title: A gene mapping bottleneck in the translational route from zebrafish to human.
abstract: Among a diversity of animal models of disease, the zebrafish is a promising model organism for enabling novel translational biomedical research. To fully achieve the latter, a key requirement is to match molecular readouts measured in zebrafish with information relevant to health and disease in humans. A fundamental step in this direction is to accurately map gene sequences from zebrafish to humans. Despite significant progress in genome annotation, this remains an intricate and time-consuming challenge. Here we discuss major obstacles that we had to overcome to systematically map genes from zebrafish to human. We identified important disparities, as well as partial agreements, between five public zebrafish-to-human homology resources. There is still a need for standardized, comprehensive genomic mappings between zebrafish and humans. Without this, efforts to use zebrafish as a powerful translational research tool will be stalled.
authors: NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (formerly CRP-Santé) , Luxembourg, Luxembourg ; Vrije Universiteit Amsterdam , Amsterdam, Netherlands.
authors: Niek
authors: N
authors: de Klein
authors: Vital-IT Systems Biology Division, Swiss Institute of Bioinformatics (SIB) , Lausanne, Switzerland.
authors: Mark
authors: M
authors: Ibberson
authors: Vital-IT Systems Biology Division, Swiss Institute of Bioinformatics (SIB) , Lausanne, Switzerland.
authors: Isaac
authors: I
authors: Crespo
authors: NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (formerly CRP-Santé) , Luxembourg, Luxembourg.
authors: Sophie
authors: S
authors: Rodius
authors: NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (formerly CRP-Santé) , Luxembourg, Luxembourg.
authors: Francisco
authors: F
authors: Azuaje
keywords: genome annotation; orthology inference; translational research; zebrafish; zebrafish-to-human gene mapping
references: Dis Model Mech. 2010 Sep-Oct;3(9-10):517-23
references: 20354112
references: Stem Cell Res. 2014 Nov;13(3 Pt B):542-55
references: 25127427
references: Nucleic Acids Res. 2001 Jan 1;29(1):11-6
references: 11125038
references: Nucleic Acids Res. 2014 Jan;42(Database issue):D7-17
references: 24259429
references: Database (Oxford). 2011 Nov 13;2011:bar049
references: 22083790
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9
references: 16845079
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Nature. 2013 Apr 25;496(7446):498-503
references: 23594743
references: Science. 2006 Sep 29;313(5795):1929-35
references: 17008526
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90
references: 23193272
references: Nat Rev Cancer. 2013 Sep;13(9):624-36
references: 23969693
references: Nat Rev Cancer. 2007 Jan;7(1):54-60
references: 17186018
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
references: 23193258
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D822-9
references: 21036866
references: Trends Genet. 2013 Nov;29(11):611-20
references: 23927865
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694