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• Psychophysiological Investigation of Myocardial Ischemia (PIMI-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 investigate psychophysiological factors related to both symptomatic and asymptomatic cardiac ischemia.Background: An important hypothesis has been generated from current research in this area: manifestations and expressions of cardiac ischemia are influenced by specified psychophysiological mechanisms.Participants: The study population consisted of 196 participants recruited from four clinical units, all of which were clinical units for the Asymptomatic Cardiac Ischemia Pilot (ACIP). Participants eligible for PIMI were identified throughout the screening process established for the enrollment of participants in ACIP.Design: The primary goal of PIMI was to test the hypothesis, "Manifestations and expressions of cardiac ischemia are influenced by specific psychophysiological mechanisms." The specific relationships investigated were:Patients who are susceptible to mental stress ischemia (indexed by new left ventricular wall motion abnormalities) would display more ischemia during daily activities and would have ambulatory ischemia at lower heart rate and activity level thresholds than patients who are not susceptible. Cardiovascular and catecholamine reactivity to mental stress would be a predictive of severity of mental stress ischemia and of ambulatory ischemia. Β-edorphin responses to mental stress and to exercise would be predictive of asymptomatic ischemia. Patients with systematic ischemia and those with asymptomatic ischemia would show differences in each of the following at rest and after response to stresses (exercise and/or mental tests). Mental stress would produce different hormonal and perceptual responses than exercise. Asymptomatic ischemia would be associated with a lesser severity of ischemia than symptomatic ischemia. The location of the ischemic myocardium would be inferior in a higher proportion of patients with asymptomatic ischemia than of patients with symptomatic ischemia. The latency internal that would be the onset of ST segment depression and the onset of ischemic pain would be related to somatic sensory perception, autonomic nervous system reflux control of the heart, Β-endorphin responses, and psychosocial characteristics.

  Study phs004183

• Illumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001002598

• ProjectMinE :llumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001003383

• Massive Genomic Rearrangment Acquired in a Single Catastrophic Event During Cancer Development

  Cancer is driven by mutation. Using Agilent exome hybridisation capture and Illumina GA massively parallel sequencing technology, we aim to sequence ~1600 microRNAs plus the protein coding genome of 25 matched human renal cancer samples. Bespoke algorithms are being developed to identify the somatically acquired point mutations, insertions and deletions in these samples. This project will give unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with renal cancer development.Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00000000029

• REDS-IV-P Epidemiology, Surveillance and Preparedness of the Novel SARS-CoV-2 Epidemic (RESPONSE)

  Leveraging access to the blood supply and blood donors, the REDS-IV-P program began conducting the RESPONSE study (REDS-IV-P Epidemiology, Surveillance and Preparedness of the Novel SARS-CoV-2 Epidemic) in early 2020 in order to 1) evaluate if SARS-CoV-2 RNA was found in blood donations in the U.S. using an assay that could potentially be used to screen the blood supply if evidence of SARS-CoV-2 transfusion-transmission became apparent 2) conduct serosurveys using optimized assays/algorithms to monitor antibody reactivity in blood donor populations over time, 3) enroll SARS-CoV-2 positive donors and others into a longitudinal cohort study to answer fundamental questions about the evolution of viremia and immune responses, and 4) establish a sharable biorepository that includes specimens collected early on in the infection and potentially large volumes of plasma from infected/convalescent donors.Screening for SARS-CoV-2 RNAemia was completed using a SARS-CoV-2 nucleic acid test (NAT) performed on retained blood donor minipool samples from six geographic regions in the US. The study also included serosurveillance (i.e. testing for antibody directed against the SARS-CoV2 spike protein) of donations from the same six regions to document accruing seroincidence in blood donor populations and to project these rates in the general population. To enrich for donors with acute SARS-CoV-2 infection, another part of the study focused on donors reporting post-donation information (PDI) consistent with COVID-19 by testing plasma from all available PDI donations for SARS-CoV-2 RNA by NAT. Subjects who were diagnosed with COVID-19 based on PDI reports or who tested positive by SARS-CoV-2 NAT on index donation plasma were enrolled into a longitudinal follow-up study which collected multiple samples for up to one-year post-infection. The longitudinal follow-up study also enrolled community members who reported a new positive SARS-CoV-2 NAT test in the prior 7-14 days. The specific aims of the RESPONSE study were to: Establish the incidence of SARS-CoV-2 RNAemia in blood donations from the American Red Cross (ARC) regions in Los Angeles, Boston, and Minneapolis metropolitan areas, Bloodworks Northwest (BWNW), New York Blood Center (NYBC), and Vitalant San Francisco Bay Area, monthly between March and September of 2020 Conduct serosurveys to study antibody reactivity in same six areas as above monthly for March to August 2020 Document rates of Post Donation Information (PDI) reports to determine PDI rates relevant to SARS-CoV-2 clinical disease and test index donation plasma from PDI donors for SARS-CoV-2 RNA Enroll SARS-CoV-2 infected subjects into a longitudinal cohort study to answer fundamental questions on the evolution of viremia, early immune responses and waning of immunity over 3-12 months of follow-up Establish a sharable biorepository of samples from all of the above Aims for future research The data from Aims 3 and 4 above is being made available in BioData Catalyst.Biospecimens for these Aims are managed by Vitalant Research Institute (VRI). More information on biospecimens is available.

  Study phs003578

• PhIP-Seq data

  Inflammatory bowel diseases (IBD), e.g. Crohn’s disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. We leveraged a high-throughput phage-displayed immunoprecipitation sequencing (PhIP-seq) workflow to identify antibodies against 344,000 antimicrobial, immune and food antigens in 497 IBD patients.

  Study EGAS00001007054

• The Dutch Microbiome Project: Defining the (un)healthy gut microbiome

  The Dutch Microbiome Project (DMP) data includes raw data generated by shotgun metagenomic sequencing of faecal samples of 8,208 Dutch individuals, processed microbiome data analysed using Biobakery2 tools (including taxonomy, pathway, virulence factors and antibiotic resistance gene profiles), and basic phenotypes (age and sex, BMI). Data is made available in two randomly assigned batches to facilitate the data access and maintenance. Access to this dataset requires a minimal access procedure (data access form at https://forms.gle/eHeBdXJMXbVvCJRc8 or email request to the data access committee (DAC) of this study, listed at DAC EGAC00001001996, https://ega-archive.org/dacs/EGAC00001001996). This access procedure is to ensure that the data is being requested for research/scientific purposes only and thus complies with the informed consent signed by Lifelines participants, which specifies that the collected data will not be used for commercial purposes. Submitted data access forms will be evaluated by the DAC and Lifelines, and a response to requests will be given within two weeks. For requests from verified academic parties, access will be given without further delay. For requests from commercial parties, Lifelines will perform a pre-DPIA (Data Privacy Impact Assessment) to assess the risks of the proposed processing of personal data (e.g. purpose, storage, access, archiving, etc.) with respect to the GDPR (EU privacy laws) subject rights. Based on the outcome of the pre-DPIA, Lifelines will decide whether sharing data with the commercial entity is allowed and/or whether additional measures have to be taken.

  Study EGAS00001005027

• Framingham Cohort

  Startup of Framingham Heart Study. Cardiovascular disease (CVD) is the leading cause of death and serious illness in the United States. In 1948, the Framingham Heart Study (FHS) -- under the direction of the National Heart Institute (now known as the National Heart, Lung, and Blood Institute, NHLBI) -- embarked on a novel and ambitious project in health research. At the time, little was known about the general causes of heart disease and stroke, but the death rates for CVD had been increasing steadily since the beginning of the century and had become an American epidemic. The objective of the FHS was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke. Design of Framingham Heart Study. In 1948, the researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In April 2002 the Study entered a new phase: the enrollment of a third generation of participants, the grandchildren of the original cohort. The first examination of the Third Generation Study was completed in July 2005 and involved 4,095 participants. Thus, the FHS has evolved into a prospective, community-based, three generation family study. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University. Research Areas in the Framingham Heart Study. Over the years, careful monitoring of the FHS population has led to the identification of the major CVD risk factors -- high blood pressure, high blood cholesterol, smoking, obesity, diabetes, and physical inactivity -- as well as a great deal of valuable information on the effects of related factors such as blood triglyceride and HDL cholesterol levels, age, gender, and psychosocial issues. Risk factors have been identified for the major components of CVD, including coronary heart disease, stroke, intermittent claudication, and heart failure. It is also clear from research in the FHS and other studies that substantial subclinical vascular disease occurs in the blood vessels, heart and brain that precedes clinical CVD. With recent advances in technology, the FHS has enhanced its research capabilities and capitalized on its inherent resources by the conduct of high resolution imaging to detect and quantify subclinical vascular disease in the major blood vessels, heart and brain. These studies have included ultrasound studies of the heart (echocardiography) and carotid arteries, computed tomography studies of the heart and aorta, and magnetic resonance imaging studies of the brain, heart, and aorta. Although the Framingham cohort is primarily white, the importance of the major CVD risk factors identified in this group have been shown in other studies to apply almost universally among racial and ethnic groups, even though the patterns of distribution may vary from group to group. In the past half century, the Study has produced approximately 1,200 articles in leading medical journals. The concept of CVD risk factors has become an integral part of the modern medical curriculum and has led to the development of effective treatment and preventive strategies in clinical practice. In addition to research studies focused on risk factors, subclinical CVD and clinically apparent CVD, Framingham investigators have also collaborated with leading researchers from around the country and throughout the world on projects involving some of the major chronic illnesses in men and women, including dementia, osteoporosis and arthritis, nutritional deficiencies, eye diseases, hearing disorders, and chronic obstructive lung diseases. Genetic Research in the Framingham Heart Study. While pursuing the Study's established research goals, the NHLBI and the Framingham investigators has expanded its research mission into the study of genetic factors underlying CVD and other disorders. Over the past two decades, DNA has been collected from blood samples and from immortalized cell lines obtained from Original Cohort participants, members of the Offspring Cohort and the Third Generation Cohort. Several large-scale genotyping projects have been conducted in the past decade. Genome-wide linkage analysis has been conducted using genotypes of approximately 400 microsatellite markers that have been completed in over 9,300 subjects in all three generations. Analyses using microsatellite markers completed in the original cohort and offspring cohorts have resulted in over 100 publications, including many publications from the Genetics Analysis Workshop 13. Several other recent collaborative projects have completed thousands of SNP genotypes for candidate gene regions in subsets of FHS subjects with available DNA. These projects include the Cardiogenomics Program of the NHLBI's Programs for Genomics Applications, the genotyping of ~3000 SNPs in inflammation genes, and the completion of a genome-wide scan of 100,000 SNPs using the Affymetrix 100K Genechip. Framingham Cohort Phenotype Data. The phenotype database contains a vast array of phenotype information available in all three generations. These will include the quantitative measures of the major risk factors such as systolic blood pressure, total and HDL cholesterol, fasting glucose, and cigarette use, as well as anthropomorphic measures such as body mass index, biomarkers such as fibrinogen and CRP, and electrocardiography measures such as the QT interval. Many of these measures have been collected repeatedly in the original and offspring cohorts. Also included in the SHARe database will be an array of recently collected biomarkers, subclinical disease imaging measures, clinical CVD outcomes as well as an array of ancillary studies. The phenotype data is located here in the top-level study phs000007 Framingham Cohort. To view the phenotype variables collected from the Framingham Cohort, please click on the "Variables" tab above. The Framingham Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, 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 phs000007 Framingham Cohort. phs000342 Framingham SHARe phs000282 Framingham CARe phs000363 Framingham SABRe phs000307 Framingham Medical Resequencing phs000401 Framingham ESP Heart-GO phs000651 Framingham CHARGE-S phs000724 Framingham DNA Methylation phs001610 Framingham T2D-GENES phs002558 Framingham ADSP phs002559 Framingham BRIDGET phs002560 Framingham Cholesterol phs002611 Framingham Post-Mortem Brain Tissue phs002938 Framingham Molecular QTL The unflagging commitment of the research participants in the NHLBI FHS has made more than a half century of research success possible. For decades, the FHS has made its data and DNA widely available to qualified investigators throughout the world through the Limited Access Datasets and the FHS DNA Committee, and the SHARe database will continue that tradition by allowing access to qualified investigators who agree to the requirements of data access. With the SHARe database, we continue with an ambitious research agenda and look forward to new discoveries in the decades to come.

  Study phs000007

• Genomic Sequencing of Solitary Fibrous Tumors

  Solitary fibrous tumors (SFTs) are rare mesenchymal tumors that can be benign or malignant. In this study, we sequenced and analyzed the exomes of 17 SFT matched tumor and normal pairs. This study appertains to a large endeavor to characterize cancers as part of the Slim Initiative for Genomic Medicine in the Americas (SIGMA) project.

  Study phs000568

• Prevention of Viral Hepatitis and HIV in Drug Users - A Hepatitis B Model for HIV and an HB Vaccine Model for HIV Vaccine Trials in Drug Users (DASH)

  The goal of the proposed study is to use the Hepatitis B virus (HBV) vaccine as a model for a future Human Immunodeficiency Virus (HIV) vaccine trial, examining the efficacy of community-based outreach intervention as well as an accelerated vaccine schedule as a method for increasing acceptance/adherence with HBV vaccination protocols among not-in-treatment drug users. This study also examined the effect of HBV vaccination coupled with community-based outreach intervention on reducing the incidence of HIV, HBV and Hepatitis C Virus (HCV) infections and the frequency of needle use and sexual risk behaviors related to these viral transmissions. A secondary purpose is to assess the antibody response after HBV vaccination as a measurement of immunological response in drug users.

  Study phs002331