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• Center for Common Disease Genomics [CCDG] - Cardiovascular: The Bangladesh Risk of Acute Vascular Events (BRAVE) Study

  The Bangladesh Risk of Acute Vascular Events (BRAVE) study is a hospital-based case-control study in Bangladesh which was established by the Cardiovascular Epidemiology Unit of Cambridge University in the UK in partnership with the key local cardiology and research centres to examine environmental, genetic, lifestyle and biochemical determinants of myocardial infarction (MI) among this South Asian population. By the end of 2016, this study has recruited ~8000 clinically confirmed first-ever MI cases (with a significant proportion being early-onset MI), and ~8000 healthy controls frequency-matched by age and sex. This site hosts data from ~500 whole genomes and ~1500 whole exomes (50% cases and 50% controls)

  Study phs001398

• Single Cell Analysis of Psoriasis Resolution following IL-23 Blockade

  Full-thickness skin biopsies were obtained from five individuals with severe psoriasis who were receiving risankizumab treatment. Skin biopsies were taken from lesional and non-lesional sites at baseline, and from lesional sites at day 3 and day 14 of therapy. All biopsies were taken from site-matched areas on the lower back/buttocks. Single-cell RNA sequencing was performed using a 10x Genomics platform. Myeloid and fibroblast populations showed the strongest change in gene expression after 3 days. An inflammatory, transient WNT5A+/IL24+ fibroblast state was identified, which was elevated in abundance in lesional skin versus non lesional skin, and decreased after 14 days of treatment. R1 and R2 FASTQs files are available.

  Study phs003351

• NHLBI TOPMed: Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE)

  ECLIPSE was a longitudinal observational study of 2164 COPD subjects and a smaller number of smoking controls (337) and nonsmoking controls (245) followed regularly for three years, with three chest CT scans (at baseline, one year, and three years) (Vestbo et al., 2008, PMID: 18216052). Subjects were enrolled at clinical centers in the US, Canada, Europe, and New Zealand. Inclusion criteria included subjects ages 40-75, at least 10 pack-years of smoking, and spirometry in GOLD grades 2-4 (COPD cases) or normal spirometry with post-bronchodilator FEV1 >85% (predicted) and FEV1/FVC>0.7 (controls). Study visits were performed at enrollment, three months, and every six months thereafter with spirometry, questionnaires, and other clinical evaluations. The ECLIPSE CT scans have been analyzed with the VIDA software for emphysema and airway phenotypes. ECLIPSE has provided key insights into the clinical epidemiology of COPD, including COPD exacerbations (Hurst, et. al., 2010, PMID: 20843247) and lung function decline in COPD (Vestbo, et. al., 2011, PMID: 21991892). ECLIPSE has been used in a number of genetic studies of COPD susceptibility and protein biomarkers (Faner, et. al., 2014, PMID: 24310110). Genome-wide gene expression microarray data are available in 147 induced sputum samples from COPD subjects and 248 peripheral blood samples from COPD and control subjects. Phenotype data for ECLIPSE subjects is available through dbGaP phs001252.

  Study phs001472

• The Cardiogenics study

  Cardiogenics is an European collaborative project, it started in January 2007 and was funded by the European Commission through its Sixth Framework Program (reference LSHM -CT-2006-037593) until 2011. It involved several laboratories from France (INSERM UMRS937), Germany (Lübeck University; Regensburg University), United Kingdom (the Welcome Trust Sanger Institute; University of Leicester) and Sweden (Uppsala University Hospital) and was coordinated by a management group composed of scientists from these different institutions. Under the coordination of the management group the laboratories are still developing projects using Cardiogenics data sets. As part of the Cardiogenics project, RNA from monocytes and macrophages of 363 patients with coronary artery disease and 395 healthy individuals was prepared and genome-wide expression was assessed in both cell types using the Illumina HumanRef 8 v3 Beadchip . The DNA of all these individuals was genotyped using the Human 610 Quad custom arrays. Both data sets were used to conduct eQTL analyses. A subsample of subjects included in an allelic-imbalance substudy were also genotyped using the Illumina Human Custom 1.2M array. Detailed description of these datasets can be found in Shah S et al. Circ Cardiovs Genet 2011; Rotival M et al. Plos Genet 2011, Almlöf et al. Plos One 2012 and Garnier S et al. Plos Genet 2013

  Study EGAS00001000411

• NIH RECOVER: A Multi-Site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults

  The NIH Researching COVID to Enhance Recovery (RECOVER) initiative comprises a set of three combined retrospective and prospective, longitudinal, observational meta-cohort studies with nested case-control studies designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection (PASC or Post-COVID syndrome) in a diverse study population representative of the general COVID-19 population in the US. Enrolled patients with and without known SARS-CoV-2 infection will be observed for clinical signs and symptoms of PASC and will be assessed for risk and resiliency factors and potential mediating factors associated with the severity and progression of PASC. The objective of the RECOVER initiative is to enhance knowledge of recovery from SARS-CoV-2 infections in order to support development of novel diagnostic and therapeutic interventions. Overarching scientific objectives are as follows: Characterize the incidence and prevalence of sequelae of SARS-CoV-2 infection. Characterize the spectrum of clinical symptoms, subclinical organ dysfunction, natural history, and distinct phenotypes identified as sequelae of SARS-CoV-2 infection.Define the biological mechanisms underlying pathogenesis of the sequelae of SARS-CoV-2 infection. The RECOVER observational studies comprise three cohorts across the lifespan (adult, pediatric, and tissue pathology (autopsy)). The data collection and data analysis plans for each cohort have been harmonized to use common data elements where feasible. Brief descriptions of each cohort are provided in the following paragraphs:1) NIH RECOVER: A Multi-site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults (this study)The RECOVER adult cohort study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals who will enter the cohort with and without SARS-CoV-2 infection and at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study will be conducted in the United States and subjects will be recruited through inpatient, outpatient, and community-based settings. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptom screen will be reported by subjects or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical examinations and radiologic examinations will be performed at local study sites with cross-site standardization. A summary of information available by request in the RECOVER Adult Cohort (this study) can be reviewed via the "Adult Cohort Dataset Release Notes" and the "REDCap Codebook for the Adult Cohort" documents.2) The RECOVER Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study: A Multi-Center Observational Study (data not yet released)The RECOVER pediatric study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals ages newborn-25 years who will enter the cohort with and without SARS-CoV-2 infection at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study recruit participants inpatient, outpatient, and community-based settings in the United States. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptoms will be reported by participants or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical and radiologic examinations will be performed at local study sites with cross-site standardization.3) NIH RECOVER: A Multi-site Pathology Study of Post-Acute Sequelae of SARS-CoV-2 Infection (data not yet released)The RECOVER tissue pathology study is a cross-sectional study designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection in a diverse population representative of the general COVID-19 population in the US. The autopsy study will characterize the pathology of PASC in (i) non-hospitalized patients who die 30 days or later from symptom onset of COVID-19, and (ii) hospitalized patients who die 30 days or later after discharge from a hospitalization for COVID-19. The study will include decedents who had previously fully recovered from SARS-CoV-2 infection (i.e., >30 days from onset in non-hospitalized, or >30 days from discharge in hospitalized patients), and decedents who meet clinical criteria of PASC as defined by the recent World Health Organization publication (see Section 5.4 below). The autopsy study will also explore the pathology of acute SARS-CoV-2 infection in a smaller subset of patients who died 15-30 days from symptom onset. This protocol defines the common set of clinical data elements, autopsy procedures for tissue collection, core measures, pathology protocols, shared pathology tissues, data elements, and methodology. Each investigator site is expected to perform autopsies on the decedents to address the pathophysiology of the potential long-term effects of SARS-CoV-2 infection on human health. The Consortium analysis plan aims to address research questions by incorporating: 1) tissue obtained from autopsies performed at each Phase II participant's site; and 2) tissue available from other pathology investigators/autopsy sites within the Consortium.

  Study phs003463

• Bulk Iso-Seq from brain tissue and exosomes isolated from brain tissue using long-read PacBio sequencing of poly-adenylated transcripts

  Human brain sEVs were isolated from postmortem human brain tissue. RNA was extracted from both the source brain tissue and sEVs and prepared for long-read sequencing. cDNA was sequenced on the PacBio Sequel II. The data provided have undergone processing using the tool ccs (v6.0.0) to generate circula consensus reads. For further processing, it is recommended to follow the guidelines at https://isoseq.how/, starting with using lima to remove cDNA primers.

  Dataset EGAD50000000043

• Development and Validation of a Prognostic and Predictive 32-Gene Signature for Gastric Cancer

  We applied this signature to a 567-patient GC cohort to establish genomic-based molecular subtypes and then used a support vector machine to build a molecular subtype-based risk-scoring model. Both source code and supplementary datasets for risk score prediction are available at https://github.com/hwanglab/Yonsei_gastric_cancer_32genes.

  Dataset EGAD00001008091

• Genetic analysis of patients with Inherited Retinal Dystrophies (IRDs) using next generation sequencing to identify the causative variants

  Genetic analysis of patients with Inherited Retinal Dystrophies (IRDs) was carried out by performing Whole Genome Sequencing (WGS). The main purpose of this study is to identify simple and complex mutations responsible for IRD in patients. WGS was performed on selected affected and unaffected individuals using the Illumina HiSeqX10. The reads were aligned to human genome 19 (hg19) and variant calling was performed using Genome Analysis Toolkit (GATK). The genotyping quality of single nucleotide variants (SNVs) and indels was assessed using the variant quality score recalibration approach implemented in GATK. Copy number variations (CNVs) were called using Genome STRiP and SpeedSeq. This large set of whole genome sequencing data from different ethnicity can be stored and shared through dbGaP. This data could serve as a source for checking frequencies of variants or the pathogenicity of selected variants in different ethnicities.

  Study phs001619

• The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

  Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that in other non- Africans.

  Study EGAS00001001959

• Exploring Extracellular Vesicle microRNAs in Usher Syndrome Type 1B: Tear-Derived EVs as Indicators of Retinal Health

  The goal of this study was to explore extracellular vesicles (EVs) from human tears and iPSC-derived RPE cells as biomarkers for Usher syndrome type 1B (USH1B), a rare inherited disorder causing deafness and retinitis pigmentosa. Researchers found that tear EVs showed higher levels and diversity of miRNAs, making them a promising non-invasive source for diagnosing USH1B. In contrast to patient-derived RPE cells, which did not express MYO7A protein despite similar expression levels in controls, the study identified specific microRNA signatures associated with retinal degeneration in both tear EVs and RPE-derived EVs. The findings suggest that tear EVs can serve as a useful biomarker for USH1B diagnosis, monitoring, and therapeutic development. Overall, this research aims to contribute to our understanding of disease mechanisms and identify potential targets for treatment in patients with Usher syndrome type 1B.

  Study EGAS50000001200