Undiagnosed Diseases Network (UDN)
Ontology highlight
ABSTRACT: The Undiagnosed Diseases Network (UDN) is an initiative to facilitate the diagnosis of conditions that have eluded diagnosis through the coordinated action of leading clinical and research centers. The purpose of this cooperative research network is to establish a national network added to and building upon the NIH Undiagnosed Diseases Program (NIH UDP). The objectives of this program are to:
SECONDARY ACCESSION(S): PRJNA350185PRJNA350184
REPOSITORIES: dbGaP
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Project description:To facilitate a better understanding of the molecular heterogeneity of breast cancer and to uncover gene-survival associations that segregate with distinct molecular subtypes, we recently compiled a meta-analytical database of over 2,000 human breast tumor expression profiles variously annotated for clinical and pathological variables and derived from various institutions worldwide. This database was utilized for the breast tumor study cited below: Nagalla, et. al., Genome Biology, 2013. While the majority of the tumor expression profiles included in this database derived from publicly accessible microarray repositories, a number of the samples had not been previously published. Here, we describe the origin of these samples and provide their associated clinical and pathological annotations with the hope that other investigators will be able to utilize these data in their own research. Breast tumor samples derived from the Institut Jules Bordet (IJB; Belgium), John Radcliffe Hospital (JRH; Oxford) and the National University Hospital (NUH, Singapore) were profiled on the Affymetrix U133A platform. The number of tumors profiled (n) and the corresponding dates of tumor diagnosis are as follows. IJB: n=41, 1994-2001; JRH: n=8, 1990-1993; and NUH: n=100, 2000-2002.
2013-03-21 | E-GEOD-45255 | biostudies-arrayexpress
Project description:Impairment of oligodendrocyte (OL) myelinogenic potential, rather than inability of oligodendrocyte precursors to differentiate, is implicated in remyelination failure in demyelinating diseases such as multiple sclerosis. However, the mechanisms underlying myelinogenesis and age-related decline in remyelination remain elusive. Here, we identify a mature-OL-active transcriptional regulator Dor as a critical mediator of CNS myelination and remyelination. Genomic occupancy and transcriptomic analyses revealed that Dor interacts with Sox10 and targets the enhancers of myelinogenesis-regulatory genes including a newly identified OL-enriched nuclear factor Prr18 required for OL maturation. Metabolomic profiling showed that Dor is critical for alpha-ketoglutarate (alpha-KG) production and lipid biosynthesis. Supplementation with alpha-KG enhanced lipid biosynthesis and restored OL maturation defects in Dor-mutant mice while reversing the age-associated decline in remyelination efficiency and memory deficits in aging mice. Thus, our findings connect the OL-active Dor regulatory activity to alpha-KG-mediated lipid metabolism in mature OLs to thereby facilitate myelin production and remyelination.
2024-07-05 | GSE233592 | GEO
Project description:Impairment of oligodendrocyte (OL) myelinogenic potential, rather than inability of oligodendrocyte precursors to differentiate, is implicated in remyelination failure in demyelinating diseases such as multiple sclerosis. However, the mechanisms underlying myelinogenesis and age-related decline in remyelination remain elusive. Here, we identify a mature-OL-active transcriptional regulator Dor as a critical mediator of CNS myelination and remyelination. Genomic occupancy and transcriptomic analyses revealed that Dor interacts with Sox10 and targets the enhancers of myelinogenesis-regulatory genes including a newly identified OL-enriched nuclear factor Prr18 required for OL maturation. Metabolomic profiling showed that Dor is critical for alpha-ketoglutarate (alpha-KG) production and lipid biosynthesis. Supplementation with alpha-KG enhanced lipid biosynthesis and restored OL maturation defects in Dor-mutant mice while reversing the age-associated decline in remyelination efficiency and memory deficits in aging mice. Thus, our findings connect the OL-active Dor regulatory activity to alpha-KG-mediated lipid metabolism in mature OLs to thereby facilitate myelin production and remyelination.
2024-07-05 | GSE261859 | GEO
Project description:Impairment of oligodendrocyte (OL) myelinogenic potential, rather than inability of oligodendrocyte precursors to differentiate, is implicated in remyelination failure in demyelinating diseases such as multiple sclerosis. However, the mechanisms underlying myelinogenesis and age-related decline in remyelination remain elusive. Here, we identify a mature-OL-active transcriptional regulator Dor as a critical mediator of CNS myelination and remyelination. Genomic occupancy and transcriptomic analyses revealed that Dor interacts with Sox10 and targets the enhancers of myelinogenesis-regulatory genes including a newly identified OL-enriched nuclear factor Prr18 required for OL maturation. Metabolomic profiling showed that Dor is critical for alpha-ketoglutarate (alpha-KG) production and lipid biosynthesis. Supplementation with alpha-KG enhanced lipid biosynthesis and restored OL maturation defects in Dor-mutant mice while reversing the age-associated decline in remyelination efficiency and memory deficits in aging mice. Thus, our findings connect the OL-active Dor regulatory activity to alpha-KG-mediated lipid metabolism in mature OLs to thereby facilitate myelin production and remyelination.
2024-07-05 | GSE233591 | GEO
Project description:<p><font color="#FF0000"><b>Note: Data Use Restrictions:</b> <ul> <li>The data <i><u>must only</u></i> be used for genetic research projects solely in the area of health-related social-network research.</li> </ul> </font> </p> <p>This study compiles detailed information on family and social ties linked to participants in the offspring cohort of the Framingham Heart Study. The investigators took computerized information from self-report data used by the FHS for over 30 years to facilitate health exam scheduling. These tracking sheets asked participants to identify people close to them, which were assumed by the investigators to indicate a social tie. Individuals are listed as "egos" (if the ties are from their perspective) and/or "alters" (if they are linked as a friend or family members to one of the other participants). All egos were FHS offspring participants while alters could be FHS participants in any cohort or non-participants. This information was combined with internal FHS pedigree data on family ties to list family member alters (as well as the nature of their relationship). The resultant dataset therefore includes each ego-alter tie, the nature of their relationship and the start and end dates for their ties for each of seven waves for the offspring study.</p> <p>Due to privacy concerns, all exam dates for individuals are listed relative to the initial FHS exam date. The study investigators chose a random, confidential date, to which all initial exam dates are linked (by number of months from random date to initial exam date). With this information, researchers can have access to the temporal relationships among participants' exam dates while remaining unaware of the actual exam dates for individual participants.</p> <p>During each clinic exam cycle, the participants undergo a detailed examination including physical examination, medical history, laboratory testing, and electrocardiogram. Over the years, other tests (that may not be performed at every exam cycle) have included pulmonary function, lifestyle, physical function, cognitive function questionnaires, and various noninvasive cardiovascular tests including echocardiograms. This study involves phenotypic data from these exams including (when available) basic body measurements (height, weight, blood pressure), laboratory values (blood sugar levels, LDL levels), information on smoking and alcohol use, and tests of depression and cognitive functioning.</p> <p><b>Important links to apply for individual-level data</b> <ol> <li><a href="http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000153.v8.p7" target="_blank">Data Use Certification Requirements (DUC)</a></li> <li><a href="GetPdf.cgi?id=phd001183.1" target="_blank">Instructions to Request Authorized Access</a></li> <li><a href="http://view.ncbi.nlm.nih.gov/dbgap-controlled" target="_blank">Apply here for controlled access to individual level data</a></li> <li><a href="GetPdf.cgi?id=phd000317" target="_blank">Participant Protection Policy FAQ</a></li> </ol> </p> <p>In 1948, researchers recruited men and women from the town of Framingham, Massachusetts, beginning the first round of extensive physical examinations and lifestyle interviews that would later be analyzed for common patterns related to CVD development.</p> <p>Initially, the Framingham Heart Study enrolled 5,209 men and women from the Framingham area who were between the ages of 28 and 62 years. Beginning in 1971, the Framingham Heart Study enrolled 5,124 men and women, who were either offspring of the original cohort or spouses of those offspring. In 2002, 4,095 third generation participants (men and women) were enrolled.</p>
| phs000153 | dbGaP
Project description:Our hypothesis was that conducting proteomic analysis on clinical laboratory samples which are intended for the fecal calprotectin test would enable the develop-ment of a highly sensitive and specific non-invasive stool test based on mass spec-trometry. To investigate this hypothesis, we combined and applied our expertise in basic research, clinical practice, and bioinformatics to develop a precise ma-chine-learning model for the accurate diagnosis of active IBD from symptomatic non-IBDpatients.
2024-02-01 | PXD047585 | Pride
Project description:Clostridioides difficile is a major cause of healthcare-associated diarrhea in adult patients. Laboratory diagnosis of C. difficile infection (CDI) is challenging as there is no single test combining high sensitivity and specificity, rapid turnaround time and cost efficiency. They also offer no or little correlation with the clinical outcome. Recently, host-based methods have shown satisfactory performance for the diagnosis of infectious diseases. The aim of this study was to discover CDI-specific host biomarkers that correlate with disease stage and severity.
2021-09-09 | PXD020117 | Pride
Project description:The diagnosis of Systemic Lupus Erythematosus (SLE) is challenging due to its heterogeneous clinical presentation and lack of robust biomarkers for laboratory testing to distinguish it from other autoimmune or infectious diseases. Current diagnostic criterion relies on a combination of clinical examination and laboratory tests, and it does not readily distinguish between those with active clinical disease from those that are clinically quiescent. Several groups have attempted to apply emerging high throughput profiling technologies to diagnose SLE. Despite showing promising diagnostic potential, many of them are expensive and technically challenging for routine clinical uses. Here we report a pilot study of applying a technically simple and highly customisable leukocyte capture antibody microarray to profile healthy (n=24) and SLE patients (n=60) of various disease activities. Our analysis reveals a set of surface antigen biomarkers that have significant association with SLE. In addition, we present a computational method to calculate a score from the entire microarray profile to obtain a score that correlate most reliably with SLE disease activity. Although the current version of our microarray alone does not match the discriminatory power of the standard laboratory tests (serum dsDNA, complements C3 and C4), the combination of the two yields a test with significantly increased discriminatory ability than what can be achieved individually. This work paves the way for a customised SLE-specific antibody microarray for accurate diagnosis and monitoring of SLE that can be readily translated to routine clinical use.
2013-02-21 | GSE27293 | GEO
Project description:Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases
| PRJNA285944 | ENA
Project description:<p><font color="#FF0000"><b>Note: Data Use Restrictions:</b> <ul> <li>The data <i><u>must only</u></i> be used for genetic research projects solely in the area of health-related social-network research.</li> </ul> </font> </p> <p>This study compiles detailed information on family and social ties linked to participants in the offspring cohort of the Framingham Heart Study. The investigators took computerized information from self-report data used by the FHS for over 30 years to facilitate health exam scheduling. These tracking sheets asked participants to identify people close to them, which were assumed by the investigators to indicate a social tie. Individuals are listed as "egos" (if the ties are from their perspective) and/or "alters" (if they are linked as a friend or family members to one of the other participants). All egos were FHS offspring participants while alters could be FHS participants in any cohort or non-participants. This information was combined with internal FHS pedigree data on family ties to list family member alters (as well as the nature of their relationship). The resultant dataset therefore includes each ego-alter tie, the nature of their relationship and the start and end dates for their ties for each of seven waves for the offspring study.</p> <p>Due to privacy concerns, all exam dates for individuals are listed relative to the initial FHS exam date. The study investigators chose a random, confidential date, to which all initial exam dates are linked (by number of months from random date to initial exam date). With this information, researchers can have access to the temporal relationships among participants' exam dates while remaining unaware of the actual exam dates for individual participants.</p> <p>During each clinic exam cycle, the participants undergo a detailed examination including physical examination, medical history, laboratory testing, and electrocardiogram. Over the years, other tests (that may not be performed at every exam cycle) have included pulmonary function, lifestyle, physical function, cognitive function questionnaires, and various noninvasive cardiovascular tests including echocardiograms. This study involves phenotypic data from these exams including (when available) basic body measurements (height, weight, blood pressure), laboratory values (blood sugar levels, LDL levels), information on smoking and alcohol use, and tests of depression and cognitive functioning.</p> <p><b>Important links to apply for individual-level data</b> <ol> <li><a href="http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000153.v3.p3" target="_blank">Data Use Certification Requirements (DUC)</a></li> <li><a href="GetPdf.cgi?id=phd001183.1" target="_blank">Instructions to Request Authorized Access</a></li> <li><a href="http://view.ncbi.nlm.nih.gov/dbgap-controlled" target="_blank">Apply here for controlled access to individual level data</a></li> <li><a href="GetPdf.cgi?id=phd000317" target="_blank">Participant Protection Policy FAQ</a></li> </ol> </p> <p>In 1948, researchers recruited men and women from the town of Framingham, Massachusetts, beginning the first round of extensive physical examinations and lifestyle interviews that would later be analyzed for common patterns related to CVD development.</p> <p>Initially, the Framingham Heart Study enrolled 5,209 men and women from the Framingham area who were between the ages of 28 and 62 years. Beginning in 1971, the Framingham Heart Study enrolled 5,124 men and women, who were either offspring of the original cohort or spouses of those offspring. In 2002, 4,095 third generation participants (men and women) were enrolled.</p>
| phs000153.v5.p5 | EGA