SegAnnDB: interactive Web-based genomic segmentation

Toby D Hocking; Valentina Boeva; Guillem Rigaill; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Wilfrid Richer; Franck Bourdeaut; Miyuki Suguro; Masao Seto; Francis Bach; Jean-Philippe Vert

doi:10.1093/bioinformatics/btu072

SegAnnDB: interactive Web-based genomic segmentation

Bioinformatics. 2014 Jun 1;30(11):1539-46. doi: 10.1093/bioinformatics/btu072. Epub 2014 Feb 3.

Affiliations

¹ Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, France.
² Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, FranceDepartment of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, FranceDepartment of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, France.
³ Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, FranceDepartment of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, France.

Abstract

Motivation: DNA copy number profiles characterize regions of chromosome gains, losses and breakpoints in tumor genomes. Although many models have been proposed to detect these alterations, it is not clear which model is appropriate before visual inspection the signal, noise and models for a particular profile.

Results: We propose SegAnnDB, a Web-based computer vision system for genomic segmentation: first, visually inspect the profiles and manually annotate altered regions, then SegAnnDB determines the precise alteration locations using a mathematical model of the data and annotations. SegAnnDB facilitates collaboration between biologists and bioinformaticians, and uses the University of California, Santa Cruz genome browser to visualize copy number alterations alongside known genes.

Availability and implementation: The breakpoints project on INRIA GForge hosts the source code, an Amazon Machine Image can be launched and a demonstration Web site is http://bioviz.rocq.inria.fr.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Chromosome Breakpoints
DNA Copy Number Variations*
Genomics / methods
Internet
Software*

Grants and funding

280032/ERC_/European Research Council/International