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Cited by 80Genomics and Rare DiseasesCRISPR and Genetic EngineeringGenetic Associations and Epidemiology

MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays

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Rubin, Alan F., Stone, Jeremy, Bianchi, Aisha Haley, Capodanno, Benjamin J., Da, Estelle Y., Dias, Mafalda, Esposito, Daniel, Frazer, Jonathan +20 more·2025·Genome Biology
DOI 10.1186/s13059-025-03476-yPMC PMC11753097
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Abstract

Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB (https://www.mavedb.org/) with four key improvements to the MAVE community’s database of record: more available data including over 7 million variant effect measurements, an improved data model supporting assays such as saturation genome editing, new built-in exploration and visualization tools, and powerful APIs for data federation and streamlined submission and access. Together these changes support MaveDB’s role as a hub for the analysis and dissemination of MAVEs now and into the future.

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  • MaveDB follows strict data and documentation standards, mandating HGVS nomenclature for variant representation, embodying FAIR principles for data sharing, and complying with GA4GH frameworks.

    “This follows strict data and documentation standards, mandating HGVS nomenclature for variant representation and embodying FAIR (findable, accessible, interoperable, and reusable) principles for data sharing, and compliance with GA4GH (Global Alliance for Genomics and Health) frameworks.”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [41]

    The Background (page unavailable) says MaveDB emphasizes HGVS compliance and is improving compatibility with the GA4GH Variant Representation Specification; Construction and content (page unavailable) describes validation using MAVE-HGVS. The paper supports standardized, discoverable data sharing, but does not establish a mandate to use HGVS nomenclature, explicit adoption of FAIR principles, or compliance with GA4GH frameworks. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • MaveDB includes application programming interfaces and visualisation tools that simplify data analysis, making it a valuable resource for the genomics community.

    “The inclusion of application programming interfaces and visualisation tools further simplifies data analysis, making MaveDB a valuable resource for the genomics community (41).”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [41]

  • The creation of the publicly accessible MaveDB database is a key step taken by the community towards meeting needs for cross-study standardisation and a data repository.

    “A key step taken by the community towards meeting the needs for cross-study standardisation and a data repository has been the creation of the publicly accessible MaveDB database (41).”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [41]

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Authors
Rubin, A. F., Stone, J., Bianchi, A. H., Capodanno, B. J., Da, E. Y., Dias, M., Esposito, D., Frazer, J., Fu, Y., Grindstaff, S. B., Harrington, M. R., Li, I., McEwen, A. E., Min, J. K., Moore, N., Moscatelli, O. G., Ong, J., Polunina, P. V., Rollins, J. E., Rollins, N. J., Snyder, A. E., Tam, A., Wakefield, M. J., Ye, S. S., Starita, L. M., Bryant, V. L., Marks, D. S., & Fowler, D. M.
Affiliations
  • The University of Melbourne (AU)
  • Brotman Baty Institute (US)
  • University of Washington (US)
  • Walter and Eliza Hall Institute of Medical Research (AU)
  • Universitat Pompeu Fabra (ES)
  • University of Freiburg (DE)
  • The Graduate Center, CUNY (US)
  • Harvard University (US)
  • The Royal Melbourne Hospital (AU)
  • Broad Institute (US)
Corresponding author
  • Rubin, Alan F.
  • Marks, Debora S.
  • Fowler, Douglas M.
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2025-01-21
Volume
26
Issue
1
Pages
13-13
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-025-03476-y
PMC
PMC11753097
OpenAlex
W4406674953
Cited by
80
References
4
Citations by year
2026: 50 · 2025: 30
FWCI
41.58
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by-nc-sa)
  • PubMed Central (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
Funders
  • Alex's Lemonade Stand Foundation for Childhood Cancer
  • Ministerio de Ciencia e Innovación (PID2022-140793NA-I00, PID2022)
  • National Institutes of Health
  • National Human Genome Research Institute (RM1HG010461, UM1HG011969, R01HG013025)
  • National Institute of General Medical Sciences (T32GM007454)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (DP2HD088158)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
MaveDB, MAVE, genetic variants, variant effect prediction, saturation genome editing, functional assays, data federation, data model
MeSH terms
Humans, Software, Genetic Variation, Databases, Genetic, Data Curation

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