tetramers (Tetramer). CD4+, gut-homing Tetramer+ and Tetramer- effector-memory T (TEM) cells at d6 were subjected to bulk RNA-seq (n=7).

  Study EGAS00001004988

• A transcriptome atlas of human skeletal muscles

  We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.

  Study EGAS00001005904

• Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature

  To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki Disease (KD), bacterial infections and viral infections. Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020-April 2021 were prospectively recruited. Whole blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C to those from children with KD, definite bacterial and viral infections. Data deposited here comprises samples from patients recruited into the DIAMONDS study.

  Study EGAS00001007409

• NHLBI GO-ESP: Heart Cohorts Exome Sequencing Project (Siblings with Ischemic Stroke Study, SWISS)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. The Siblings with Ischemic Stroke Study (SWISS) is an affected sibpair (ASP) study of patients and their brothers/sisters who have had similar strokes. The study was conducted to determine the genes that contribute to an individual's risk of developing an ischemic stroke (a stroke due to sudden interruption of blood flow to a part of the brain). Over 600 people have participated in SWISS, with the coordination of the recruitment and flow of the samples occurring at the Mayo Clinic, Jacksonville, FL, under the direction of James F. Meschia, MD. The University of Virginia (Stephen S. Rich, PhD) served as the analytic site for the genetic data. Participants were excluded from SWISS if they had stroke following an invasive cerebrovascular or cardiovascular procedure, if their stroke occurred shortly following an aneurismal subarachnoid hemorrhage, if the stroke occurred in the setting of a mechanical aortic or mitral valve, if the patient had definite CNS vasculitis or if the patient had a Mendelian mitochondrial stroke disorder, including CADASIL, MELAS, Fabry disease, sickle cell anemia or homocysteinemia. For the NHLBI ESP, the youngest 51 ASPs (102 individuals) from SWISS were selected to undergo exome sequencing. These ASPs were selected from among all SWISS participants, excluding those pedigrees with individuals who had TOAST subtypes of stroke of other etiology or of stroke with undetermined etiology. In addition, the affected siblings were required to have the same TOAST subtype (both small vessel (lacunar) or both large vessel (atherosclerotic)). Of those selected, 98 samples passed initial quality control metrics, and 94 completed exome sequencing and were deposited in dbGaP. An additional set of 590 samples from the SWISS collection has been genotyped on the ExomeChip that contained a subset of rare/infrequent variants identified by exome sequencing. These samples include 495 affected individuals (from multiple affected family members) as well as 95 unaffected family members. These genetic and phenotypic data also will reside in dbGaP.

  Study phs000327

• Maintenance of Brain Tumor Profile on Organotypic Brain Slice Culture (OBSC)

  We used uncultured tumor resection tissue from an NF2 mutation-driven grade II meningioma (MG-II) to investigate whether tumors engrafted onto organotypic brain slice cultures (OBSCs) maintained the genetic profile of the parent tumor. We prepared three groups of samples for whole exome sequencing (WES) from the same pool of dissociated MG-II tissue. Group HT is the original uncultured human tumor tissue (n = 3). Group CL is the parent tumor tissue expanded in standard in vitro cell culture until the minimum number of cells required for WES had grown. Because of initial cell loss and subsequent clonal expansion, this required six passages over the span of approximately one month (n = 3). Group BSHT is the uncultured tumor resection tissue engrafted onto OBSCs and subsequently dissected from the OBSCs at the conclusion of our standardized assay length (4 days; n = 4). WES analysis showed that tumor tissue engrafted onto OBSCs maintained a significant genetic resemblance to the parent tumor, while tumor tissue expanded in vitro displayed a distinctly different profile. Furthermore, the mutational profiles of all four BSHT biological replicates were markedly similar, indicating that each OBSC-engrafted tumor indeed contained a representative sample of the original patient tumor. A closer look at the hallmark NF2 mutations existing within all samples revealed that while all samples from the original tumor (HT1-3) and the OBSC-engrafted tumor (BSHT1-4) maintain the frame shift deletion at V24, this mutation was lost in all samples expanded in vitro (CL1-3) and replaced by mutations in other areas. Together, this data suggests that the rapid assay design and tumor-accommodating niche of our OBSC platform enables effective maintenance of the original patient tumor profile. The BBsplit algorithm from the BBtools suite was run on all samples to eliminate rat DNA contamination in the BSHT samples as well as to account for any biases that may result as a part of that process. Only the reads that were binned to the human reference were used for subsequent analysis. Reads were then mapped to the GRCh38 version of the human genome with BWA v0.7.17 and realigned together with ABRA2 v.23. Quality control was implemented using the GATK/Picard v4.1.7.0 toolkit. Somatic variants were called for each sample using the MuTect2 algorithm v4.1.7.0. Variants were merged into a single cohort variant call file and then converted to MAF via vcf2maf v1.6.21 tool. Variants were annotated using VEP v87. To identify mutations with potentially high biological impact, multiple filtering steps were applied to somatic mutation calling. First, we selected only the somatic variants that passed all filters from the MuTect2 FilterMutectCalls algorithm and second, only high/moderate impact (change coding) variants as defined by the VEP annotation were further analyzed. Over 1900 single nucleotide variants (SNVs) were detected across all samples. Figures that summarized the results were generated using maftools.

  Study phs003268

• The Human Virome in Children and its Relationship to Febrile Illness

  Definition of the human microbiome is an important scientific priority. This study will expand the scope of the investigation to include viruses, which account for a substantial proportion of infectious disease morbidity and mortality, especially in children. The long-term goal of this project is to describe the human virome in children and to investigate its relevance to febrile illnesses in children. The project will also seek to understand the relationship of the immune system to the composition of the virome. Thus, the project's specific aims are 1) To elucidate the spectrum of viruses that can be detected using non-biased, high throughput sequencing on samples of blood, respiratory, and gastrointestinal secretions from healthy children and to use this information as a basis for understanding the role of viruses in acute febrile illnesses without an obvious source, and 2) to investigate the effect of various forms of immunosuppression on the spectrum of viruses detected in children, and to use this information as a basis for understanding the role of viruses in acute febrile illnesses occurring in these children. Our preliminary studies show that diverse viruses can be detected in children having undiagnosed fever. To carry out the specific aims, well children will be enrolled prior to having elective surgery, and febrile otherwise well children will be enrolled from the Emergency Department at St. Louis Children's Hospital. Immunocompromised children will be recruited from hematopoietic stem cell and solid organ transplant clinics, the HIV/AIDS clinic, and the rheumatology/immunology clinic from the same hospital. Children with fever will have samples obtained at the time of the febrile illness and at 1 and 6-month follow-up visits. Selected samples from each study group will be analyzed at the Genome Center at Washington University (GCWU) using next generation 454 high throughput sequencing to detect and sequence all viral sequences present. We anticipate detecting and sequencing a broad range of viruses, including previously unrecognized agents. A variety of techniques will be used to investigate the significance of viruses detected. Virus-specific PCR assays will be used to determine the frequency and extent of viruses detected by sequencing, using the full range of samples collected. Host response to the detected viruses will be investigated using serologic analysis, cytokine profiling, and microarrays to characterize host gene expression. These studies will take advantage of follow-up samples to compare the acute response with the response in the convalescent period. This study will draw upon the expertise and technological assets of one of the world's most powerful sequencing centers to provide the research community with a comprehensive sequence data base of the viruses that are present in children, which can be used to improve our understanding of the causes of febrile illnesses in young children, many of which are currently undiagnosed.

  Study phs000264

• Resuscitation Outcomes Consortium Pragmatic Trial of Airway Management in out-of-Hospital Cardiac Arrest (ROC PART-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To determine the effect of an initial airway management strategy using laryngeal tube (LT) insertion, compared with endotracheal intubation (ETI), on survival among adults with out-of-hospital cardiac arrest (OHCA).Background: Out-of-hospital cardiopulmonary arrest (OHCA) affects more than 350,000 adults in the United States each year, with only a low percentage of patients surviving to hospital discharge. Emergency medical services (EMS) paramedics commonly perform ETI or insertion of supraglottic airways (SGAs), such as the LT, on patients with OHCA to facilitate oxygenation and protect the lungs from aspiration of vomitus. Because SGA insertion is rapid, simple, and requires less training compared to ETI, many EMS agencies have incorporated this as the primary method of ventilation during OHCA resuscitation. However, the optimal method for OHCA advanced airway management is unknown.Participants: A total of 3004 patients were included; 1505 assigned to initial LT and 1499 assigned to initial ETI.Design: PART was a multicenter cluster-crossover randomized trial. The trial included 27 EMS agencies associated with US sites of the Resuscitation Outcomes Consortium (ROC). The EMS agencies were grouped into 13 randomization clusters. Each cluster selected a crossover interval of 3 or 5 months. Within each cluster, treatment assignments for consecutive intervals were computer-randomized in blocks of 2 to ensure balanced exposure to both airway groups. Crossovers between study groups could occur more than once. Treatment assignments were initial LT insertion or initial ETI. Neuromuscular blocking agents or video laryngoscopy was permitted for initial intubation efforts. The trial did not limit the number of initial LT insertion or ETI attempts. If the initial insertion efforts were unsuccessful, EMS personnel performed rescue airway management using any available airway technique. EMS personnel followed local protocols for confirmation of airway placement and management of OHCA, including field termination of resuscitation efforts. Patients receiving bag-valve mask (BVM) ventilation only were retained in their assigned treatment group per intention-to-treat principles. The trial did not prescribe clinical care at the receiving hospitals, including use of EMS airway, targeted temperature management, percutaneous coronary intervention, or the timing of withdrawal of life-sustaining therapy.The primary outcome was 72-hour survival. Secondary outcomes included return of spontaneous circulation, survival to hospital discharge, and favorable neurological status at hospital discharge (Modified Rankin Scale score ≤3). Conclusions: Among adults with OHCA, a strategy of initial LT insertion was associated with significantly greater 72-hour survival compared with a strategy of initial ETI. These findings suggest that LT insertion may be considered as an initial airway management strategy in patients with OHCA, but limitations of the pragmatic design, practice setting, and ETI performance characteristics suggest that further research is warranted.

  Study phs003902

• SC_DDD-G-5

  Post-QC (pre-imputation) genotype data for N=2,166, a subset of trios described in EGAD00010001602. These data form N=722 complete trios in which the proband has a neurodevelopmental phenotype (Niemi et al. Nature 2018). Includes HPO phenotype terms for patients. Samples were genotyped on the Illumina HumanOmniExpress BeadChip

  Dataset EGAD00010001606

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Shotgun Proteomics; Glioblastoma samples from 11 patients were obtained at initial and recurrent tumor stages. Proteins were extracted, identified and quantified via tandem mass spectrometry based on a TMT isobaric labelling approach. Quatitative proteomics reveals 146 differentially abundant proteins using a patient-matched statistical modelling. Analysis of proteolytic processing reveals differential proteolytic patterns in recurrent tumors. Proteogenomics reveals the presense of 30 single-amino acid variants present in glioblastoma tumor and 1 of those as increased in recurrent tumor.

  Dataset EGAD00010002350

• Whole Genome Sequencing of HCC

  The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Dataset EGAD00001003994

• Rheumatoid Arthritis Finger Stick RNA Sequence Data

  This is a longitudinal study of 355 blood samples collected weekly from 5 patients with Rheumatoid Arthritis with varying disease activity over the course of one to five years. Blood samples were self collected from finger sticks and mailed from home. RNA was extracted, purified and sequenced.

  Study phs003179

• Multi-Omic Analysis of Von Willebrand Factor Regulation in Endothelial Colony Forming Cells

  This study evaluated the multi-omic analysis of endothelial cells with a focus on von Willebrand factor regulation, and investigated aspects of endothelial regulation in the context of blood disorders. The data available at dbGaP consist of multi-omic analyses of these cells. 

  Study phs002731

• Familial Exome Sequencing in Rare Pediatric Phenotypes

  To discover novel candidate genes associated with rare Mendelian phenotypes, we will conduct individual genomic and phenotypic characterization using genome-wide array, pedigree exome sequencing, candidate genotyping, and pertinent clinical testing to define phenotype. Pedigrees included in this submission will have a variety of clinical pathological phenotypes.

  Study phs000553

• Understanding the Biology of Language Impairment through Whole Genome Sequencing

  This study involves the whole genome sequencing of a cohort of 390 individuals assessed for language ability, IQ, and behavior as schoolchildren. The primary goal of the study is to identify genes, regulatory elements, and pathways which may underlie variation in language ability within an average population. 

  Study phs002255

• Genetics of Fuchs Corneal Dystrophy

  This grant proposal continues to expand our understanding of the clinical presentation of Fuchs corneal dystrophy, and its underlying genetic basis, which will lead to the development of better therapeutic models and treatment for a common corneal dystrophy that affects 4% of the US population over age 40.

  Study phs001834

• BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

  RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000808

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731

• RnaSeq data from 414 tumor samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.

  Dataset EGAD50000000733

• Base modification analysis using single molecule real-time sequencing

  This dataset was generated using single-molecule real-time sequencing for both training and testing purposes. The DNA samples isolated from human buffy coats or placenta of healthy individuals (n=4,) were prepared in a way that four types of base modifications were incorporated, including unmodified controls, 5mC, 5hmC, and 6mA. The sequence data for each sample consists of subreads produced by single-molecule real-time sequencing and stored in a bam format. Details of the specific experiments conducted in this study are outlined in our manuscript.

  Dataset EGAD50000000541

• Epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages

  Immune memory is key to effective antimicrobial responses, but the impact of mRNA vaccines on this process is not fully understood. Our research shows that SARS-CoV-2 mRNA vaccines alter the epigenetic profile of human macrophages, specifically enhancing histone acetylation, which is linked to immune training. Significant epigenetic changes, along with increased cytokine release, require two vaccine doses. However, these effects diminish over time but can be restored with a booster dose six months later, maintaining a strong pro-inflammatory response.

  Dataset EGAD50000000495

• Sequencing data of the ampulla and fimbriae of the fallopian tube in pre-menopausal women

  A total of 10 pre-menopausal patients were recruited for this study. Sequencing of both the fimbriae and ampullary region of the fallopian tubes was performed using 10x Genomics single-cell RNA-seq and ATAC-seq. For one patient, data were sequenced across 4 lanes, while the remaining patients' data were sequenced in 2 lanes each, resulting in a total of 44 sequencing datasets for each platform.

  Dataset EGAD50000000889

• Clinical Outcomes for 344 Diffuse Large B-Cell Lymphoma Patients

  This dataset contains clinical outcomes for 344 Diffuse Large B-Cell Lymphoma patients. For each subject we have recorded AGE (binarized: > 60, <= 60), SEX (male or female), LDH (serum lactate dehydrogenase), ECOG (Performance status 3 or 4), STAGE (Disease stage III or IV according to the Ann Arbor staging system), EXBM (Two or more extranodal sites of disease (outside of a lymph node), BSYMP (Presence of B symptoms), and BM (Bone marrow involvement). All data are delivered as a single XLSX file with one row per patient.

  Dataset EGAD50000001536

• Multi-omic dataset utilized in the analysis of a phase II study of epigenetic priming followed by nivolumab in lung cancer

  This dataset includes sequence files from whole exome sequencing and bulk RNA sequencing of tissue and blood biospecimens from a phase II clinical trial investigating epigenetic priming followed by immune checkpoint blockade in non-small cell lung cancer (NSCLC; NCT01928576). There are 78 whole exome sequencing files and 36 bulk RNA sequencing files included in this dataset.

  Dataset EGAD50000001336

• WES data of pediatric cancer patients with P/LP variants in HBOC-related genes

  The current study aimed to identify (likely) pathogenic germline variants(LP/PVs) in 25 adult-onset HBOC-related genes within a cohort of 372 pediatric cancer patients. For this purpose we performed (paired-end) whole exome sequencing (WES) using Ilumina sequencing technology. The files uploaded here belong to the 27 individuals with such a LP/PV. The project provides insight into the prevalence and spectrum of such variants in childhood cancer, contributing to the understanding of genetic predisposition in pediatric oncology.

  Dataset EGAD50000001561

• Trial of Onco-Panel for Geneprofiling to Estimate both Adverse events and Response by cancer treatment (TOP-GEAR)

  Bam files and fastq files in a hospital-based prospective study (TOP-GEAR project, the 2nd stage) to investigate the feasibility and utility of NGS-based analysis of 114 cancer-associated genes (the NCC Oncopanel test). DOI: 10.1111/cas.13969

  Study JGAS000662

• RIP-SeqRaw data

  This dataset contains 15 paired FASTQ files from the PTBP1 project. Sequencing data were generated using bulk directional RNA-seq and RIP-seq experiments performed on a NovaSeq 6000 platform (2×100 bp paired-end reads). The dataset comprises two groups of samples: controls and patients. For each group, both input and immunoprecipitated samples are available. Patient samples correspond to skin biopsies from individuals affected by a neurodevelopmental disorder associated with variable skeletal dysplasia and disproportionate short-limbed short stature.

  Dataset EGAD50000001723

• Targeted panel sequencing of two patient-derived melanoma cell lines

  Targeted panel sequencing was conducted on patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). The parental cell line was generated from disseminated cancer cells (DCCs) obtained from a lymph node sample of a melanoma patient. The resistant cell line was generated from the parental one through exposure to Vemurafenib. Normal peripheral blood lymphocytes from the same patient served as the control for comparison. Sequencing on NovaSeq6000. Fastq files.

  Dataset EGAD50000001745

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• Japanese Alzheimer's disease neuroimaging initiative

  Japanese ADNI aims to establish imaging and biofluid markers that can predict and monitor the progression of changes in the brains of elderly individuals with AD, mild cognitive impairment (MCI) or normal cognition, and eventually be used as a surrogate markers for the clinical trials of DMDs for AD.

  Study JGAS000051

• Whole exome sequence analysis in sporadic amyotrophic lateral sclerosis

  To identify a susceptible gene for amyotrophic lateral sclerosis, exome sequence analysis was conducted in patients with amyotrophic lateral sclerosis and control subjects to perform whole genome association studies. In this data set, exome sequencing data of 11 patients with amyotrophic lateral sclerosis was included.

  Study JGAS000013

• An imputation reference panel of HLA variants in Japanese

  We constructed a human leukocyte antigen (HLA) imputation reference panel of Japanese ancestry, which includes genotype data of HLA alleles and single nucleotide polymorphisms (SNPs) in the major histocompatibility complex (MHC) region of 908 healthy Japanese controls. Variant locations are based on NCBI build 36.

  Study JGAS000018

• comprehensive genetic analysis and database construction for head and neck cancer

  The main purpose is to conduct comprehensive genetic analysis of head and neck malignant tumor tissue and patient-derived blood, and to construct a database for it. By analyzing these databases, we aim to clinically identify recurrence and metastasis prediction markers and establish new molecular target therapies.

  Study JGAS000214

• Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo).

  Dataset EGAD50000000677

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• RNAseq of human breast cancer tumors from the PEARL study

  Formalin fixed, paraffin-embedded human breast cancer tumor samples had RNA extracted using the Thermo Scientific KingFisher Flex instrument and the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit; Total RNA libraries were created using the Bravo Automated Liquid-Handling Platform and the TruSeq Stranded Total RNA Library Prep Gold Kit; libraries were sequenced on the Illumina NovaSeq 6000 machine using a 2x50 bp paired-end configuration to target a read depth of 120 million clusters per library.

  Dataset EGAD00001015613

• fibroblast RNAseq from a GINS3 patient and two parents

  RNA-seq was performed from 3 separate GINS3 patient fibroblast cultures and 1 replicate of fibroblasts derived from each of the two parents. RNA-seq libraries were generated with NEBNext Ultra II Directional RNA library prep for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and sequenced on Illumina NextSeq500 with paired-end 150 bp read length. SIRV Set 3 (Lexogen) spike-ins were added. Two fastq files are provided for each RNAseq sample.

  Dataset EGAD00001008571

• ICU transcriptomics: Assessing the role of the host immune response in patients with ventilator-associated pneumonia

  This is a study of 100 patients with the aim to provide transcriptomic sequencing data analysis of cells isolated from bronchioalveolar lavage and blood samples from critically ill patients with pneumonia on an intensive care unit in order to investigate the host contribution to disease. 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/

  Dataset EGAD00001015407

• WGS of primary mesothelioma cell lines

  Mesothelioma is an aggressive cancer associated with previous exposure to asbestos and dismal prognosis. Since a pemetrexed/cisplatin combination was introduced for treatment of mesothelioma, no new first- or second-line therapies have been discovered. Thus, to better understand what drives mesothelioma carcinogenesis and to identify potential targets for therapy, in this project we aim at performing WGS analysis of a panel of mesothelioma cells lines.

  Dataset EGAD00001009641

• 33 Paired (Normal-Tumor1-Tumor2) MM whole-exome data

  Samples were sequenced from 33 multiple myeloma patients including tumor presentation and relapse samples and a matched patient control sample. Tumor DNA was isolated from CD138-positive plasma cells. Control DNA originated from peripheral blood leukapheresis products collected after induction therapy. Libraries were prepared using the SureSelectQXT sample prep kit and the SureSelect Clinical Research Exome kit (Agilent), with additional baits covering the Ig and MYC loci. Paired-end sequencing was performed to an average sequencing depth of 118× on a HiSeq2500 (Illumina).

  Dataset EGAD00001002165

• Cancer and germline exomes consisting of FASTQ reads from melanoma, lung and colon cancer samples

  Cancer and germline exomes consisting of FASTQ reads from 6 individuals (4 melanoma, 1 lung and 1 colon cancer). Exome sequencing was performed on illumina with a depth of 100x to 200x. 2 Melanoma datasets contain reads from 2 different tumor regions 2 Melanoma datasets contain reads from 1 tumor region and from a tumor derived cell line 1 Melanoma dataset contains reads from 2 healthy tissues Colon and lung datasets contain both 1 matched germline-tumor pair

  Dataset EGAD00001007950

• pan-cancer plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 266 different human donors. The first, pan-cancer, cohort covers 25 high-grade to metastatic cancer types (8 cancer patients per type) and a control group (8 healthy donors). The validation cohort comprises additional plasma samples from ovarian, prostate and uterine cancer patients (12 per type) as well as additional samples from controls (22 new and 8 repeated). Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

  Dataset EGAD00001009713

• Chronic lymphocytic leukemia driven by paradoxical ERK activation during BRAF inhibitor treatment

  Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (&gt;97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (&gt;90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations.

  Dataset EGAD00001000997

• Multiple myeloma Total Therapy trial patient sequencing

  DNA was obtained from either CD138+ cells from the bone marrow of multiple myeloma patients (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using the HyperPlus kit (KAPA Biosystems). After PCR amplification the libraries were hybridized with probes against either a targeted panel consisting of 140 genes and chromosomal regions (Nimblegen) using SeqCap reagents (Nimblegen). Hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Dataset EGAD00001004373

• Combined Telomerase Vaccination and Pembrolizumab in Advanced Melanoma: WES and RNA sequencing of biopsies from a Phase I Trial

  This dataset contains whole-exome and RNA sequencing of biopsies obtained from patients enrolled in a phase I clinical trial investigating the UV1 vaccine in combination with pembrolizumab in patients with advanced melanoma.

  Dataset EGAD00001011074

• WCDT Hi-C assays performed mCRPC biopsies

  Paired FASTQ files from a Hi-C assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument.

  Dataset EGAD00001009408

• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• Targeted gene panel sequencing of matched diagnosis-remission-relapse B cell precursor acute lymphoblastic leukemia samples

  Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

  Dataset EGAD00001004977

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• snRNA-seq BAM files from 10x Multiome profiling of human fetal liver hematopoiesis

  This dataset provides snRNA-seq BAM files from a single-nucleus multiome study of 53 human fetal liver samples (5–18 post-conception weeks). Live CD45+CD235- cells were sorted from dissociated tissue, and isolated nuclei were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Raw sequencing data were processed and aligned to GRCh38-2020-A-2.0.0 using Cell Ranger ARC v2.0.2.

  Dataset EGAD50000002337

• IBD_Whole_Genome_Sequencing

  Whole genome sequences at 15X depth of patients with Inflammatory Bowel Disease. 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 EGAS00001002754

• Repeated_clinical_malaria_episodes_are_associated_with_modification_of_the_immune_system_in_children_

  Repeated clinical malaria episodes are associated with modification of the immune system in children.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 EGAS00001003167

• Microinjection_of_hIPSC_derived_intestinal_organoids_with_Salmonella_Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are 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 EGAS00001001253

• Targeted gene expression analysis on FFPE specimen from NSCLC patients

  This study measured the expression of a panel of over 300 cancer immunotherapy-relavant genes in tumors after neoadjuvant chemoimmunotherapy. It was performed on RNA from FFPE tumor tissue. Differential gene expression analysis was performed between patients achieving or not achieving an event-free survival of 12 months.

  Study EGAS50000001140

• RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue.

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001008071

• Molecular characterisation of paediatric PDX cells before and after 3D RASTRUM bioprintin

  This dataset is a part of the publication and contains source data for comparative analysis of the molecular (TSO500, RNAseq) characteristics between patient-derived xenograft (PDX) cells from high-risk paediatric neuroblastoma and sarcoma models before and after 3D bioprinting using RASTRUM Bioprinter.

  Study EGAS00001008220

• Perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma: Primary phase 2 trial results with ctDNA residual disease analyses

  This data set includes sequence files from whole genome sequencing of tumor (n=28), normal (n=28), and blood (n=113) specimens from a phase 2 clinical trial of neoadjuvant nivolumab and nivolumab/ipilimumab in resectable diffuse pleural mesothelioma (NCT03918252).

  Study EGAS50000001195

• HipSci_RNASEQ_PID

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Platelet and bleeding disorders patients

  Study EGAS00001001990

• Genome-wide array data from Eivissan and Menorcan Individuals

  22 and 20 genome-wide array data for Eivissan and Menorcan healthy unrelated volunteers, respectively. The affymetrix Human Origins array was used to genotype these individuals. The variant set was lifted over to the hg38 human genome reference. A single gziped VCF file can be found.

  Study EGAS50000000423

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00001000585

• Multi-omics analysis of CUD in the VS

  The aim was to molecularly characterize the human ventral striatum in CUD. For this, we generated epigenomic, transcriptomic, and proteomic datasets at the bulk-level, performed integrative multi-omics analyses and further analyzed CUD-associated transcriptomic changes at a cell type-specific level using snRNA-seq.

  Study EGAS50000000623

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00000000059

• An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors

  A pilot study examining genetic determinants associated with elite long term non progression and rapid progression using exome sequencing of individuals at the extremes of the distribution of HIV control and progression. Data can only be used for HIV related research.

  Study EGAS00001000057

• Combination pembrolizumab and radiotherapy induces systemic anti-tumor immune responses in immunologically-cold non-small cell lung cancer

  This data set includes sequence files from whole exome sequencing and RNA sequencing from serial tissue and blood biospecimens from a phase 2 clinical trial of stereotactic body radiation therapy (SBRT) followed by pembrolizumab in metastatic non-small cell lung cancer (NSCLC; NCT02492568).

  Study EGAS50000000277

• An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease

  We established and validated sequence capture based NGS testing approach for all genes known for cystic and polycystic kidney disease including PKD1. This setup overcomes the complication of unspecific capture of pseudogenes by applying a mapping algorithm efficiently and specifically aligning reads to the PKD1 locus.

  Study EGAS00001001003

• Expression profiles of DLL1 positive and negative subpopulations in metastatic colorectal cancer organoids under cetuximab treatment

  Bulk RNA sequencing was performed on metastatic colorectal cancer (mCRC) organoids subjected to cetuximab treatment and FACS-sorted according to DLL1 positivity. This study is part of a larger set of studies focused on investigating cetuximab induced populations in mCRC organoids

  Study EGAS50000001780

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Study EGAS50000000141

• Immunodeficiency_

  We are doing single-cell RNAseq from B cells from monozygotic twins discordant for common variable immunodeficiency 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/

  Study EGAS00001002667

• Cellular Analysis of Resistance and Evolution (CARE) IDH-mutant glioma dataset

  In IDH-mutant glioma, genetic evolution and cellular heterogeneity across and within tumors may drive therapeutic resistance. Here, we analyzed 35 longitudinal patients by single-nucleus RNA-sequencing with a subset also characterized by bulk tumor DNA sequencing to better understand IDH-mutant glioma evolution.

  Study EGAS50000001727

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Study EGAS00001000575

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase II. 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 EGAS00001002461

• _Isotype_resolved_sequencing_of_B_cell_receptor__in_sorted_memory_populations

  Optimisation of ex vivo Memory B cell Expansion/Differentiation for Interrogation of Rare Peripheral Memory B Cell Subset Responses 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/

  Study EGAS00001002633

• Family-based GWAS for CRSwNP

  AbstractOur goal was to identify genetic markers and genes associated with susceptibility to chronic rhinosinusitis with nasal polyps using a family-based genome-wide association study.MethodsPatients with CRSwNP and controls were recruited. SNP association values were generated using DFAM (implemented in PLINK) and Efficient Mixed Model Association eXpedited (EMMAX).

  Study EGAS00001002665

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase III. 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 EGAS00001002787

• Predictor_ChemoNEAR_TNBC

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict.

  Study EGAS00001002806

• Genomic analysis of Japanese gastric cancer (345 gastric cancers of NCC)

  As a contribution to the International Cancer Genome Consortium, whole exome sequencing of 345 Japanese gastric cancer (345 gastric cancers of NCC) with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer.

  Study EGAS00001002884

• Stratified Medicine Paediatrics (SMPaeds): molecular profiling of relapsed paediatric cancer

  We profiled a large heterogenous cohort of matched diagnostic-relapse tumour tissue and plasma-derived cell free DNA (cfDNA) from patients with relapsed and progressive solid tumours of childhood. Tumour DNA and cfDNA were analysed by targeted panel sequencing and low coverage whole genome sequencing.

  Study EGAS50000000549

• ENGAGE___Amendment__500_genes_exon_sequencing_

  The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes

  Study EGAS00001000137

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Study EGAS50000000107

• Paired whole exome sequence of subcutaneous panniculitis-like T-cell lymphoma.

  Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare subtype of peripheral T-cell lymphoma affecting younger cases and associated with hemophagocytic lymphohistiocytosis. To clarify molecular pathogenesis of SPTCL, we analyzed paired tumor and germline DNAs from 13 patients by whole exome sequencing.

  Study EGAS00001003282

• Non-invasive prediction of immunotherapy response (NIPIT) project

  This project aims to find transcriptomic biomarkers for immunotherapy response prediction in several cancer types. So far, we have performed poly-A RNA-seq using whloe blood and peripheral blood mononuclear cells from 33 non-small cell lung cancer patients, collected before and after the start of immunotherapy.

  Study EGAS50000000266

• High_powered_complex_trait_association_mapping_through_whole_genome_sequencing_of_a_selected_subpopulation_of_the_INGI_Val_Borbera_genetic_isolate

  The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.

  Study EGAS00001000398

• Variables of mass cytometry (CyTOF) innate immune cell counts

  For 61 COVID-19 patients we performed a CyTOF analysis to characterize the innate immune landscape associated with disesase severity. For this study, 37 analyzed populations have been included, speccialy focused in monocyte-macrophague subpopulations. For more information, please consult DOI: 10.3389/fimmu.2022.1094644

  Study EGAS50000000588

• Genotype variables of the 61 COVID-19 patient cohort used in the main project of data integration

  We selected SNPs with a minor allele frequency (MAF) higher than 10% in the Caucasian population from the Ensembl database. Specifically, we selected ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788) for the present analysis. For more information, please refer to:

  Study EGAS50000000589

• High-resolution analyses of human sperm dynamic methylome reveals thousands of novel age-related epigenetic alterations

  Age-dependent modifications of the germ cells epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging. A cohort study was designed to investigate the effects of age and fertility status on sperm DNA methylation.

  Study EGAS00001004168

• WES for CNV-verified CTCs enriched by high-throughout microfluidic device from entire cancer patient leukopak

  WES analysis (illumina platform, PE150, 100x coverage) was performed on a pool of copy number variation (CNV)-verified CTCs that were enriched using high-throughout microfluidic device from entire leukopak from patients with metastatic prostate cancer (GU-1 and GU-2).

  Study EGAS50000000724