PUBLICATION
An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains
- Authors
- Holden, L.A., Wilson, C., Heineman, Z., Dobrinski, K.P., Brown, K.H.
- ID
- ZDB-PUB-181114-17
- Date
- 2018
- Source
- Zebrafish 16(1): 29-36 (Journal)
- Registered Authors
- Dobrinski, Kim P.
- Keywords
- array CGH, reciprocal comparison, strain variation
- MeSH Terms
-
- Animals
- DNA Copy Number Variations*
- Fish Proteins/genetics*
- Genome*
- Species Specificity
- Zebrafish/genetics*
- PubMed
- 30418105 Full text @ Zebrafish
Citation
Holden, L.A., Wilson, C., Heineman, Z., Dobrinski, K.P., Brown, K.H. (2018) An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains. Zebrafish. 16(1):29-36.
Abstract
Zebrafish (Danio rerio) are a widely utilized model system for human disorders, but common laboratory strains have distinct behavioral and physiological differences. Accompanying these known strain differences, commonly used "wildtype" zebrafish strains have both shared and unique suites of single nucleotide polymorphisms and copy number variants (CNVs). Despite this, genomic variation is often ignored in study design, and the actual strain used is often not adequately reported. The goal of this study was to assess CNVs across three common laboratory strains of zebrafish-AB, Tubingen (TU), and WIK-and provide these data as a tool for the zebrafish community. Herein we identified 1351 CNV regions within the most recent genome assembly (GRCz11) covering 1.9% of the zebrafish genome (31.7 Mb). CNVs were found across all chromosomes, and 2200 genes (5121 transcripts) lie within ±5 kb of identified CNVs, pointing to likely cis regulatory actions of CNVs on nearby gene neighbors. We have created a Public Session accessible on the UCSC Genome Browser to view CNVs from this study titled "danRer11 zebrafish CNV across strains" as a tool for the zebrafish community.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping