ArticleScientific reports2020
High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Whole genome resequencing reveals the genetic basis of stature in short-statured Indian cattle.Scientific reports · 2026Article
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population.BMC genomics · 2025Article
- Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.BMC genomics · 2025Article
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- Genome-wide association studies for economically important traits in mink using copy number variation.Scientific reports · 2024Article
- Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy.PloS one · 2024Article
- Molecular Cytogenetics in Domestic Bovids: A Review.Animals : an open access journal from MDPI · 2023Review
- In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.Genetics, selection, evolution : GSE · 2023Review
- Article
- Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.Frontiers in veterinary science · 2023Review
- Genome-wide detection of copy number variation in American mink using whole-genome sequencing.BMC genomics · 2022Article
- DNA sequence features underlying large-scale duplications and deletions in human.Journal of applied genetics · 2022Article
- Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.Nature communications · 2022Article
- Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle.Animals : an open access journal from MDPI · 2021Article
- Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple methods to detect copy number variants (CNV) relying on different types of data have been developed and CNV have been shown to have an impact on phenotypes of numerous traits of economic importance in cattle, such as reproduction and immunity. Further improvements in CNV detection are still needed in regard to the trade-off between high-true and low-false positive variant identification rates. Instead of improving single CNV detection methods, variants can be identified in silico with high confidence when multiple methods and datasets are combined. Here, CNV were identified from whole-genome sequences (WGS) and genotype array (GEN) data on 96 Holstein animals. After CNV detection, two sets of high confidence CNV regions (CNVR) were created that contained variants found in both WGS and GEN data following an animal-based (n = 52) and a population-based (n = 36) pipeline. Furthermore, the change in false positive CNV identification rates using different GEN marker densities was evaluated. The population-based approach characterized CNVR, which were more often shared among animals (average 40% more samples per CNVR) and were more often linked to putative functions (48 vs 56% of CNVR) than CNV identified with the animal-based approach. Moreover, false positive identification rates up to 22% were estimated on GEN information. Further research using larger datasets should use a population-wide approach to identify high confidence CNVR.
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