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• Heart Failure Network - Nitrate's Effect on Activity Tolerance in Heart Failure with Preserved Ejection Fraction (HFN NEAT-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. Related StudiesEcho images are available with HFN-NEAT Imaging.ObjectivesTo determine the effect of isosorbide mononitrate on daily activity in patients with heart failure and preserved ejection fraction.Background Nitrates are commonly prescribed for symptom relief in patients with heart failure. Early studies in patients with heart failure with a reduced ejection fraction concluded that long-acting nitrates improve activity tolerance; however, approximately half of heart failure patients have preserved ejection fraction. The effects of nitrates in patients with heart failure and a preserved ejection fraction have not been extensively studied and the overall effect of nitrates on activity tolerance in such patients is uncertain. ParticipantsThere were a total of 110 participants enrolled with 51 participants assigned to receive isosorbide mono-nitrate first and placebo second, and 59 participants assigned to receive placebo first and isosorbide mononitrate second. Design Enrolled participants underwent baseline assessments, including echocardiography, quality-of-life scores, 6-minute walk test distance, and NT-proBNP levels. participants were also supplied with two kinetic activity monitors containing high-sensitivity triaxis accelerometers, to be worn 24 hours per day. The accelerometer measurements were expressed as arbitrary accelerometer units and stored every 15 minutes equaling 96 data points per day. The 15-minute cumulative accelerometer units were totaled over a 24-hour period to provide daily accelerometer units. Participants were assigned to one of two treatment groups: 6 weeks of placebo first with crossover to 6 weeks of isosorbide mononitrate, or 6 weeks of isosorbide mononitrate first with crossover to 6 weeks of placebo. The study drugs were prepared as 30-mg tablets of isosorbide mononitrate and matching placebo. During each 6-week period, participants were instructed to take no study drug for the first 2 weeks followed by one tablet (30 mg daily) for 1 week, two tablets (60 mg once daily) for 1 week, and four tablets (120 mg once daily) until the next study visit, for a treatment duration of at least 2 weeks and up to 4 weeks. After each 6-week period, participants returned to the study center to repeat end-point assessments. The primary outcome for the study was the comparison of average daily accelerometer units during the period in which participants were receiving the 120-mg dose of isosorbide mononitrate compared to the period in which participants received the placebo. Other secondary end points included the 6-minute walk distance and the post-walk Borg dyspnea score, scores on the Kansas City Cardiomyopathy Questionnaire and the Minnesota Living with Heart Failure Questionnaire, and NT-proBNP levels. In addition, participants completed a questionnaire indicating in which period (first, second, no preference) they felt better. Conclusions Participants were active for fewer hours of the day during the 120-mg phase of receipt of isosorbide mononitrate as compared with placebo. Furthermore, during all study-drug regimens combined (30 mg to 120 mg), participants were less active during receipt of isosorbide mononitrate as compared with placebo. There was no significant effect of isosorbide mononitrate on secondary outcomes.

  Study phs003548

• Prevention and Early Treatment of Acute Lung Injury (PETAL) Network - Functional, Imaging, and Respiratory Evaluation in CORAL (PETAL FIRE CORAL-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.Biospecimens: Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from PETAL FIRE CORAL include plasma and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent and biospecimens may not be used to produce commercial products.Objectives: To examine the recovery from COVID-19 disease following acute hospitalization with an emphasis on functional, imaging, and respiratory evaluation, and assess the feasibility of conducting a larger study to evaluate variables associated with differential recovery.Background: The BLUE CORAL study, dbGaP phs003419, was intended to address the knowledge gaps and provide critical data to help guide clinical care, public health, and scientific efforts regarding SARS-CoV-2 (COVID-19) recovery. The understanding and treatment of long-term sequelae of COVID-19, referred to variously as post-acute sequelae of COVID-19 (PASC), post-acute COVID, long COVID, or long-haul COVID, is fundamental to patient recovery. These long-term consequences are common and increasingly recognized, although heterogeneous in manifestation, and can result in a failure to return to baseline level of health. At the time of the FIRE CORAL study, there were limited studies that collected objective assessments following hospital discharge for a wide spectrum of patients surviving COVID-19.Participants: FIRE CORAL enrolled adult participants as a subset of those enrolled in the BLUE CORAL study with a recent COVID-19 hospitalization and that completed the 1- or 3-month post-hospital telephone long-term outcomes assessment. The target enrollment for this pilot study cohort was 80 participants.Design: FIRE CORAL was a multicenter prospective cohort study of participants recovering from COVID-19 disease with in-person follow-up, as an extension of the BLUE CORAL study. The study consisted of a battery of assessments objectively measuring pulmonary function, abnormalities on lung imaging, and functional status. Participants were to attend and perform initial in-person testing at 3 to 9 months after hospital discharge. Participants with abnormal findings on pulmonary function testing or chest imaging during their initial assessment or those with persistent respiratory symptoms were eligible to repeat study procedures 3 months later with a subsequent visit at 12 months. All participants were invited to return for in-person follow up at 12 months after hospital discharge. Assessments included high-resolution chest CT scan without contrast, spirometry, lung volume assessment, diffusing capacity measured by single breath measurement, Six Minute Walk Test, Short Physical Performance Battery, St. George's Respiratory Questionnaire, and Functional Assessment of Chronic Illness Therapy-Fatigue scale. Demographic and hospitalization data are available as part of the BLUE CORAL study.The primary aim of the FIRE CORAL study was to examine the feasibility of conducting rigorous in-person follow-up testing of participants discharged from the hospital following COVID-19 illness to assist with planning for a larger study to evaluate variables associated with differential recovery. The secondary aim was to describe the pulmonary, imaging, and functional recovery following COVID-19 hospitalization in a diverse population of patients.

  Study phs004130

• Heart Failure Network - Imaging from Nitrate's Effect on Activity Tolerance in Heart Failure with Preserved Ejection Fraction (HFN NEAT-Imaging)

  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 isosorbide mononitrate on daily activity in patients with heart failure and preserved ejection fraction.Background: Nitrates are commonly prescribed for symptom relief in patients with heart failure. Early studies in patients with heart failure with a reduced ejection fraction concluded that long-acting nitrates improves activity tolerance; however, approximately half of heart failure patients have preserved ejection fraction. The effects of nitrates in patients with heart failure and a preserved ejection fraction have not been extensively studied and the overall effect of nitrates on activity tolerance in such patients is uncertain.Subjects: There were a total of 110 patients enrolled with 51 patients assigned to receive isosorbide mono-nitrate first and placebo second, and 59 patients assigned to receive placebo first and isosorbide mononitrate second.Design: Enrolled subjects underwent baseline assessments, including echocardiography, quality-of-life scores, 6-minute walk test distance, and NT-proBNP levels. Subjects were also supplied with two kinetic activity monitors containing high-sensitivity triaxis accelerometers, to be worn 24 hours per day. The accelerometer measurements were expressed as arbitrary accelerometer units and stored every 15 minutes equaling 96 data points per day. The 15-minute cumulative accelerometer units were totaled over a 24-hour period to provide daily accelerometer units.Subjects were assigned to one of two treatment groups: 6 weeks of placebo first with crossover to 6 weeks of isosorbide mononitrate, or 6 weeks of isosorbide mononitrate first with crossover to 6 weeks of placebo. The study drugs were prepared as 30-mg tablets of isosorbide mononitrate and matching placebo. During each 6-week period, patients were instructed to take no study drug for the first 2 weeks followed by one tablet (30 mg daily) for 1 week, two tablets (60 mg once daily) for 1 week, and four tablets (120 mg once daily) until the next study visit, for a treatment duration of at least 2 weeks and up to 4 weeks. After each 6-week period, patients returned to the study center to repeat end-point assessments. The primary outcome for the study was the comparison of average daily accelerometer units during the period in which patients were receiving the 120-mg dose of isosorbide mononitrate compared to the period in which patients received the placebo. Other secondary end points included the 6-minute walk distance and the post-walk Borg dyspnea score, scores on the Kansas City Cardiomyopathy Questionnaire and the Minnesota Living with Heart Failure Questionnaire, and NT-proBNP levels. In addition, subjects completed a questionnaire indicating in which period (first, second, no preference) they felt better. Conclusions: Patients were active for fewer hours of the day during the 120-mg phase of receipt of isosorbide mononitrate as compared with placebo. Furthermore, during all study-drug regimens combined (30 mg to 120 mg), patients were less active during receipt of isosorbide mononitrate as compared with placebo. There was no significant effect of isosorbide mononitrate on secondary outcomes.

  Study phs004254

• EGA file encryption types

  EGA file encryption The European Genome-Phenome Archive (EGA) stands as a significant initiative in the field of genomics, facilitating the secure storage and sharing of vast amounts of genomic data. Jointly hosted by the Centre for Genomic Regulation (CRG) and the European Bioinformatics Institute (EMBL-EBI), the EGA offers a robust infrastructure for managing encrypted data, ensuring the privacy and integrity of sensitive genomic information. Both CRG and EMBL-EBI play pivotal roles in the EGA, each institution bringing unique expertise in managing different types of encryptions. EMBL-EBI EGACryptor encryption system, while CRG utilises Crypt4GH, resulting in two distinct encryption file types: cip and c4gh, respectively. How can I check the file encryption? To access your dataset of interest on the European Genome-Phenome Archive (EGA) and determine the corresponding encryption file extension, please follow these step-by-step instructions: Utilise the search or navigation features provided on the EGA website to locate the dataset you are interested in. Once you find the dataset webpage, click on the "Files" tab, typically located on the dataset's webpage. Upon reaching the "Files" tab, you will be presented with a table containing comprehensive information about the files associated with the dataset. This table will include various columns, such as "File Name," "Size," and "Location." The "Location" column is particularly relevant for determining the encryption file extension. Figure 1: File table showing all the information available for the files in a dataset. This table is specific for each dataset. To identify the encryption file extension corresponding to a specific file, locate the "Location" column in the table. If the file is archived in Spain, the file will have the .c4gh extension, indicating that it is encrypted using Crypt4gh. Conversely, if the file is archived in the UK, the encrypted file extension will be .cip, indicating the usage of EGACryptor for encryption. It is worth noting that a file can be available in both locations, meaning it will be accessible with both file extensions (.c4gh and .cip). This allows users to choose the encryption method that aligns with their preferred platform or analysis tools.

  Documentation check-encryption-type

• Honolulu Heart Program (HHP-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. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from HHP include DNA, plasma, serum, and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: The initial objectives of the Honolulu Heart Program were to: 1) estimate morbidity and mortality from coronary heart disease and stroke among Japanese men in Honolulu; 2) compare morbidity and mortality from coronary heart disease and stroke among Japanese men in Japan, Honolulu, and San Francisco; 3) investigate relationships among risk factors, coronary heart disease, and stroke in Japanese men in Honolulu; 4) compare distributions of risk factors among men in Japan, Honolulu, and San Francisco, and relate similarities and differences in risk factors to the occurrence of disease in these areas and in other populations, including Framingham and Puerto Rico; 5) conduct an autopsy study, and to relate pathological findings to morbidity and mortality data; and 6) investigate relationships between risk factors and pathological evidence of atherosclerosis and its complications.Background: The Honolulu Heart Program was initiated in 1965 by the NHLBI as a prospective study of environmental and biological causes of cardiovascular disease among Japanese Americans living in Hawaii. This population was known to have low incidence of coronary heart disease and higher incidence of stroke. The study provided opportunities to investigate relationships among disease frequencies, pathologic findings, and disease predictors in the cohort and to compare the findings in this population with those in other populations, especially cohorts of Japanese men resident in Japan or the U.S.Participants: There were 8006 participants.Design: The study began in 1965 with the first examination of a cohort of 8,006 Japanese-American men residing on the island of Oahu, Hawaii who were born during the period 1900-1919. The first examination was completed in 1968 and was followed by the initiation of a second examination that same year. Three subsequent sub-examinations (Lipoprotein Exams I, II and III) were conducted between 1970 and 1982 to collect lipid measurements on a subset of those who participated in Exam II. The fourth examination of surviving members of the original cohort was conducted during 1991-93 and collected data on 3,741 men. Morbidity and mortality follow-up continues through grant and contract-supported efforts, and the current HHP dataset includes events through 1998.

  Study phs003907

• Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP): CO-CREATE-Ex: Community-engaged Optimization of COVID-19 Rapid Evaluation And TEsting Experiences

  Cases of COVID-19 infection in San Diego have persistently remained high in the county's central and southern communities near the US/Mexico border, home to primarily Latino residents who have been one of the ethnic minority communities most impacted by COVID-19. To address this, our Phase I RADx-UP project partnered with San Ysidro Health (SYH), a federally qualified health center, and the Global Action Research Center (Global ARC), a social change organization, to co-create and demonstrate the impact of a PCR-based COVID-19 testing program in San Ysidro. To date, we have administered approximately 15,000 PCR tests for >10,000 community members (92% Latino) and received requests from SYH to scale-out the testing program to additional primary care clinic sites. Responsive to RFA-OD-22-006, we will continue working with our community (Global ARC) and clinical (SYH) partners to refine, specify, implement, and evaluate an implementation strategy bundle that optimizes COVID-19 testing, expanding beyond current PCR testing to focus on FDA-authorized COVID-19 rapid antigen testing. Use of self-administered rapid antigen tests will allow participants to build capacity to self-test and use health information technology to access additional clinic services. Based on initial implementation mapping with the project's established Community and Scientific Advisory Board, three implementation strategies were prioritized to accelerate sustained uptake of rapid COVID-19 testing. These three strategies include: (1) current, walk-up onsite free testing; (2) promotores-led COVID-19 test counseling and preventive care reminders; (3) vending machines that dispense FDA-authorized self-testing kits. Our primary objectives are to: 1) refine and operationalize our multi-component implementation strategy bundle and a related set of measures of success for rapid FDA- authorized COVID-19 testing and 2) implement and evaluate impact of our innovative, multilevel, and multicomponent implementation strategy bundle to optimize COVID-19 rapid testing among underserved, Latino communities using a roll-out implementation optimization study design across four clinics over 18 months. The COVID-19 pandemic has underscored the urgent and essential need to engage invested community parties continuously and meaningfully in public health research to reduce health disparities. This proposal is well-positioned to provide a set of strategies and measures of success that can be used in settings serving underserved communities while maintaining flexibility to adjust to the changing COVID-19 landscape.

  Study phs003686

• New set of services for all users unveiled at the EGA

  The European Genome-phenome Archive (EGA) releases today a brand-new website as well as a set of improved services for users, comprising a revamped Submitter Portal with an improved API and data brokering functionality for submitters, as well as a new DAC Portal for Data Access Committee members to easily manage data access requests. The EGA team has been working hard over the past months on these improvements that will provide a better experience for the users. Discover them below! Visit our new EGA website and check the new functionalities and updated guides Our new website is live, with a fresh look and updated features to discover all the novelties. The homepage now includes three pathways to guide our users, depending on whether they want to deposit, download or manage data within the Archive. One of the most outstanding developments is the introduction of a streamlined process for requesting access to data: EGA Users can now directly request access to their preferred datasets through the website using their EGA accounts. Additionally, users can customise their profile, oversee active sessions, and manage the public keys, essential for our latest array of services, alongside a range of other features. Another major change is our new Help Desk contact method: a built-in website form tailored for user inquiries. This system, called "Need Help?", can be easily located on the top right-hand side of the website. It will encompass both EGA and Federated EGA node users' requests. We will detail its use soon, so stay tuned. Register your metadata to the EGA easily with our new Submitter Portal The new Submitter Portal makes the submission process quicker and more intuitive. The process is currently divided into sections that the user will know beforehand by taking the tour that the EGA team has created to guide users through the Portal before starting the first submission. Do not complete your data submissions alone! Our Submitter Portal now includes a collaboration mode so that every submission can be completed by authorised collaborators with an EGA Profile. There are a lot more features that we will be detailing from now on in incoming posts. A new platform for Data Access Committee Members The new DAC Portal brings novelties for individuals engaged in governance, legal, technical, operational roles, or those acting as data stewards. DAC members will be able to easily manage DACs, policies, and data access requests with the new Portal. Take the tour now to check them out! Help us improve the services completing the EGA Survey As part of our ongoing journey to improve your experience, we have created an EGA User Survey. This questionnaire covers a wide range of aspects such as user experience, support and data accessibility, among others. Participate now and take the opportunity to suggest your own improvements. Help us enhance your experience in this new era for the EGA. Subscribe to the EGA Mailing List and stay tuned In the next weeks we will share more information about the possibilities of the new services. You can easily join the EGA Mailing List to receive all the updates.

  Blog new-set-of-services-at-EGA

• Data Quality Control

  Data Quality Control High-throughput sequencing techniques have become the leading method to study, decode and discover the genomic origins of biological phenomenons. EGA provides a secure archival of such identifiable genomics data with the purpose of data-upcycling, i.e. to re-use these data for research. High-quality data standards are essential to ensure the quality and credibility of the research. Moreover, a quality check report can assure a researcher beforehand about the data that they will request access, therefore saving time and effort. The EGA has developed a File Quality Control Report (QC Report) to provide generic quality control reports for Fastq, SAM/BAM/CRAM, and VCF files deposited at EGA. This QC Report will allow users to get information regarding the files submitted within a specific dataset. The data requesters will obtain information such as the quality of reads, mapped reads, number of variants, and other features before starting the requesting process, which will save the efforts and time.Accessing file quality control reportsIn each dataset page, the user can explore the files that it contains by clicking the "files" tab. The Quality Control report of a file has two sections. The first one, contains general information about the file, such as the inferred assembly, total reads, the dataset or study where it comes from, etc. The second section contains plots that summarise interesting information about the file, for example, the base coverage distribution, base quality or mapped reads. The description of each plot is accessible by clicking the "i" button at the top-right corner of each plot box. Technical Description For analysing the fastq, SAM/BAM/CRAM and VCF files, the EGA applies a set of tools widely used in the bioinformatics community. FASTQ: FastQC, recognised as the gold standard tool by the community.Per base sequence quality, per sequence quality scores, per base sequence content, per sequence GC content, sequence duplication levels, etc.SAM/BAM/CRAM: samtools, also the gold standard, generates results plots useful to get an overall idea of the quality of the file.base coverage distribution, base quality, % of mapped reads, % of both mates mapped, singletons, duplicates, etc.VCF: vcftools and bcftools, combined with a custom script to infer the genome assembly.site frequency distribution, Ts/Tv, base changes, indel distribution, etc.

  Documentation access/request-data/quality-control-reports

• FASTQ files of total RNA-Seq data of POPS control samples

  Placental biopsies (n = 64 female placentas, n = 67 male placentas) were selected from healthy pregnancies from the POPs cohort. These patients had no evidence of hypertension at booking and during pregnancy, did not experience pre-eclampsia, Hemolysis, Elevated Liver enzymes, and Low Platelets (HELLP) syndrome, gestational diabetes, or diabetes mellitus type I or type II and other obstetric complications. They delivered live babies with a birth weight percentile in the normal range (20-80th percentile), with no evidence of slowing in fetal growth trajectory. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003457

• eMERGE Network's Multi-Center Pilot of Pharmacogenetic Sequencing in Clinical Practice

  eMERGE-PGx is a multi-site test of the concept that sequence information can be coupled to electronic medical records (EMRs) for use in healthcare. The promise of personalized medicine - health care guided by each individual's biological characteristics - is being fostered by increasingly powerful and economical methods to acquire clinically relevant biomarkers from large numbers of people. One therapeutic area that seems especially ripe for an early test of the personalized medicine concept is pharmacogenomics (PGx) - the idea that individual variation in drug response includes a genomic component. Drug response variation is an accepted feature of virtually all drug treatments, and contemporary molecular biologic tools continue to identify key genes mediating drug metabolism, transport, and targets. Importantly, common variation in these genes is an increasingly well-recognized contributor, sometimes with large effects, to variation in drug responses. As a result, recommendations for genotype-guided therapy are increasing. These evidence-based recommendations, if implemented in health care practice, could reduce adverse drug events and improve time to therapeutic response. Through eMERGE-PGx, we are developing strategies for the optimal implementation of genetic sequence data into the clinical environment with the ultimate goal of improving patient care. Site and participants include: Children's Hospital of Pennsylvania (CHOP): The Center for Applied Genomics (CAG) at the Children's Hospital of Philadelphia (CHOP) is a high-throughput, highly automated genotyping and sequencing facility equipped with state-of-the-art genotyping and sequencing platforms. Children who are treated at the Children's Hospital Healthcare Network and their parents may be eligible to take part in a major initiative to collect more than 100,000 blood samples, covering a wide range of pediatric diseases. The PGx population selected for sequencing with the PGRNseq panel at CHOP is 1,650 children from CAG's biorepository with well-documented drug-related severe adverse events (SAEs) or EHR-based drug response profiles. SAEs were extracted from EPIC records and from CHOP's Adverse Event (AE) database, which documents every AE at CHOP. These AEs are classified by a medical review panel according to the causal relationship with the suspected drug into 'doubtful', 'possible', and 'probable'. Individuals with events classified as probable, severe and objective, were selected for sequencing. The drugs more frequently associated with adverse events are antibiotics, antineoplastics, immunosuppressants and psychotropic drugs. This cohort constitutes 50% of the target population. The remaining subjects were selected using EHR-based algorithms that we have developed and validated at CAG for identifying patients not responding to ADHD medication (primarily atomoxetine) and patients refractory to antiepileptic treatment from responders. Cincinnati Children's Hospital Medical Center/Boston's Children's Hospital (CCHMC/BCH): 811 CCHMC samples were obtained from children, adolescents or young adults exposed to medication or at risk for needing medication of study interest. 55% of participants were exposed to one or more opioids and their DNA source was a CCHMC study-specific biobank; while 27% of participants were at risk for needing an opioid for surgical pain management and were newly recruited. The remainder of the cohort was exposed to methylphenidate and their DNA samples were obtained from a CCHMC study-specific biobank. The focus of Boston Children's Hospital eMERGE PGx project is on individuals with epilepsy. Samples were taken from a current pharmacogenomics study already in place through which DMET analysis was run and used as confirmation for PGRN-Seq results. A total of 109 samples were sent for PGRN-Seq analysis at University of Washington. The remaining 141 epilepsy samples were from Children's Hospital of Philadelphia and underwent testing with PGRN-Seq at CHOP. Geisinger Health System: A research cohort of adult Geisinger Clinic patients was enrolled from community-based primary care clinics of the Geisinger Health System. Patients were eligible for enrollment if they were a primary care patient of a Geisinger Clinic physician and were scheduled for a non-emergent clinic visit. All data are from Geisinger patients who consent to participate in the MyCode project. MyCode participants agree to provide biological samples for broad research use, including genomic analysis, and for linking of sample data to information in the participant's Geisinger health record. The consent also permits sharing of de-identified data for research purposes. Group Health(GH)/University of Washington (UW): Potential GH participants for the PGx project were enrolled in the eMERGE Network through the Northwest Institute of Genetic Medicine (NWIGM) biorepository, and provided the appropriate consent to receive clinically relevant genetic results (N~6300). Participants were eligible if aged 50 - 65 years old at the time of their enrollment into the NWIGM repository, living, enrolled in GH's integrated group practice, and had completed an online Health Risk Appraisal. The selection algorithm was based on several data sources from the EHR at Group Health: 1. Demographics - participants with self-reported race as Asian or African ancestry were prioritized and selected to enrich for non-European ancestry; 2. Diagnosis and procedure codes - participants were selected if found to have a history of hypertension, atrial fibrillation (AF,) or congestive heart failure (CHF). Participants with a history of arrhythmia were added if the entire selection algorithm did not generate 900 individuals. We also enriched for participants with EHR evidence of actionable indications related to PGRNSeq genes. Participants were selected if found to have an ICD9 code for malignant hyperthermia, hypertension, atrial fibrillation, congestive heart failure or long QT syndrome (LQTS); 3. Laboratory values - if a participant had any laboratory event of creatine kinase (CK) > 1000, and were dispensed statins within 6 months of the event, then they were selected; and 4. Medications - participants were excluded if ever on carbamazepine or had a current regimen of warfarin. Essentia Institute of Rural Health, Marshfield Clinic, Pennsylvania State University (Marshfield): For this study, 750 subjects were selected and enrolled into PGx based on Vanderbilt's algorithm designed to enrich for patients who are most likely to receive one of three common drugs (Clopidogrel, Warfarin or Simvastatin) in the next 2-3 years. These patients were sent a letter of invitation and description of the PGx project. Follow-up phone calls were made, and interested subjects came in for a one time meeting to discuss the project and go through the informed consent with the research coordinator. If they were interested they signed the consent and HIPAA forms and gave blood. Subjects were chosen and enrolled into PGx independently of previous biobank participation. Mayo Clinic: The Right Drug, Right Dose, Right Time - Using Genomic Data to Individualize Treatment (The RIGHT Protocol) enrolled 1013 patients to test the hypothesis that prescribers could deliver genome-guided drug therapy at the point-of-care by using pharmacogenomic data preemptively integrated in the electronic medical record. Complete details regarding the study population have been previously described (Bielinski et al., 2014). Icahn School of Medicine at Mount Sinai School (Mt Sinai): Our study site is the Primary Care Associates (PCA) practice group of the Mount Sinai Faculty Practice Associates (FPA) of the Mount Sinai Medical Center in New York City. This practice has 12 physician providers. All patient encounters are documented and managed with EpicCare ambulatory electronic medical record. Active PCA Patients eligible for enrollment fulfilled the following criteria: a) age 50 or older receiving clinical care at Mount Sinai FPA PCA practice with at least one practice encounter within 18 months prior to commencement of enrollment; b) no history or current use of clopidogrel, warfarin, or simvastatin. Eligible patients were invited to participate through de novo recruitment by letter sent by their provider. Interested patients were screened for eligibility and enrolled to participate in the eMERGE PGX study on site by a dedicated research coordinator. In addition to de novo enrollment from clinical practice, patients of FPA PCA who had previously enrolled in Mount Sinai's BioMe Biobank program AND fulfilled eligibility criteria as stated under a) and b) were identified by chart review and samples sequenced at CIDR using PGRNseq platform (N=300). PGRNseq data from 291 samples passed stringent quality control and are included in the current data set. Furthermore, 56 of these patients carrying known and validated 'actionable' variants affecting prescribing of clopidogrel, warfarin, and/or simvastatin were enrolled in the eMERGE PGX study following invitation through recontacting by the Principal Investigator of the BioMe Program. Northwestern University: Participants for this study were recruited from the General Internal Medicine (GIM) clinic at Northwestern Medical Group (NMG). Patients were selected for invitation to participate if they had been seen a minimum of two times over the last four years, having a high likelihood to receive a prescription for warfarin, Plavix, or a statin, and are seeing a physician who has agreed to allow their patients to be contacted for the study. We utilized an algorithm developed at Vanderbilt and tailored to our population which uses our EHR to estimate the probability that individuals will receive a prescription for warfarin, Plavix, or a statin in the next three years. Participants were sent a letter explaining the study prior to their GIM appointment and offered participation at the time of their visit. Participants were consented on-site and blood drawn after consent was obtained. The GIM clinic consists of 39 primary care physicians who provide approximately 80,000 patient encounters per year. As with any large primary care clinic, a significant proportion of patients in GIM clinic suffer from a variety of chronic health conditions, such as diabetes, hypertension, and coronary artery disease. Over 50,000 individuals have been seen by GIM doctors in the past 5 years; 11,562 of these patients have evidence of a statin prescription in the EHR, 3,436 have evidence of a warfarin prescription, and 1,872 have evidence of a Plavix prescription. Vanderbilt University: The more than 1000 participants enrolled into Vanderbilt's eMERGE PGx study were newly recruited from the Cardiology and Internal Medicine Clinics and the Hillsboro Medical Group within Vanderbilt University Medical Center (VUMC). Patients were selected based on a predictive algorithm estimating the patient's likelihood of receiving Clopidogrel, Warfarin, and/or Simvastatin. The algorithm identifies primarily older middle-aged patients, and the mean age of the study group is 74. The cohort is approximately 45% female with 75% of subjects self-identified as EA and 24% as AA. Subjects were consented in person by study personnel following a routine clinic visit and an introduction to the study staff by their doctor. VUMC is a comprehensive health care facility dedicated to patient care, research, and the education of health care professionals. Translational research into the causes and treatment of disease as well as studying fundamental biological properties is the primary focus of discovery at Vanderbilt. Clinical research is conducted in Vanderbilt University Hospital, the Nashville Veterans Administration Hospital, Meharry General Hospital and in their associated outpatient clinics. These hospitals and clinics, all associated with the Vanderbilt system, each have full time Vanderbilt faculty and medical housestaff and provide clinical care and participate in research programs. The Vanderbilt Clinic is comprised of more than 95 adult outpatient specialty practices and received over 1.5 million ambulatory visits in 2012-13. The Vanderbilt Heart and Vascular Institute offers a comprehensive heart program offering diagnosis, medical treatment, minimally invasive therapies, surgical intervention and disease management, tailored to each individual's unique needs. All programs within the Vanderbilt Clinic have survival figures that surpass the national average.

  Study phs000906