Aneuvis: Web-based exploration of numerical chromosomal variation in single cells

Daniel G. Piqué, Grasiella A. Andriani, Elaine Maggi, Samuel E. Zimmerman, John M. Greally, Cristina Montagna, Jessica C. Mar

Research output: Contribution to journalArticle

Abstract

Background: Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. However, the ability to quantify and visualize differences in chromosome number between experimentally-defined groups (e.g. control vs treated) obtained from single-cell experiments is currently limited by the lack of user-friendly software. Results: Aneuvis is a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed single cell whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. Conclusions: Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation. Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis.

Original languageEnglish (US)
Article number336
JournalBMC Bioinformatics
Volume20
Issue number1
DOIs
StatePublished - Jun 17 2019

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Web-based
Web Application
Cell
Chromosomes
Chromosome
Carcinogenesis
Numerics
Cytogenetics
Sequencing
User Interface
User interfaces
Genome
Quantify
Software
Visualization
Genes
Cells
Research Personnel
Statistics
Perturbation

Keywords

  • Aneuploidy
  • Automated hypothesis testing
  • Fluorescence in situ hybridization
  • Multi-experiment comparison
  • Numerical chromosomal variation
  • Single-cell genomics
  • Visualization

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Aneuvis : Web-based exploration of numerical chromosomal variation in single cells. / Piqué, Daniel G.; Andriani, Grasiella A.; Maggi, Elaine; Zimmerman, Samuel E.; Greally, John M.; Montagna, Cristina; Mar, Jessica C.

In: BMC Bioinformatics, Vol. 20, No. 1, 336, 17.06.2019.

Research output: Contribution to journalArticle

Piqué, Daniel G. ; Andriani, Grasiella A. ; Maggi, Elaine ; Zimmerman, Samuel E. ; Greally, John M. ; Montagna, Cristina ; Mar, Jessica C. / Aneuvis : Web-based exploration of numerical chromosomal variation in single cells. In: BMC Bioinformatics. 2019 ; Vol. 20, No. 1.
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