The European Genome-phenome Archive (EGA) is a permanent archive that promotes distribution and sharing of genetic and phenotype data consented for specific approved uses, but not fully open public distribution. The EGA follows strict protocols for information management, data storage, security and dissemination. Authorized access to the data is managed in partnership with the data providing organizations. The EGA includes major reference data collections for human genetics research.
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| http://dx.doi.org/10.1038/ng.3312 | DOI Listing |
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A WFS1 variant disrupting acceptor splice site uncovers the impact of alternative splicing on beta cell apoptosis in a patient with Wolfram syndrome.
Diabetologia
January 2025
Unit of β Cell Biology, Diabetes Research Institute, IRCCS San Raffaele Hospital, Milan, Italy.
Aims/hypothesis: Wolfram syndrome 1 (WS1) is an inherited condition mainly manifesting in childhood-onset diabetes mellitus and progressive optic nerve atrophy. The causative gene, WFS1, encodes wolframin, a master regulator of several cellular responses, and the gene's mutations associate with clinical variability. Indeed, nonsense/frameshift variants correlate with more severe symptoms than missense/in-frame variants.
View Article and Find Full Text PDFAnalyzing sex imbalance in EGA and dbGaP biological databases: Recommendations for better practices.
iScience
October 2024
Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.
Precision medicine aims at tailoring treatments to individual patient's characteristics. In this regard, recognizing the significance of sex and gender becomes indispensable for meeting the distinct healthcare needs of diverse populations. To this end, continuing a trend of improving data quality observed since 2014, the European Genome-phenome Archive (EGA) established a policy in 2018 that mandates data providers to declare the sex of donor samples, aiming to enhance data accuracy and prevent imbalance in sex classification.
View Article and Find Full Text PDFAn interconnected data infrastructure to support large-scale rare disease research.
Gigascience
January 2024
Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
The Solve-RD project brings together clinicians, scientists, and patient representatives from 51 institutes spanning 15 countries to collaborate on genetically diagnosing ("solving") rare diseases (RDs). The project aims to significantly increase the diagnostic success rate by co-analyzing data from thousands of RD cases, including phenotypes, pedigrees, exome/genome sequencing, and multiomics data. Here we report on the data infrastructure devised and created to support this co-analysis.
View Article and Find Full Text PDFCohort profile: DNA methylation in the Northern Ireland Cohort for the Longitudinal Study of Ageing (NICOLA) - recruitment and participant characteristics.
BMJ Open
September 2024
Centre for Public Health, Queen's University Belfast, Belfast, UK.
Purpose: Epigenetic modifications including DNA methylation (DNAm) are proposed mechanisms by which social or environmental exposures may influence health and behaviours as we age. The Northern Ireland Cohort for the Longitudinal Study of Ageing (NICOLA) DNAm cohort, established in 2013, is one of several worldwide, nationally representative prospective studies of ageing with biological samples from participants who consented to multiomic analysis.
Participants: NICOLA recruited 8478 participants (8283 aged 50 years or older and 195 spouses or partners at the same address aged under 50 years).
Identification of tumor rejection antigens and the immunologic landscape of medulloblastoma.
Genome Med
August 2024
UF Brain Tumor Immunotherapy Program, Preston A. Wells Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA.
Article Synopsis
- Current treatments for high-risk medulloblastoma are ineffective due to tumor heterogeneity, highlighting the need for personalized immunotherapy approaches.
- A study analyzed the genetic profiles of 170 medulloblastoma tumors to identify potential tumor rejection antigens that could enhance the effectiveness of immune responses.
- The results indicated that patients expressed various immunogenic antigens, with higher proportions of tumor-associated antigens compared to neoantigens, particularly noting the presence of cancer-testis and new neurodevelopmental antigens across most molecular subgroups.
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