MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Daniel Esposito; Jochen Weile; Jay Shendure; Lea M Starita; Anthony T Papenfuss; Frederick P Roth; Douglas M Fowler; Alan F Rubin

doi:10.1186/s13059-019-1845-6

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Genome Biol. 2019 Nov 4;20(1):223. doi: 10.1186/s13059-019-1845-6.

Authors

Daniel Esposito¹, Jochen Weile^{2

3

4

5}, Jay Shendure^{6

7

8}, Lea M Starita^{6

7}, Anthony T Papenfuss^{1

9

10

11

12}, Frederick P Roth^{13

14

15

16

17}, Douglas M Fowler^{18

19

20}, Alan F Rubin^{21

22

23}

Affiliations

¹ Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
² The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
³ Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
⁴ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁵ Department of Computer Science, University of Toronto, Toronto, ON, Canada.
⁶ Department of Genome Sciences, University of Washington, Seattle, WA, USA.
⁷ Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
⁸ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
⁹ Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
¹⁰ Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
¹¹ Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
¹² Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia.
¹³ The Donnelly Centre, University of Toronto, Toronto, ON, Canada. fritz.roth@utoronto.ca.
¹⁴ Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada. fritz.roth@utoronto.ca.
¹⁵ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. fritz.roth@utoronto.ca.
¹⁶ Department of Computer Science, University of Toronto, Toronto, ON, Canada. fritz.roth@utoronto.ca.
¹⁷ Canadian Institute for Advanced Research, Toronto, ON, Canada. fritz.roth@utoronto.ca.
¹⁸ Department of Genome Sciences, University of Washington, Seattle, WA, USA. dfowler@uw.edu.
¹⁹ Canadian Institute for Advanced Research, Toronto, ON, Canada. dfowler@uw.edu.
²⁰ Department of Bioengineering, University of Washington, Seattle, WA, USA. dfowler@uw.edu.
²¹ Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. alan.rubin@wehi.edu.au.
²² Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia. alan.rubin@wehi.edu.au.
²³ Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. alan.rubin@wehi.edu.au.

Abstract

Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.

Keywords: Deep mutational scanning; Genome interpretation; Large-scale mutagenesis; MAVE; Massively parallel reporter assays; Multiplexed assay of variant effect; Personalized medicine.

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

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