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Drogaris C, Zhang Y, Zhang E, Nazarova E, Sarrazin-Gendron R, Wilhelm-Landry S, Cyr Y, Majewski J, Blanchette M, Waldispühl J. ARGV: 3D genome structure exploration using augmented reality. BMC Bioinformatics 2024; 25:277. [PMID: 39192184 DOI: 10.1186/s12859-024-05882-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
Over the past two decades, scientists have increasingly realized the importance of the three-dimensional (3D) genome organization in regulating cellular activity. Hi-C and related experiments yield 2D contact matrices that can be used to infer 3D models of chromosome structure. Visualizing and analyzing genomes in 3D space remains challenging. Here, we present ARGV, an augmented reality 3D Genome Viewer. ARGV contains more than 350 pre-computed and annotated genome structures inferred from Hi-C and imaging data. It offers interactive and collaborative visualization of genomes in 3D space, using standard mobile phones or tablets. A user study comparing ARGV to existing tools demonstrates its benefits.
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Affiliation(s)
| | - Yanlin Zhang
- School of Computer Science, McGill University, Montréal, QC, H3A 0E9, Canada
| | - Eric Zhang
- School of Computer Science, McGill University, Montréal, QC, H3A 0E9, Canada
| | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, QC, H3A 0E9, Canada
| | | | | | - Yan Cyr
- Beam Me Up Inc., 5925 Monkland Ave, Suite, 100, Montréal, H4A 1G7, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1B1, Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, Montréal, QC, H3A 0E9, Canada
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, QC, H3A 0E9, Canada.
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