cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60645/bdc-orn2-79s2
title: NHLBI TOPMed: Genetic Epidemiology of COPD (COPDGene)

description: 
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States, and the only leading cause of death that is steadily increasing in frequency. This project established a racially diverse cohort that is sufficiently large and appropriately designed for genome-wide association analysis of COPD. A total of 10,720 subjects were recruited, including control smokers and nonsmokers, definite COPD cases (GOLD Stage 2 to 4), and subjects not included in either group (GOLD 1 and PRISm). This cohort is being used for cross-sectional analysis, and long-term longitudinal follow-up visits after five years and after ten years are also being performed. The primary focus of the study is to identify the genetic risk factors that determine susceptibility for COPD and COPD-related phenotypes. Detailed phenotyping of both cases and controls, including chest CT scan assessment of emphysema and airway disease, will allow identification of genetic determinants for the heterogeneous components of the COPD syndrome.

The aims for this study are:
 1. Precise phenotypic characterization of COPD subjects using computed tomography, as well as clinical and physiological measures, that will provide data to enable the broad COPD syndrome to be decomposed into clinically significant subtype; 1. Genome-wide association studies will identify genetic determinants for COPD susceptibility that will provide insight into clinically relevant COPD subtypes; 1. Distinct genetic determinants influence the development of emphysema and airway disease. The TOPMed analysis will include approximately 10,500 subjects with whole genome sequencing after quality control is completed. 
Comprehensive phenotypic data for COPDGene subjects is available through dbGaP study [phs000179](study.cgi?study_id=phs000179).
DOI: 10.60645/bdc-30vn-m45p
title: NHLBI TOPMed: Genetic Epidemiology of COPD (COPDGene)

description: 
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States, and the only leading cause of death that is steadily increasing in frequency. This project established a racially diverse cohort that is sufficiently large and appropriately designed for genome-wide association analysis of COPD. A total of 10,720 subjects were recruited, including control smokers and nonsmokers, definite COPD cases (GOLD Stage 2 to 4), and subjects not included in either group (GOLD 1 and PRISm). This cohort is being used for cross-sectional analysis, and long-term longitudinal follow-up visits after five years and after ten years are also being performed. The primary focus of the study is to identify the genetic risk factors that determine susceptibility for COPD and COPD-related phenotypes. Detailed phenotyping of both cases and controls, including chest CT scan assessment of emphysema and airway disease, will allow identification of genetic determinants for the heterogeneous components of the COPD syndrome.

The aims for this study are:
 1. Precise phenotypic characterization of COPD subjects using computed tomography, as well as clinical and physiological measures, that will provide data to enable the broad COPD syndrome to be decomposed into clinically significant subtype; 1. Genome-wide association studies will identify genetic determinants for COPD susceptibility that will provide insight into clinically relevant COPD subtypes; 1. Distinct genetic determinants influence the development of emphysema and airway disease. The TOPMed analysis will include approximately 10,500 subjects with whole genome sequencing after quality control is completed. 
Comprehensive phenotypic data for COPDGene subjects is available through dbGaP study [phs000179](study.cgi?study_id=phs000179).
DOI: 10.60645/bdc-pjk5-az92
title: NHLBI TOPMed: Genetic Epidemiology of COPD (COPDGene)

description: 
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States, and the only leading cause of death that is steadily increasing in frequency. This project established a racially diverse cohort that is sufficiently large and appropriately designed for genome-wide association analysis of COPD. A total of 10,720 subjects were recruited, including control smokers and nonsmokers, definite COPD cases (GOLD Stage 2 to 4), and subjects not included in either group (GOLD 1 and PRISm). This cohort is being used for cross-sectional analysis, and long-term longitudinal follow-up visits after five years and after ten years are also being performed. The primary focus of the study is to identify the genetic risk factors that determine susceptibility for COPD and COPD-related phenotypes. Detailed phenotyping of both cases and controls, including chest CT scan assessment of emphysema and airway disease, will allow identification of genetic determinants for the heterogeneous components of the COPD syndrome.

The aims for this study are:
 1. Precise phenotypic characterization of COPD subjects using computed tomography, as well as clinical and physiological measures, that will provide data to enable the broad COPD syndrome to be decomposed into clinically significant subtype; 1. Genome-wide association studies will identify genetic determinants for COPD susceptibility that will provide insight into clinically relevant COPD subtypes; 1. Distinct genetic determinants influence the development of emphysema and airway disease. The TOPMed analysis will include approximately 10,500 subjects with whole genome sequencing after quality control is completed. 
Comprehensive phenotypic data for COPDGene subjects is available through dbGaP study [phs000179](study.cgi?study_id=phs000179).
DOI: 10.60645/bdc-7o97-1y7n
title: NHLBI TOPMed: Genetic Epidemiology of COPD (COPDGene)

description: 
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States, and the only leading cause of death that is steadily increasing in frequency. This project established a racially diverse cohort that is sufficiently large and appropriately designed for genome-wide association analysis of COPD. A total of 10,720 subjects were recruited, including control smokers and nonsmokers, definite COPD cases (GOLD Stage 2 to 4), and subjects not included in either group (GOLD 1 and PRISm). This cohort is being used for cross-sectional analysis, and long-term longitudinal follow-up visits after five years and after ten years are also being performed. The primary focus of the study is to identify the genetic risk factors that determine susceptibility for COPD and COPD-related phenotypes. Detailed phenotyping of both cases and controls, including chest CT scan assessment of emphysema and airway disease, will allow identification of genetic determinants for the heterogeneous components of the COPD syndrome.

The aims for this study are:
 1. Precise phenotypic characterization of COPD subjects using computed tomography, as well as clinical and physiological measures, that will provide data to enable the broad COPD syndrome to be decomposed into clinically significant subtype; 1. Genome-wide association studies will identify genetic determinants for COPD susceptibility that will provide insight into clinically relevant COPD subtypes; 1. Distinct genetic determinants influence the development of emphysema and airway disease. The TOPMed analysis will include approximately 10,500 subjects with whole genome sequencing after quality control is completed. 
Comprehensive phenotypic data for COPDGene subjects is available through dbGaP study [phs000179](study.cgi?study_id=phs000179).
DOI: 10.60645/bdc-d0wv-rx9i
title: NHLBI TOPMed: The Cleveland Family Study (CFS)

description: 
The [Cleveland Family Study](https://sleepdata.org/datasets/cfs) (CFS) is one cohort involved in the WGS project. The CFS was designed to provide fundamental epidemiological data on genetic and non-genetic risk factors for sleep disordered breathing (SDB). In brief, the CFS is a family-based study that enrolled a total of 2284 individuals from 361 families between 1990 and 2006. The sample was selected by identifying affected probands who had laboratory diagnosed obstructive sleep apnea. All first degree relatives, spouses and available second degree relatives of affected probands were studied. In addition, during the first 5 study years, neighborhood control families were identified through a neighborhood proband, and his/her spouses and first degree relatives. Each exam, occurring at approximately 4 year intervals, included new enrollment as well as follow up exams for previously enrolled subjects. For the first three visits, data, including an overnight sleep study, were collected in the participants' homes while the last visit occurred in a general clinical research center (GCRC). Phenotypic characterization of the entire cohort included overnight sleep apnea studies, blood pressure, spirometry, anthropometry and questionnaires. The GCRC exam (n=735 selected individuals) included more comprehensive phenotype data on a focused subsample of the larger cohort, to permit linking SDB phenotypes with cardio-metabolic phenotypes, with an interest in identifying genetic loci that are associated with these related phenotypes. In this last round of data collection, a subset of 735 individuals was selected based on expected genetic informativity by choosing pedigrees where siblings had extremes of the apnea hypopnea index (AHI). Participants underwent detailed phenotyping including laboratory polysomnography (PSG), ECG, spirometry, nasal and oral acoustic reflectometry, vigilance testing, and blood and urine collection before and after sleep and after an oral glucose tolerance test. A wide range of biochemical measures of inflammation and metabolism were assayed by a Core Laboratory at the University of Vermont.

994 individuals were sequenced as part of TOPMed Phase 1, including 507 African-Americans and 487 European-Americans. Among the sequenced individuals, 156 were probands with diagnosed sleep apnea, an additional 706 were members of families with probands, and 132 were from neighborhood control families. 

298 individuals were sequenced as part of TOPMed Phase 3.5, including 169 African-Americans and 129 European-Americans. Among the newly sequenced individuals, 33 were probands with diagnosed sleep apnea, an additional 214 were members of families with probands, and 51 were from neighborhood control families.

Please note: Phenotype and pedigree data are available through "NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe)", [phs000284](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000284).
DOI: 10.60645/bdc-33pf-pte6
title: NHLBI TOPMed: Genetics of Cardiometabolic Health in the Amish

description: 
The Amish Complex Disease Research Program includes a set of large community-based studies focused largely on cardiometabolic health carried out in the Old Order Amish (OOA) community of Lancaster, Pennsylvania ([http://medschool.umaryland.edu/endocrinology/amish/research-program.asp](http://medschool.umaryland.edu/endocrinology/amish/research-program.asp)). The OOA population of Lancaster County, PA immigrated to the Colonies from Western Europe in the early 1700's. There are now over 30,000 OOA individuals in the Lancaster area, nearly all of whom can trace their ancestry back 12-14 generations to approximately 700 founders. Investigators at the University of Maryland School of Medicine have been studying the genetic determinants of cardiometabolic health in this population since 1993. To date, over 7,000 Amish adults have participated in one or more of our studies.

Due to their ancestral history, the OOA may be enriched for rare variants that arose in the population from a single founder (or small number of founders) and propagated through genetic drift. Many of these variants have large effect sizes and identifying them can lead to new biological insights about health and disease. The parent study for this WGS project provides one (of multiple) examples. In our parent study, we identified through a genome-wide association analysis a haplotype that was highly enriched in the OOA that is associated with very high LDL-cholesterol levels. At the present time, the identity of the causative SNP - and even the implicated gene - is not known because the associated haplotype contains numerous genes, none of which are obvious lipid candidate genes. A major goal of the WGS that will be obtained through the NHLBI TOPMed Consortium will be to identify functional variants that underlie some of the large effect associations observed in this unique population.
DOI: 10.60645/bdc-wbqx-f971
title: PGRN-RIKEN:Genetic Determinants of Cardiovascular Events while on Statins

description: 
Coronary heart disease (CHD) is an important public health problem in developed countries. Statins are effective in the prevention and treatment of CHD; nevertheless, many patients receiving statins still suffer cardiovascular events (CV) such as heart attack. Identifying genetic variants responsible for differential clinical responses to statins will not only allow individual patients at high residual risk to be targeted for additional therapies, but also will define new biologic pathways contributing to statin response, and thus new targets for future therapies. Accordingly, the goal of this study is to identify genetic variants associated with clinical CV in patients receiving statins.

Subjects identified for study are of European descent and include 1718 subjects with CV while on statins (cases) and 4172 subjects without CV while on statins (controls). Key research resources utilized in this effort include VanderbiltD&#39;s BioVU DNA databank and associated Synthetic Derivative database of clinical information, and software tools developed to identify drugs and clinical events using Electronic Health Record-derived structured and unstructured (&#34;free text&#34;) data. Most cases and controls identified include three data types: ICD-9 codes, medication regimens, and medical test results. Genotyping, using IlluminaD&#39;s Infinium HumanOmniExpressExome BeadChip (OmniExpressExome), was performed by the RIKEN Integrative Medical Sciences Center (IMS) and supported by the Pharmacogenomics Research Network (PGRN)-RIKEN IMS Global Alliance.
DOI: 10.5281/zenodo.18503882
title: The effect of aerobic methane oxidation on accumulation of AMPA in soil

description: The deposited data were collected as part of a research project entitled: Effect of glyphosate on the biological methane oxidation in agricultural soils, funded by the National Science Centre Poland as part of the OPUS-21 project (no.: 2021/41/B/NZ9/03130). The project aims to investigate the response of methanotrophic bacteria to glyphosate and adjuvants. The analyses include determining the impact of compounds on methanotrophic activity, abundance and composition of methanotrophic bacterial communities.

The research was conducted between 16.05.2022 and 30.09.2025 at the Department of Environmental Biogeochemistry of the Institute of Agrophysics, Polish Academy of Sciences; The John Paul II Catholic University of Lublin and Medical University of Lublin.

The collection contains research results concerning the impact of glyphosate on the rates of: methane oxidation, oxygen depletion, carbon dioxide increase, glyphosate degradation and aminomethylphosphonic acid accumulation in the Gleysol, Leptosol and Fluvisol soils.

The data was compiled on the basis of laboratory tests.
description: The results presented in `Taxonomy Gleysol.xlsx`, `Taxonomy Leptosol.xlsx` and `Taxonomy Fluvisol.xlsx` were obtained using research equipment: Illumina PE250 platform

The results presented in file `GC, GF, AMPA raw data.xlsx` were obtained using research equipment: gas chromatograph (8890 GC, Agilent Technology, USA) and liquid chromatograph (1290 Infinity II series, Agilent Technology, USA) coupled with mass spectrometry (Triple quadrupole mass spectrometer 6470 QQQ LC/MS equipped with a Jet Stream ion source, Agilent Technologies, USA).
description: The data set consists of the following files:

Taxonomy Gleysol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Gleysol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

Taxonomy Leptosol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Leptosol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

Taxonomy Fluvisol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Fluvisol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

GC, GF, AMPA raw data.xlsx – raw data obtained from gas chromatography and liquid chromatography coupled with mass spectrometer of the glyphosate-free and glyphosate-exposed soils.

Methodology of GF and AMPA determination.docx - information describing the methodology of glyphosate and aminomethylphosphonic acid determination in soil samples.

Microcosm and gas chromatography methodology.docx - information describing the methodology related to gas chromatography measurements.
DOI: 10.5281/zenodo.18503881
title: The effect of aerobic methane oxidation on accumulation of AMPA in soil

description: The deposited data were collected as part of a research project entitled: Effect of glyphosate on the biological methane oxidation in agricultural soils, funded by the National Science Centre Poland as part of the OPUS-21 project (no.: 2021/41/B/NZ9/03130). The project aims to investigate the response of methanotrophic bacteria to glyphosate and adjuvants. The analyses include determining the impact of compounds on methanotrophic activity, abundance and composition of methanotrophic bacterial communities.

The research was conducted between 16.05.2022 and 30.09.2025 at the Department of Environmental Biogeochemistry of the Institute of Agrophysics, Polish Academy of Sciences; The John Paul II Catholic University of Lublin and Medical University of Lublin.

The collection contains research results concerning the impact of glyphosate on the rates of: methane oxidation, oxygen depletion, carbon dioxide increase, glyphosate degradation and aminomethylphosphonic acid accumulation in the Gleysol, Leptosol and Fluvisol soils.

The data was compiled on the basis of laboratory tests.
description: The results presented in `Taxonomy Gleysol.xlsx`, `Taxonomy Leptosol.xlsx` and `Taxonomy Fluvisol.xlsx` were obtained using research equipment: Illumina PE250 platform

The results presented in file `GC, GF, AMPA raw data.xlsx` were obtained using research equipment: gas chromatograph (8890 GC, Agilent Technology, USA) and liquid chromatograph (1290 Infinity II series, Agilent Technology, USA) coupled with mass spectrometry (Triple quadrupole mass spectrometer 6470 QQQ LC/MS equipped with a Jet Stream ion source, Agilent Technologies, USA).
description: The data set consists of the following files:

Taxonomy Gleysol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Gleysol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

Taxonomy Leptosol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Leptosol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

Taxonomy Fluvisol.xlsx – taxonomical data from Next Generation Sequencing method of DNA obtained from the Fluvisol unexposed to glyphosate. Primers used: 515F (5’-GTGYCAGCMGCCGCGGTAA) and 806R (5’-GGACTACNVGGGTWTCTAAT).

GC, GF, AMPA raw data.xlsx – raw data obtained from gas chromatography and liquid chromatography coupled with mass spectrometer of the glyphosate-free and glyphosate-exposed soils.

Methodology of GF and AMPA determination.docx - information describing the methodology of glyphosate and aminomethylphosphonic acid determination in soil samples.

Microcosm and gas chromatography methodology.docx - information describing the methodology related to gas chromatography measurements.
DOI: 10.60645/bdc-5v38-0y33
title: NHLBI TOPMed: Genome-Wide Association Study of Adiposity in Samoans

description: 
The individuals sequenced here represent a small subset of the parent study (described below) and were carefully selected for the purpose of creating a Samoan-specific reference panel for imputation back into the parent study. The INFOSTIP algorithm of Gusev et. al. (2012) (PMID: [22135348](http://www.ncbi.nlm.nih.gov/pubmed/22135348)) was used to optimally choose the individuals for sequencing.

The research goal of the parent study (dbGaP ID [phs000914](./study.cgi?study_id=phs000914)) is to identify genetic variation that increases susceptibility to obesity and cardiometabolic phenotypes among adult Samoans using genome-wide association (GWAS) methods. DNA from peripheral blood and phenotypic information were collected from 3,119 adult Samoans, 23 to 70 years of age. The participants reside throughout the independent nation of Samoa, which is experiencing economic development and the nutrition transition. Genotyping was performed with the Affymetrix Genome-Wide Human SNP 6.0 Array using a panel of approximately 900,000 SNPs. Anthropometric, fasting blood biomarkers and detailed dietary, physical activity, health and socio-demographic variables were collected. We are replicating the GWAS findings in an independent sample of 2,500 Samoans from earlier studies. After replication of genomic regions and informative SNPs in those regions, we will determine sequences of the important genes, and determine the specific genetic variants in the sequenced genes that are associated with adiposity and related cardiometabolic conditions. We will also identify gene by environment interactions, focusing on dietary intake patterns and nutrients.
DOI: 10.60645/bdc-d2z4-c71t
title: NHLBI TOPMed: Genomic Activities such as Whole Genome Sequencing and Related Phenotypes in the Framingham Heart Study

description: 
The Framingham Heart Study (FHS) is a prospective cohort study of 3 generations of subjects who have been followed up to 65 years to evaluate risk factors for cardiovascular disease. Its large sample of ~15,000 men and women who have been extensively phenotyped with repeated examinations make it ideal for the study of genetic associations with cardiovascular disease risk factors and outcomes. DNA samples have been collected and immortalized since the mid-1990s and are available on ~8000 study participants in 1037 families. These samples have been used for collection of GWAS array data and exome chip data in nearly all with DNA samples, and for targeted sequencing, deep exome sequencing and light coverage whole genome sequencing in limited numbers. Additionally, mRNA and miRNA expression data, DNA methylation data, metabolomics and other 'omics data are available on a sizable portion of study participants. 

This project will focus on deep whole genome sequencing (mean 30X coverage) in ~4100 participants and imputed to all with GWAS array data to more fully understand the genetic contributions to cardiovascular, lung, blood and sleep disorders. Also available are aptamer proteomic profiling, RNAseq and 850K array DNA methylation data that predominantly overlap with participants with WGS data.

Comprehensive phenotypic and pedigree data for study participants are available through dbGaP [phs000007](./study.cgi?study_id=phs000007).