High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data

Butty, Adrien M.; Chud, Tatiane C. S.; Miglior, Filippo; Schenkel, Flavio S.; Kommadath, Arun; Krivushin, Kirill; Grant, Jason R.; Häfliger, Irene M.; Drögemüller, Cord; Cánovas, Angela; Stothard, Paul; Baes, Christine F. (2020). High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Scientific reports, 10(1), p. 8044. Springer Nature 10.1038/s41598-020-64680-3

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Häfliger, Irene Monika; Drögemüller, Cord and Baes, Christine Francoise

Subjects:

500 Science > 590 Animals (Zoology)
600 Technology > 610 Medicine & health
600 Technology > 630 Agriculture

ISSN:

2045-2322

Publisher:

Springer Nature

Language:

English

Submitter:

Cord Drögemüller

Date Deposited:

19 May 2020 10:59

Last Modified:

24 May 2020 02:43

Publisher DOI:

10.1038/s41598-020-64680-3

PubMed ID:

32415111

BORIS DOI:

10.7892/boris.144138

URI:

https://boris.unibe.ch/id/eprint/144138

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