Discovering CNVs in the 1000g project with SurVIndel2
Ontology highlight
ABSTRACT:
INSTRUMENT(S): -
ORGANISM(S): Homo Sapiens
SUBMITTER: Hong Kong Genome Institute
PROVIDER: PRJEB71638 | EVA | 2024-01-05
REPOSITORIES: EVA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 1000g-CNV.no_HLA_EBV_decoy.vcf.csi | Other | |||
| 1000g-CNV.no_HLA_EBV_decoy.vcf.gz | Vcf | |||
| 1000g-CNV.no_HLA_EBV_decoy.vcf.gz.csi | Vcf |
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Project description:Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.
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Project description:Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.? 19 zebrafish from 3 laboratory strains and one native population were analyzed using a strain specific reference for each group
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