Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking

Human Mutation, Journal Year: 2022, Volume and Issue: unknown

Published: May 10, 2022

The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism discover novel disease-gene relationships. It operates as federated network connecting databases holding relevant data using common application programming interface, where two or more users are looking for match the same gene (two-sided matchmaking). Seven years from its launch, it is clear that MME making outstanding contributions understanding morbid anatomy of genome. number unique genes present across has steadily increased over time; there currently >13,520 (~68% all protein-coding genes) connected MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, RD-Connect Genome-Phenome Analysis Platform. collective set accessible includes than 120,000 cases 12,000 contributors 98 countries. discovery potential new relationships happening daily international collaborative teams moving these advances forward publication, now numbering well 500. Expansion sharing into routine clinical practice by clinicians, genetic counselors, laboratories ensured access even individuals with undiagnosed rare diseases. Tens thousands patients their family members have been directly indirectly impacted discoveries facilitated two-sided matchmaking. supports further connections literature (PubCaseFinder) human model organism resources (Monarch Initiative) scientists (ModelMatcher). Efforts underway explore additional approaches at variant level only one querier (one-sided Genomic proven utility past 7 will continue facilitate come.

Language: Английский

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Implementation of precision medicine in healthcare—A European perspective

Journal of Internal Medicine, Journal Year: 2023, Volume and Issue: 294(4), P. 437 - 454

Published: July 17, 2023

The technical development of high-throughput sequencing technologies and the parallel targeted therapies in last decade have enabled a transition from traditional medicine to personalized treatment care. In this way, by using comprehensive genomic testing, more effective treatments with fewer side effects are provided each patient-that is, precision or (PM). several European countries-such as England, France, Denmark, Spain-the governments adopted national strategies taken "top-down" decisions invest infrastructure for PM. other Sweden, Germany, Italy regionally organized healthcare systems-the profession has instead "bottom-up" initiatives build competence networks enable equal access review, we summarize key learnings at level on implementation process establish sustainable governance organization PM regional, national, EU/international levels. We also discuss critical ethical legal aspects implementing PM, importance real-world data performing clinical trials evidence generation, well need improved reimbursement models, increased cross-disciplinary education patient involvement. summary, represents paradigm shift, modernization all relevant stakeholders-that healthcare, academia, policymakers, industry, patients-must be involved system transformation create sustainable, non-siloed ecosystem that benefits our patients society large.

Language: Английский

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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Journal of Proteome Research, Journal Year: 2023, Volume and Issue: 22(2), P. 287 - 301

Published: Jan. 10, 2023

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community other fields supported by mass spectrometry since its inception 20 years ago. Here we describe general operation of PSI, including leadership, working groups, yearly workshops, document process which proposals are thoroughly publicly reviewed in order to be ratified as PSI standards. We briefly current state many existing standards, some remain same when originally developed, have undergone subsequent revisions, become obsolete. Then set currently being developed described, with an open call participation forging next generation Finally, synergies collaborations organizations look future how will continue promote sharing thus accelerate progress field proteomics.

Language: Английский

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Will variants of uncertain significance still exist in 2030?

The American Journal of Human Genetics, Journal Year: 2023, Volume and Issue: 111(1), P. 5 - 10

Published: Dec. 11, 2023

Language: Английский

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Challenges and opportunities in sharing microbiome data and analyses

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(11), P. 1960 - 1970

Published: Oct. 2, 2023

Language: Английский

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High-throughput sequencing in plant disease management: a comprehensive review of benefits, challenges, and future perspectives

Phytopathology Research, Journal Year: 2023, Volume and Issue: 5(1)

Published: Sept. 12, 2023

Abstract High-throughput sequencing (HTS) has instigated a paradigm shift in plant pathology, showcasing its transformative role the management of diseases. As powerful tool, HTS aids identifying pathogens and enhances disease strategies by detecting novel emerging pathogens, tracking outbreaks, contributing to developing disease-resistant cultivars. Despite these benefits, implementation faces obstacles due complexity data interpretation economic factors that affect widespread adoption. This comprehensive review summarizes strengths, limitations, opportunities associated with using managing The article also delves into prospects HTS, incorporating technological advancements, synergy complementary methodologies, capacity-building initiatives, development best practices guidelines. By acknowledging addressing while harnessing full capabilities we advocate for refined approach is critical ensuring global food security, especially context growing population climate change.

Language: Английский

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The role of biotechnology in healthcare: A review of global trends

World Journal of Advanced Research and Reviews, Journal Year: 2024, Volume and Issue: 21(1), P. 2740 - 2752

Published: Jan. 30, 2024

As healthcare systems strive to meet the evolving demands of an ever-changing landscape, biotechnology emerges as a pivotal force driving transformative advancements. This comprehensive review explores multifaceted role in healthcare, examining global trends that underscore its profound impact on diagnostics, treatment modalities, and overall landscape delivery. The study begins by elucidating fundamental principles diverse applications healthcare. From genomics personalized medicine, biotechnological innovations are reshaping understanding diseases, enabling tailored interventions based individual genetic profiles. delves into burgeoning field precision where tools empower clinicians deliver targeted therapies, optimize outcomes, minimize adverse effects. integration platforms including advanced imaging techniques liquid biopsies, is transforming early detection monitoring ushering era proactive Moreover, characterized collaborative research initiatives cross-disciplinary partnerships. interconnectedness with artificial intelligence data analytics explored, highlighting synergistic potential unlocking intricate patterns within vast datasets inform more precise effective strategies. accelerates development novel therapeutics, gene cell addresses ethical considerations, regulatory frameworks, accessibility challenges. It critically analyzes disparities adoption advancements across systems, emphasizing need for equitable access ensure benefits reach populations worldwide. In conclusion, elucidates extends beyond scientific breakthroughs encompass paradigm shift. By continents, it underscores power fostering new precision, innovation, unwavering commitment improving patient outcomes scale.

Language: Английский

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Data sharing in child and adolescent psychiatry research: Key challenges (and some potential solutions)

Open Research Europe, Journal Year: 2025, Volume and Issue: 5, P. 93 - 93

Published: March 31, 2025

Background The field of biomedical research is entering a new era, in which public data sharing increasingly the norm. There are many advantages embracing initiatives, including tackling replication crisis through enhanced transparency and publication null findings, facilitating global collaborations to accelerate progress, enhancing cost-effectiveness by reducing duplication efforts, making scientific advances more accessible public. However, there also several crucial ethical logistical challenges that must be addressed maximise benefits minimise risks. potential, recognised, risks unregulated (e.g., reidentification, misuse, lack representativeness due variability who agrees share data) have been exemplified high profile breaches directly clash with efforts make robust, accessible, global. Methods/Results Here, we narratively outline current for from perspective child adolescent psychiatry, one area where they may particularly acute. For example, early often requires caregivers consent on behalf minor – increasing responsibility researchers consider how science today evolve into future (when those individuals no longer minors). We use our consortium Autism Innovative Medicines Study - 2 Trials (AIMS-2-TRIALS; https://www.aims-2-trials.eu/) illustrate points raised this piece. Conclusions propose some potential solutions begin address sharing, focusing key priorities, shared control curation between researcher participant communities equity access groups tools resources needed conduct responsible sustainable sharing.

Language: Английский

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Playbook workflow builder: Interactive construction of bioinformatics workflows

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(4), P. e1012901 - e1012901

Published: April 3, 2025

The Playbook Workflow Builder (PWB) is a web-based platform to dynamically construct and execute bioinformatics workflows by utilizing growing network of input datasets, semantically annotated API endpoints, data visualization tools contributed an ecosystem collaborators. Via user-friendly user interface, can be constructed from building-blocks without technical expertise. output each step the workflow added into reports containing textual descriptions, figures, tables, references. To workflows, users click on cards that represent in workflow, or via chat interface assisted large language model (LLM). Completed are compatible with Common Language (CWL) published as research publications, slideshows, posters. demonstrate how PWB generates meaningful hypotheses draw knowledge across multiple resources, we present several use cases. For example, one these cases prioritizes drug targets for individual cancer patients using NIH Fund programs GTEx, LINCS, Metabolomics, GlyGen, ExRNA. created repurposed tackle similar different inputs. available from: https://playbook-workflow-builder.cloud/ .

Language: Английский

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The Data Use Ontology to streamline responsible access to human biomedical datasets

Cell Genomics, Journal Year: 2021, Volume and Issue: 1(2), P. 100028 - 100028

Published: Nov. 1, 2021

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they processed made available comply with ethical regulatory frameworks informed consent data conditions. To enable streamline access these datasets, the Global Alliance Genomics Health (GA4GH) Data Use Researcher Identities (DURI) work stream developed approved Ontology (DUO) standard. DUO is a hierarchical vocabulary machine-readable use terms consistently unambiguously represents dataset's allowable uses. has been implemented by major international stakeholders such as Broad Sanger Institutes currently used in annotation over 200,000 worldwide. Using management facilitates researchers' discovery relevant datasets. annotations increase FAIRness support linkages using common profiles integrating secondary analyses. Web Language (OWL) and, community awareness engagement, hosted an open, centralized GitHub repository. DUO, together GA4GH Passport standard, offers new, efficient, streamlined authorization framework enabled increased sharing

Language: Английский

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