Minimum information and guidelines for reporting a multiplexed assay of variant effect

Melina Claussnitzer; Victoria N Parikh; Alex H Wagner; Jeremy A Arbesfeld; Carol J Bult; Helen V Firth; Lara A Muffley; Alex N Nguyen Ba; Kevin Riehle; Frederick P Roth; Daniel Tabet; Benedetta Bolognesi; Andrew M Glazer; Alan F Rubin

doi:10.1186/s13059-024-03223-9

Minimum information and guidelines for reporting a multiplexed assay of variant effect

Genome Biol. 2024 Apr 19;25(1):100. doi: 10.1186/s13059-024-03223-9.

Authors

Melina Claussnitzer^#^{1

2}, Victoria N Parikh^#³, Alex H Wagner^#^{4

5}, Jeremy A Arbesfeld^{4

6}, Carol J Bult⁷, Helen V Firth^{8

9}, Lara A Muffley¹⁰, Alex N Nguyen Ba¹¹, Kevin Riehle¹², Frederick P Roth^{13

14

15

16}, Daniel Tabet^{13

14

15

16}, Benedetta Bolognesi¹⁷, Andrew M Glazer¹⁸, Alan F Rubin^{19

20}

Affiliations

¹ The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
² Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, 02142, USA.
³ Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, 94305, USA.
⁴ The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43215, USA.
⁵ Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
⁶ Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
⁷ The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
⁸ Wellcome Sanger Institute, Hinxton, Cambridge, UK.
⁹ Dept of Medical Genetics, Cambridge University Hospitals NHS Trust, Cambridge, UK.
¹⁰ Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA.
¹¹ Department of Biology, University of Toronto at Mississauga, Mississauga, ON, Canada.
¹² Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
¹³ Donnelly Centre, University of Toronto, Toronto, ON, Canada.
¹⁴ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
¹⁵ Department of Computer Science, University of Toronto, Toronto, ON, Canada.
¹⁶ Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
¹⁷ Institute for Bioengineering of Catalunya (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain. bbolognesi@ibecbarcelona.eu.
¹⁸ Vanderbilt University Medical Center, Nashville, TN, 37232, USA. andrew.m.glazer@vumc.org.
¹⁹ Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. alan.rubin@wehi.edu.au.
²⁰ Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia. alan.rubin@wehi.edu.au.

^# Contributed equally.

Abstract

Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.

Keywords: DMS; Deep mutational scanning; Genetic variants; Genomics; MAVE; Multiplexed assays of variant effect; Standards.

MeSH terms

Metadata*
Reproducibility of Results
Research Design*

Abstract

MeSH terms

Grants and funding