cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60645/bdc-12q7-4279
title: Genetic Risks for ALI in ARDSNet and the iSPAAR Consortium

description: 
This GWAS sub-study [phs000686](study.cgi?study_id=phs000686) contains genotype and selected phenotype of subjects available from the [phs000631](study.cgi?study_id=phs000631) study. Summary level phenotypes for the "ARDSnet and the iSPAAR Consortium: Genetic Studies" study participants can be viewed at the top-level study page [phs000631](study.cgi?study_id=phs000631) ARDSNet iSPAAR cohort. Individual level phenotype data and molecular data for all ARDSnet and the "iSPAAR Consortium: Genetic Studies" top-level study and sub-studies are available by requesting Authorized Access to the "ARDSnet and the iSPAAR Consortium: Genetic Studies" [phs000631](study.cgi?study_id=phs000631) study.

The primary goal of this study is to identify genetic factors that alter the risk of individuals for developing acute respiratory distress syndrome (ARDS)/acute lung injury (ALI), a condition characterized by severe lung inflammation and an inability to maintain adequate oxygenation levels and high mortality. We employed genome wide association studies (GWAS) comparing a group of patients with ARDS (n=1072) with a group of critically ill patients at-risk for the development of ARDS (n=1124).

Samples and phenotype information were acquired from existing cohorts assembled as part of the iSPAAR (Identification of SNPs Predisposing to Altered ALI Risk) consortium, a multi-institutional NHLBI-funded study (RC2 HL101779) focused on the identification of genetic risks for ALI and related outcomes. Cases of established ALI in iSPAAR include subjects from the Molecular Epidemiology of Acute Respiratory Distress (MEA) Study [1] enrolled at the Massachusetts General Hospital, and from the ARDSNet consortium (http://www.ardsnet.org/), an NHLBI-funded clinical research network that performs randomized clinical trials in ARDS. We employed ARDS cases from ARDSNet Fluid and Catheter Treatment Trial (FACTT)[2], the EDEN-OMEGA studies[3,4], and the Albuterol for the Treatment of ALI (ALTA) study[5]. Controls at-risk for ALI who did not develop ALI during their hospital course were obtained from the MEA study[1]. We limited genotyping to subjects of European descent and who were ? 18 years of age. The genetic variants most strongly associated (upper 1st percentile) with ALI susceptibility from this GWAS are being validated through genotyping of the variants using a custom genotyping chip in a separate set of ALI cases and "at-risk" control subjects in a study design that mirrors the GWAS. Genotypes obtained from this validation study will be available through collaboration with Dr. Wurfel and Dr. Christiani, the principal investigators on this study. Of note, a subset of these subjects were also included in the NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Acute Lung Injury), phs000334, for which whole exome sequence and exome chip genotyping were obtained. In this project, additional cases of ARDS were obtained from the Validating Acute Lung Injury biomarkers for Diagnosis (VALID) study led by Dr. Lorraine Ware of Vanderbilt University.
DOI: 10.60645/bdc-682f-1e1b
title: CATHeterization GENetics (CATHGEN)

description: 
The CATHGEN biorepository consists of biological samples collected on 9334 sequential consenting individuals undergoing cardiac catheterization at Duke University Medical Center between 2001 and 2010 inclusive. The Institutional Review Board informed consent allowed for 50 mL of blood to be collected from fasting patients through the femoral arterial sheath during the catheterization procedure. Three 7.5 mL EDTA tubes for DNA extraction are stored at -80&#176;C. The Duke Database for Cardiovascular Disease (DDCD) provides the bulk of the clinical data used for analysis. Follow-up includes mortality information gleaned from the National Death Index and Social Security Death Index plus follow-up phone calls and written questionnaires regarding MI, stroke, re-hospitalization, coronary re-vascularization procedures, smoking, exercise, and medication use.
DOI: 10.60645/bdc-7xat-d3x6
title: CATHGEN: Identification of Novel Genetic and Metabolomic CV Phenotypes

description: 
The CATHGEN biorepository consists of biological samples collected on sequential consenting individuals undergoing cardiac catheterization at Duke University Medical Center between 2001 and 2010 inclusive. The Institutional Review Board informed consent allowed for 50 mL of blood to be collected from fasting patients through the femoral arterial sheath during the catheterization procedure. Three 7.5 mL EDTA tubes for DNA extraction are stored at -80&#176;C. The Duke Database for Cardiovascular Disease (DDCD) provides the bulk of the clinical data used for analysis. Follow-up includes mortality information gleaned from the National Death Index and Social Security Death Index plus follow-up phone calls and written questionnaires regarding MI, stroke, re-hospitalization, coronary re-vascularization procedures, smoking, exercise, and medication use. This particular CAD case-control substudy is composed of N=1490 unique individuals ascertained on CAD status.
DOI: 10.60645/bdc-49rx-rh8s
title: CATHGEN: Genetic Mediators of Metabolic Cardiovascular Disease Risk

description: 
The CATHGEN biorepository consists of biological samples collected on sequential consenting individuals undergoing cardiac catheterization at Duke University Medical Center between 2001 and 2010 inclusive. The Institutional Review Board informed consent allowed for 50 mL of blood to be collected from fasting patients through the femoral arterial sheath during the catheterization procedure. Three 7.5 mL EDTA tubes for DNA extraction are stored at -80&#176;C. The Duke Database for Cardiovascular Disease (DDCD) provides the bulk of the clinical data used for analysis. Follow-up includes mortality information gleaned from the National Death Index and Social Security Death Index plus follow-up phone calls and written questionnaires regarding MI, stroke, re-hospitalization, coronary re-vascularization procedures, smoking, exercise, and medication use. This is a sequential cohort of 2022 individual collected between August 2004 through September 2007.
DOI: 10.60645/bdc-4669-sj3x
title: Family Genomics of Congenital Heart Defects

description: 
The study identified the causal mutation in a five-generation pedigree harboring a cardiac septal defect. The inheritance pattern is consistent with an autosomal dominant mutation with high penetrance. We performed whole-genome sequencing (Complete Genomics) on 21 individuals in the pedigree, of which 11 individuals are affected. We identified a single gene, [GATA4](http://www.ncbi.nlm.nih.gov/gene/2626), as primarily responsible for this cardiac phenotype in this pedigree.
DOI: 10.60645/bdc-8cdw-4r17
title: Genetic Epidemiology Network of Salt Sensitivity (GenSalt)

description: 
The GenSalt study is aimed at identifying novel genes which interact with the effect of dietary sodium and potassium intake or cold pressor on blood pressure.
DOI: 10.60645/bdc-bizm-8dmf
title: MIGen_ExS: Ottawa Heart Study

description: 
The Ottawa Heart Study is a cross-sectional case-control study designed to identify genes that predispose to angiographically defined coronary artery disease. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.
DOI: 10.60645/bdc-1wt8-pv9p
title: PGRN/PAT: diLQTS Study

description: 
The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by sequencing approximately 225 patients of European descent using next-generation targeted captured or whole exome sequencing. Data from cases and controls (1:2) were analyzed to identify both rare and common genetic variation.
DOI: 10.60645/bdc-60b6-qzy4
title: Hispanic Community Health Study /Study of Latinos (HCHS/SOL)

description: 
The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH).

The goals of the HCHS/SOL include studying the prevalence and development of disease in Hispanics/Latinos, including the role of acculturation, and identifying disease risk factors that play protective or harmful roles in Hispanics/Latinos. A total of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American backgrounds were recruited through four Field Centers affiliated with San Diego State University, Northwestern University in Chicago, Albert Einstein College of Medicine in the Bronx area of New York, and the University of Miami. Seven additional academic centers serve as scientific and logistical support centers.

Study participants aged 18-74 years took part in an extensive clinic exam and assessments to ascertain socio-demographic, cultural, environmental and biomedical characteristics. Annual follow-up interviews are conducted to determine a range of health outcomes.

**The HCHS SOL Cohort is utilized in the following dbGaP substudies.** To view genotypes, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" section of this top-level study page [phs000810](study.cgi?study_id=phs000810) HCHS SOL Cohort. 
 - [phs000555](study.cgi?study_id=phs000555) PAGE CALiCo SOL - [phs000880](study.cgi?study_id=phs000880) HCHS/SOL Omics in Latinos (Ola)- phs003457 NSRR HCHS/SOL - the data for this substudy is temporarily being released as a standalone study under [phs003543](./study.cgi?study_id=phs003543)
DOI: 10.15468/dl.pkmx5t
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ponapea hentyi",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016302-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60645/bdc-3ts1-2120
title: Hispanic Community Health Study /Study of Latinos (HCHS/SOL)

description: 
The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH).

The goals of the HCHS/SOL include studying the prevalence and development of disease in Hispanics/Latinos, including the role of acculturation, and identifying disease risk factors that play protective or harmful roles in Hispanics/Latinos. A total of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American backgrounds were recruited through four Field Centers affiliated with San Diego State University, Northwestern University in Chicago, Albert Einstein College of Medicine in the Bronx area of New York, and the University of Miami. Seven additional academic centers serve as scientific and logistical support centers.

Study participants aged 18-74 years took part in an extensive clinic exam and assessments to ascertain socio-demographic, cultural, environmental and biomedical characteristics. Annual follow-up interviews are conducted to determine a range of health outcomes.

**The HCHS SOL Cohort is utilized in the following dbGaP substudies.** To view genotypes, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" section of this top-level study page [phs000810](study.cgi?study_id=phs000810) HCHS SOL Cohort. 
 - [phs000555](study.cgi?study_id=phs000555) PAGE CALiCo SOL - [phs000880](study.cgi?study_id=phs000880) HCHS/SOL Omics in Latinos (Ola)- phs003457 NSRR HCHS/SOL - the data for this substudy is temporarily being released as a standalone study under [phs003543](./study.cgi?study_id=phs003543)
DOI: 10.15468/dl.4ru8uh
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilosella ullepitschii"
 ]
}

 The dataset includes 22 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016300-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60645/bdc-j78g-1di9
title: Hispanic Community Health Study /Study of Latinos (HCHS/SOL)

description: 
The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH).

The goals of the HCHS/SOL include studying the prevalence and development of disease in Hispanics/Latinos, including the role of acculturation, and identifying disease risk factors that play protective or harmful roles in Hispanics/Latinos. A total of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American backgrounds were recruited through four Field Centers affiliated with San Diego State University, Northwestern University in Chicago, Albert Einstein College of Medicine in the Bronx area of New York, and the University of Miami. Seven additional academic centers serve as scientific and logistical support centers.

Study participants aged 18-74 years took part in an extensive clinic exam and assessments to ascertain socio-demographic, cultural, environmental and biomedical characteristics. Annual follow-up interviews are conducted to determine a range of health outcomes.

**The HCHS SOL Cohort is utilized in the following dbGaP substudies.** To view genotypes, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" section of this top-level study page [phs000810](study.cgi?study_id=phs000810) HCHS SOL Cohort. 
 - [phs000555](study.cgi?study_id=phs000555) PAGE CALiCo SOL - [phs000880](study.cgi?study_id=phs000880) HCHS/SOL Omics in Latinos (Ola)- phs003457 NSRR HCHS/SOL - the data for this substudy is temporarily being released as a standalone study under [phs003543](./study.cgi?study_id=phs003543)
DOI: 10.60645/bdc-m8i5-1xg3
title: Hispanic Community Health Study /Study of Latinos (HCHS/SOL)

description: 
The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH).

The goals of the HCHS/SOL include studying the prevalence and development of disease in Hispanics/Latinos, including the role of acculturation, and identifying disease risk factors that play protective or harmful roles in Hispanics/Latinos. A total of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American backgrounds were recruited through four Field Centers affiliated with San Diego State University, Northwestern University in Chicago, Albert Einstein College of Medicine in the Bronx area of New York, and the University of Miami. Seven additional academic centers serve as scientific and logistical support centers.

Study participants aged 18-74 years took part in an extensive clinic exam and assessments to ascertain socio-demographic, cultural, environmental and biomedical characteristics. Annual follow-up interviews are conducted to determine a range of health outcomes.

**The HCHS SOL Cohort is utilized in the following dbGaP substudies.** To view genotypes, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" section of this top-level study page [phs000810](study.cgi?study_id=phs000810) HCHS SOL Cohort. 
 - [phs000555](study.cgi?study_id=phs000555) PAGE CALiCo SOL - [phs000880](study.cgi?study_id=phs000880) HCHS/SOL Omics in Latinos (Ola)- phs003457 NSRR HCHS/SOL - the data for this substudy is temporarily being released as a standalone study under [phs003543](./study.cgi?study_id=phs003543)
DOI: 10.60645/bdc-yo79-m9m0
title: MIGen_ExS: Italian Atherosclerosis Thrombosis and Vascular Biology

description: 
Italian Atherosclerosis Thrombosis and Vascular Biology study is a prospective, nationwide, case-control study involving 125 coronary care units in Italy. The cases were patients who were hospitalised for a first MI before the age of 45 years and underwent coronary angiography. Acute MI was defined as resting chest pain lasting more than 30 minutes, accompanied by persistent electrocardiographic changes, and confirmed by an increase in total creatine kinase or in the MB fraction to more than twice the upper normal limits. The controls were healthy subjects without a history of thromboembolic disease who were unrelated to the patients, but individually matched with them by age, gender and geographical origin. They were enrolled from among the blood donors or staff of the same participating hospitals. Recruitment of cases and controls took place between 1994 and 2007.

All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.
DOI: 10.5281/zenodo.7723201
title: Neutrophil and emergency granulopoietic drivers of sepsis immune suppression and an extreme response to infection

description: The dysregulated host response to infection leading to organ dysfunction is highly heterogeneous. It is currently poorly delineated by sepsis as a clinical syndromic classification, thus confounding immunotherapy trials. Here we establish the pathophysiology and potential therapeutic targets of a specific extreme response to infection state (sepsis response signature SRS1), characterised by immune compromise and poor outcome. We first derive a whole blood single-cell multi-omic atlas of the sepsis response (2727,993 cells, n=39), finding an increase in IL1R2+ immature neutrophils in SRS1, which we confirmed by CyTOF and RNA-sequencing (n=53). We next uncovered high activity of neutrophil STAT3 gene expression programs in SRS1, which were shared across multiple infectioius disease settings (n=1044) irrespective of the clinical definition of the patient cohorts. We observed elevated plasma G-CSF and IL-6 in SRS1, suggesting heightened emergency granulopoiesis (EG). We therefore characterised patient and healthy control hematopoietic stem cells (HSCs) using single-cell RNA/chromatin accessibility multi-omics (29,366 cells, n=27), identifying SRS1-specific EG transcriptional skewing, together with STAT3 and EG master regulator CEBPB epigenetic signatures. Our findings establish a common cellular axis present across extreme responses to infection, reveal its hematopoietic origin, and nominate G-CSF and IL-6 as potential therapeutic targets for the SRS1 state.

 

The present data deposit includes processed and quality-controlled data tables for:

1. Whole blood leukocytes profiled with the BD Rhapsody platform in a cohort of 39 sepsis patients (RNA and protein count matrices, as well as their accompanying metadata table)

2. Circulating HSCs in blood profiled with the 10X multiomics platform in a cohort of 27 sepsis patients (RNA and ATAC-seq count matrices, as well as their accompanying metadata tables)

 

IMPORTANT NOTE: The files in Version 1.0 are incomplete (missing the cell barcode list and gene/feature names).Please download Version 1.1 for the complete package (includes barcode and feature list files aligned to the matrices).
DOI: 10.5281/zenodo.7723202
title: Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis

description: Sepsis arises from diverse and incompletely understood dysregulated host response processes following infection that leads to life-threatening organ dysfunction. Here we showed that neutrophils and emergency granulopoiesis drove a maladaptive response during sepsis. We generated a whole-blood single-cell multiomic atlas (272,993 cells, n =&thinsp;39 individuals) of the sepsis immune response that identified populations of immunosuppressive mature and immature neutrophils. In co-culture, CD66b+ sepsis neutrophils inhibited proliferation and activation of CD4+ T cells. Single-cell multiomic mapping of circulating hematopoietic stem and progenitor cells (HSPCs) (29,366 cells, n =&thinsp;27) indicated altered granulopoiesis in patients with sepsis. These features were enriched in a patient subset with poor outcome and a specific sepsis response signature that displayed higher frequencies of IL1R2+ immature neutrophils, epigenetic and transcriptomic signatures of emergency granulopoiesis in HSPCs and STAT3-mediated gene regulation across different infectious etiologies and syndromes. Our findings offer potential therapeutic targets and opportunities for stratified medicine in severe infection.

 

The present data deposit includes processed and quality-controlled data tables for:

1. Whole blood leukocytes profiled with the BD Rhapsody platform in a cohort of 39 sepsis patients (RNA and protein count matrices, as well as their accompanying metadata table)

2. Circulating HSCs in blood profiled with the 10X multiomics platform in a cohort of 27 sepsis patients (RNA and ATAC-seq count matrices, as well as their accompanying metadata tables)

 

IMPORTANT NOTE: The files in Version 1.0 are incomplete (missing the cell barcode list and gene/feature names).Please download Version 1.1 for the complete package (includes barcode and feature list files aligned to the matrices).
DOI: 10.60645/bdc-ae4a-e6t1
title: The Cleveland Clinic Foundation&#39;s (CCF) Lone Atrial Fibrillation (AFIB) GWAS Study

description: 
Blood samples were taken from patients who have lone atrial fibrillation. DNA samples were processed with Illumina Hap550 and Hap 610 chips.
DOI: 10.60645/bdc-2vvv-037d
title: The Cleveland Clinic Foundation&#39;s (CCF) Lone Atrial Fibrillation (AFIB) GWAS Study

description: 
Blood samples were taken from patients who have lone atrial fibrillation. DNA samples were processed with Illumina Hap550 and Hap 610 chips.
DOI: 10.7910/dvn/th5lce
title: Replication Package for: "Remeasuring Scale in Active Management"

description: Replication package for "Remeasuring scale in active management."
Authors: Shiyang Huang, Xu Lu, Yang Song, Hong Xiang.