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• ACTIV-6: COVID-19 Outpatient Randomized Trial to Evaluate Efficacy of Repurposed Medications

  This study is a platform protocol designed to be flexible so that it is suitable for a wide range of settings within healthcare systems and in community settings where it can be integrated into routine COVID-19 testing programs and subsequent treatment plans. This platform protocol will enroll participants in an outpatient setting with a confirmed polymerase chain reaction (PCR) or antigen test for SARS-CoV-2. Each appendix will describe a repurposed medication (study drug) to meet the protocol objectives. When only one study drug/appendix is under study, allocation between study drug and placebo will be 1:1. If multiple study drugs/appendices are under study, participants will also be randomized among the study drugs for which eligibility is confirmed. Since the route of administration of each study drug may differ, the placebos may also differ. To achieve blinding and an equitable randomization probability, a two-step randomization process will be used.In the first step, the participant will be randomized m:1 active study drug to placebo, where m is the number of active study drugs for which the participant is eligible. Then, participants will be randomized among the m study drugs for which they are eligible. Participants will carry their ‘study drug' versus ‘placebo' randomization with them into the study drug appendix. In this way, a participant allocated to placebo who is randomized to study drug A will be given the placebo that matches study drug A. This achieves equal probability of exposure to a placebo or an active study drug, and equitable distribution among all study arms for which a participant is eligible. Sites will be informed to which study drug appendix the participant is randomized, but not whether they are allocated to the study drug arm or placebo arm within that appendix. For analysis, concurrent placebo participants who were eligible for the study drug appendix will be pooled. This will result in approximately a 1:1 allocation ratio for any study drug to placebo. If a study drug appendix is stopped for efficacy and becomes standard of care, the active study drug arm may serve as a concurrent placebo for other study drugs.Participants will receive complete supply of repurposed medication (study drug) or placebo with length of treatment and amount of study drug/placebo depending on the study drug appendix and arm to which they are randomized.This study is designed so that it can be done completely remotely. However, screening and enrollment may occur in person at sites and unplanned study visits may occur in person or remotely, as deemed appropriate by an investigator for safety purposes. Participants will be on-study for up to 180 days, during which they will complete various questionnaires.

  Study phs003941

• Phenotype Risk Scores Identify Patients with Unrecognized Mendelian Disease Patterns

  This study was designed to assess the phenotypic effects of rare variants. Rare variants are difficult to study in a high-throughput manner because most cohorts are underpowered to detect associations. In order to gain power to test rare variants, we use Phenotype Risk Scores (PheRS) based on features of Mendelian diseases. PheRS is calculated using claims data from an EHR that is mapped to clinical features from OMIM's clinical descriptions of Mendelian disease. We calculated PheRS for 1,204 Mendelians diseases in a cohort of 21,701 individuals genotyped on the HumanExome BeadChip. We then tested for association between these diseases and rare variants in causal genes. A phenotype risk score is calculated as the weighted sum of features for a given disease. The features are defined as a set of phecodes (consolidated ICD codes) associated with a particular Mendelian disease as described in OMIM. The weights for each phecode are calculated as the log inverse prevalence of the phecode in our cohort. For an individual, their score equals the sum of the weights for each phecode that is present in their medical record. Our study was based on a cohort of individuals with genotype data linked to de-identified electronic health records (EHR) from Vanderbilt's BioVU resource. We hope that this method will help generate phenotype-genotype correlation data on rare variants which in turn may inform rare variant interpretations use for diagnostics.

  Study phs001516

• Alpha1-Antitrypsin Deficiency Registry (AADR-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 characterize the clinical and laboratory course of patients with severe alpha 1-antitrypsin deficiency whether or not the patient is undergoing long-term augmentation therapy.Background: A hereditary disorder, patients with low serum levels of alpha-1-antitrypsin are at an increased risk for the early onset of emphysema. The only approved treatment for alpha-1-antitrypsin deficiency is augmentation therapy using a purified preparation of human alpha-1-antitryspin. Sample sizes for a randomized controlled clinical trial of augmentation therapy were determined to be infeasible; therefore, a multi-center registry was initiated in 1988 to explore the natural history of the disease and the relative efficacy of augmentation therapy in patients with a severe deficiency of alpha-1-antitrypsin.Participants: Eligible participants included individuals 18 years of age or greater for whom the Central Laboratory confirmed that the serum alpha 1-antitrypsin level is Conclusions: Participants receiving augmentation therapy had decreased mortality risk during follow-up. FEV1 decline among all participants did not differ by augmentation therapy; however, among participants with FEV1 35-49% predicted, FEV1 decline was significantly slower for participants on augmentation therapy than for those not receiving therapy. (Am J Respir Crit Care Med, 1998; 158:49-59)

  Study phs004187

• CATHeterization GENetics (CATHGEN)

  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°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.

  Study phs000703

• Exploring germline and somatic mutagenesis in the extended family with germline pathogenic variant in POLD1

  This study aimed to estimate the influence of POLD1 L474P on somatic and germline mutagenesis. We studied the mutation rate and spectra in germline and soma in an extended family harboring the POLD1 c.1421T>C p.(Leu474Pro) pathogenic variant. The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from the 16 family members, from DNA obtained single-cell derived colonies obtained from immortalized fibroblasts for 8 of 16 family members and from the same single-cell derived immortalized fibroblasts after approximately 40 passages for 6 out of 8 family members. Additionaly, study includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member.

  Study EGAS00001006434

• Fixation effects on variant-calling in a clinical resequencing panel

  Formalin fixation is the standard method for preservation of tissue for diagnostic purposes, including pathological review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic tests. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade laboratory-developed targeted resequencing assay. We examined and quantified several parameters relating to sequencing quality and variant-calling from tumor and normal colon epithelial tissues. We identify one alterative fixative, Sakura Universal Molecular Fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathological review.

  Study EGAS00001003507

• single-cell RNA-seq Case-Control study of children progressing to Type1 diabetes

  Single-cell RNA sequencing was carried out on four selected PBMC samples of Finnish children at risk of developing Type 1 diabetes and their gender age and HLA matched control children using 10X genomic platform. All four Case children were positive for multiple islet specific autoantibodies and two of them also progressed to clinical disease during the follow up whereas the control children remain negative for all autoantibodies. Age at seroconversion for Case 2, 3, 5, and 9 children is 12, 18, 24, and 18 months, respectively. Age at sampling, in months, for the pairs was as follows (Case/Control): pair 2:24/24; pair 3: 12/18; pair 5: 12/12; pair 9:24/18.

  Study EGAS00001004070

• Elucidating Mechanisms of the Graft versus Leukemia Effect of Hematopoietic Stem Cell Transplant for Acute Myeloid Leukemia

  Donor lymphocyte infusion (DLI) is an established mode of adoptive cellular therapy for treatment of relapsed disease after allogeneic hematopoietic stem cell transplantation (HSCT). For patients with acute myeloid leukemia (AML), the response rate to DLI is only 20%. Here we use next generation sequencing technologies to understand the transcriptomic and immunologic features associated with response or resistance to therapy.

  Study phs003630

• Normal brain controls for ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) used, for example, for the following studies: Mack, Witt, et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 506(7489):445-450, 2014 (see EGAS00001000443) Hovestadt, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. 510(7506):537-541, 2014 (see EGAS00001000561)

  Study EGAS00001000909

• Data access committee for genomic and clinical data produced by the Institute for Biomedical Technology.

  Dac EGAC00001000110