Search results - Portal of Medical Data Models (MDM-Portal)

dbGaP phs000944 eMERGE Clinical Center at Partners HealthCare - Eligibility

- 11/27/24 - 6 forms, 2 itemgroups, 11 items, 1 language

Itemgroups: IG.elig, IG.elig

Principal Investigator: Scott T. Weiss, MD, MS, Partners HealthCare System, Boston, MA, USA MeSH: Hypercholesterolemia,Asthma,Arthritis, Rheumatoid,Attention Deficit Disorder with Hyperactivity,Bipolar Disorder,Coronary Disease,Depression,Heart Failure,Inflammatory Bowel Diseases,Multiple Sclerosis,Schizophrenia,Stroke https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000944 The Partners HealthCare Biobank is a large research data and sample repository working within the framework of Partners Personalized Medicine. It provides researchers access to high quality, consented samples to help foster research, advance understanding of the causes of common diseases, and advance the practice of medicine. The Partners Biobank provides banked samples (plasma, serum and DNA) collected from consented patients. These samples are available for distribution to Partners HealthCare investigators with appropriate approval from the Partners Institutional Review board (IRB). They are linked to clinical data that originates in the Electronic Medical Record (EMR), as well as additional health information collected in a self-reported survey. The Partners Biobank will be genotyping 25,000 subjects with the Illumina Multiethnic Beadchip 1.6 million SNPs with exome and custom content ( 60,000 LoFs). Of the participants genotyped so far, 4929 of 4962 (99.3%) individuals have genotype data that passed the default quality thresholds for the Infinium array (call rate = 0.99). We are submitting the genotype data to dbGaP for 4929 subjects with 12 phenotypes (based on icd9 codes). We will do annual releases until we reach the full 25,000 genotyped subjects.

pht004847.v1.p1

1 itemgroup 5 items

pht005288.v1.p1

1 itemgroup 6 items

pht004844.v1.p1

1 itemgroup 2 items

pht004845.v1.p1

1 itemgroup 3 items

pht004846.v1.p1

1 itemgroup 18 items

dbGaP phs000983 Pharmacogenomics of Rheumatoid Arthritis Therapy - Eligibility

- 12/1/23 - 5 forms, 1 itemgroup, 1 item, 1 language

Itemgroup: IG.elig

Principal Investigator: Rex Chisholm, PhD, Northwestern University MeSH: Arthritis, Rheumatoid https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000983 Rheumatoid arthritis (RA) is the most common autoimmune inflammatory arthritis worldwide and affects 1.3 million adults in the USA. It has previously been studied using phenotype algorithms to identify electronic health records (EHR) case cohorts. Early genetic studies of EHR-linked cohorts of RA patients have been replicated in known associations. Further development of collections of EHR-linked cohorts for RA and other phenotypes may enable not only enhanced understanding of disease risks but also the investigation of outcomes and treatment responses.

Arthritis, Rheumatoid

pht005005.v1.p1

1 itemgroup 5 items

pht005007.v1.p1

1 itemgroup 5 items

pht005004.v1.p1

1 itemgroup 5 items

pht005006.v1.p1

1 itemgroup 7 items

dbGaP phs001340 Identification and Targeting of Inflammatory Macrophage-Fibroblast Crosstalk in Rheumatoid Arthritis - pht009154.v1.p1

- 3/2/23 - 4 forms, 1 itemgroup, 2 items, 1 language

Itemgroup: pht009154

Principal Investigator: Laura T. Donlin, PhD, Hospital for Special Surgery, New York, NY, USA MeSH: Arthritis, Rheumatoid,Arthritis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001340 Macrophages tailor their function according to the signals found in tissue microenvironments, assuming a wide spectrum of phenotypes. A detailed understanding of macrophage phenotypes in human tissues is limited. Using single-cell RNA sequencing, we defined distinct macrophage subsets in the joints of patients with the autoimmune disease rheumatoid arthritis (RA), which affects ~1% of the population. The subset we refer to as HBEGF+ inflammatory macrophages is enriched in RA tissues and is shaped by resident fibroblasts and the cytokine tumor necrosis factor (TNF). These macrophages promoted fibroblast invasiveness in an epidermal growth factor receptor-dependent manner, indicating that intercellular cross-talk in this inflamed setting reshapes both cell types and contributes to fibroblast-mediated joint destruction. In an ex vivo synovial tissue assay, most medications used to treat RA patients targeted HBEGF+ inflammatory macrophages; however, in some cases, redirecting them into a state is not expected to resolve inflammation. These data highlight how advances in our understanding of chronically inflamed human tissues and the effects of medications therein can be achieved by studies on local macrophage phenotypes and intercellular interactions. Reprinted from Kuo, Ding et al., Science Translational Medicine 2019, PMID: 31068444, with permission from American Association for the Advancement of Science.

pht009155.v1.p1

1 itemgroup 2 items

pht009156.v1.p1

1 itemgroup 2 items

pht009157.v1.p1

1 itemgroup 6 items

dbGaP phs001360 Genome-Wide Association Study in African-Americans with RA - Eligibility

- 2/28/23 - 5 forms, 1 itemgroup, 10 items, 1 language

Itemgroup: IG.elig

Principal Investigator: S. Louis Bridges, Jr., MD, PhD, University of Alabama at Birmingham, Birmingham, AL, USA MeSH: Arthritis, Rheumatoid https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001360 The Consortium for the Longitudinal Evaluation of African-Americans with Early Rheumatoid Arthritis (*CLEAR*) Registry and Repository, supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (*NIAMS*), was established in 2000 to provide a resource for the scientific community to explore genetic and non-genetic factors affecting rheumatoid arthritis (*RA*) occurrence and outcomes in African Americans. The long term objective is a database and a repository of 1,100 RA and 550 matched healthy African-American subjects. This CLEAR Registry and Repository has two arms: a longitudinal arm for subjects with early RA (enrollment from 2000 to 2005) and a cross-sectional arm for subjects with any disease duration (enrollment from 2006 to 2012). CLEAR has two components: a database and a repository. The database contains extensive demographic, socioeconomic, clinical and radiographic (radiographs of hands and feet) information and bone mineral density data from DEXA scans. The repository contains genomic DNA, plasma and serum on most of the participants. Participants in CLEAR II had RNA isolated from peripheral blood cells.

Arthritis, Rheumatoid

pht006293.v1.p1

1 itemgroup 4 items

pht006296.v1.p1

1 itemgroup 5 items

pht006294.v1.p1

1 itemgroup 3 items

pht006295.v1.p1

1 itemgroup 14 items

dbGaP phs001371 Inflammation-Induced Stabilization of mRNA in Rheumatoid Arthritis - pht006544.v1.p1

- 2/25/23 - 3 forms, 1 itemgroup, 2 items, 1 language

Itemgroup: pht006544

Principal Investigator: Lionel B. Ivashkiv, MD, Hospital for Special Surgery, New York, NY, USA MeSH: Arthritis, Rheumatoid,Arthritis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001371 During rheumatoid arthritis (RA), TNF activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches and becomes dominated by very stable transcripts. This temporal switch is due to: a) TNF-induced prolonged stabilization of previously unstable transcripts that enables progressive transcript accumulation over days and b) sustained expression and late induction of very stable transcripts. TNF- induced mRNA stabilization in RA FLS occurs during the late phase of TNF response, is MAPK-dependent, and involves several genes with pathogenic potential such as IL6, CXCL1, CXCL3, CXCL8/IL8, CCL2, and PTGS2. These results provide the first insights into genome-wide regulation of mRNA stability in RA FLS and highlight the potential contribution of dynamic regulation of the mRNA stabilome by TNF to chronic synovitis.

pht006545.v1.p1

1 itemgroup 3 items