title: Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.
abstract: We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.|College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP-Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.
authors.forename: Yuri T
authors.initials: YT
authors.lastname: Utsunomiya
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.|Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: El Hamidi Abdel
authors.initials: el HA
authors.lastname: Hay
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP-Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil.|Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil.
authors.forename: Jose Fernando
authors.initials: JF
authors.lastname: Garcia
authors.affiliation: Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D003951:Diagnostic Errors; D005260:Female; D008297:Male