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

Alan F Rubin; Jeremy Stone; Aisha Haley Bianchi; Benjamin J Capodanno; Estelle Y Da; Mafalda Dias; Daniel Esposito; Jonathan Frazer; Yunfan Fu; Sally B Grindstaff; Matthew R Harrington; Iris Li; Abbye E McEwen; Joseph K Min; Nick Moore; Olivia G Moscatelli; Jesslyn Ong; Polina V Polunina; Joshua E Rollins; Nathan J Rollins; Ashley E Snyder; Amy Tam; Matthew J Wakefield; Shenyi Sunny Ye; Lea M Starita; Vanessa L Bryant; Debora S Marks; Douglas M Fowler

doi:10.1186/s13059-025-03476-y

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

Genome Biol. 2025 Jan 21;26(1):13. doi: 10.1186/s13059-025-03476-y.

Authors

Alan F Rubin^{1

2}, Jeremy Stone³, Aisha Haley Bianchi⁴, Benjamin J Capodanno³, Estelle Y Da⁵, Mafalda Dias^{6

7}, Daniel Esposito⁵, Jonathan Frazer^{6

7}, Yunfan Fu^{5

8}, Sally B Grindstaff³, Matthew R Harrington⁴, Iris Li⁵, Abbye E McEwen^{3

4

9}, Joseph K Min⁴, Nick Moore⁵, Olivia G Moscatelli^{8

10}, Jesslyn Ong^{10

11}, Polina V Polunina¹², Joshua E Rollins¹³, Nathan J Rollins¹⁴, Ashley E Snyder³, Amy Tam¹⁵, Matthew J Wakefield^{5

8

16}, Shenyi Sunny Ye⁴, Lea M Starita^{3

4}, Vanessa L Bryant^{8

10

17}, Debora S Marks^{18

19}, Douglas M Fowler^{20

21

22}

Affiliations

¹ Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. alan.rubin@wehi.edu.au.
² Department of Medical Biology, University of Melbourne, Parkville, Australia. alan.rubin@wehi.edu.au.
³ Brotman Baty Institute for Precision Medicine, Seattle, USA.
⁴ Department of Genome Sciences, University of Washington, Seattle, USA.
⁵ Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
⁶ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
⁷ University Pompeu Fabra, Barcelona, Spain.
⁸ Department of Medical Biology, University of Melbourne, Parkville, Australia.
⁹ Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA.
¹⁰ Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
¹¹ Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia.
¹² Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.
¹³ Department of Computer Science, The Graduate Center, The City University of New York, New York, USA.
¹⁴ Seismic Therapeutics, Watertown, USA.
¹⁵ Department of Systems Biology, Harvard Medical School, Boston, USA.
¹⁶ Department of Obstetrics, Gynaecology and Newborn Health, University of Melbourne, Parkville, Australia.
¹⁷ Department of Clinical Immunology & Allergy, The Royal Melbourne Hospital, Parkville, Australia.
¹⁸ Department of Systems Biology, Harvard Medical School, Boston, USA. debbie@hms.harvard.edu.
¹⁹ Broad Institute of Harvard and MIT, Boston, USA. debbie@hms.harvard.edu.
²⁰ Brotman Baty Institute for Precision Medicine, Seattle, USA. dfowler@uw.edu.
²¹ Department of Genome Sciences, University of Washington, Seattle, USA. dfowler@uw.edu.
²² Department of Bioengineering, University of Washington, Seattle, USA. dfowler@uw.edu.

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.

Keywords: DMS; Deep mutational scanning; Functional genomics; MAVEs; Multiplexed assays of variant effect; Variant classification.

MeSH terms

Data Curation
Databases, Genetic*
Genetic Variation*
Humans
Software

Abstract

MeSH terms

Grants and funding