ArticleDevelopment (Cambridge, England)2015
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish.
Article in Development (Cambridge, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatiotemporal coordination of Slit-Robo repulsion and neurturin-Gfrα attraction guides multipolar migration during retinal lamination.Cell reports · 2026Article
- Article
- A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish.PLoS genetics · 2025Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.bioRxiv : the preprint server for biology · 2025Article
- Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish.Communications biology · 2025Review
- Article
- FishSNP: a high quality cross-species SNP database of fishes.Scientific data · 2024Article
- Importin 13-dependent axon diameter growth regulates conduction speeds along myelinated CNS axons.Nature communications · 2024Article
- Generation and application of endogenously floxed alleles for cell-specific knockout in zebrafish.Developmental cell · 2023Article
- Morphological and sensorimotor phenotypes in a zebrafish CHARGE syndrome model are domain-dependent.Genes, brain, and behavior · 2023Article
- Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes.Scientific reports · 2023Article
- A Critical Review of Zebrafish Neurological Disease Models-2. Application: Functional and Neuroanatomical Phenotyping Strategies and Chemical Screens.Oxford open neuroscience · 2023Article
- Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish.Nature communications · 2022Article
- Voltage-gated sodium channelProceedings of the National Academy of Sciences of the United States of America · 2022Article
- longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth.Development (Cambridge, England) · 2021Article
- Environmental and Molecular Modulation of Motor Individuality in Larval Zebrafish.Frontiers in behavioral neuroscience · 2021Article
- A fish is not a mouse: understanding differences in background genetics is critical for reproducibility.Lab animal · 2021Review
- Article
- Neuronal activity disrupts myelinated axon integrity in the absence of NKCC1b.The Journal of cell biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Single nucleotide polymorphisms (SNPs) are the benchmark molecular markers for modern genomics. Until recently, relatively few SNPs were known in the zebrafish genome. The use of next-generation sequencing for the positional cloning of zebrafish mutations has increased the number of known SNP positions dramatically. Still, the identified SNP variants remain under-utilized, owing to scant annotation of strain specificity and allele frequency. To address these limitations, we surveyed SNP variation in three common laboratory zebrafish strains using whole-genome sequencing. This survey identified an average of 5.04 million SNPs per strain compared with the Zv9 reference genome sequence. By comparing the three strains, 2.7 million variants were found to be strain specific, whereas the remaining variants were shared among all (2.3 million) or some of the strains. We also demonstrate the broad usefulness of our identified variants by validating most in independent populations of the same laboratory strains. We have made all of the identified SNPs accessible through 'SNPfisher', a searchable online database (snpfisher.nichd.nih.gov). The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser. The SNPfisher tools will facilitate the use of SNP variation in zebrafish research as well as vertebrate genome evolution.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.