title: Identification of copy number variations and common deletion polymorphisms in cattle.
abstract: BACKGROUND
  Recently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain CNV region has been found to be associated with the onset of diseases. Therefore, CNV is now known as an important genomic variation in biological mechanisms. However, most CNV studies have only involved the human genome. The study of CNV involving other animals, including cattle, is severely lacking.
  
  
  RESULTS
  In our study of cattle, we used Illumina BovineSNP50 BeadChip (54,001 markers) to obtain each marker's signal intensity (Log R ratio) and allelic intensity (B allele frequency), which led to our discovery of 855 bovine CNVs from 265 cows. For these animals, the average number of CNVs was 3.2, average size was 149.8 kb, and median size was 171.5 kb. Taking into consideration some overlapping regions among the identified bovine CNVs, 368 unique CNV regions were detected. Among them, there were 76 common CNVRs with > 1% CNV frequency. Together, these CNVRs contained 538 genes. Heritability errors of 156 bovine pedigrees and comparative pairwise analyses were analyzed to detect 448 common deletion polymorphisms. Identified variations in this study were successfully validated using visual examination of the genoplot image, Mendelian inconsistency, another CNV identification program, and quantitative PCR.
  
  
  CONCLUSIONS
  In this study, we describe a map of bovine CNVs and provide important resources for future bovine genome research. This result will contribute to animal breeding and protection from diseases with the aid of genomic information.
authors.affiliation: Laboratory of Genomic Diversity, Department of Life Science, Sogang University, Shinsu-dong, Mapo-gu, Seoul, Republic of Korea.
authors.forename: Joon Seol
authors.initials: JS
authors.lastname: Bae
authors.forename: Hyun Sub
authors.initials: HS
authors.lastname: Cheong
authors.forename: Lyoung Hyo
authors.initials: LH
authors.lastname: Kim
authors.forename: Suk
authors.initials: S
authors.lastname: NamGung
authors.forename: Tae Joon
authors.initials: TJ
authors.lastname: Park
authors.forename: Ji-Yong
authors.initials: JY
authors.lastname: Chun
authors.forename: Jason Yongha
authors.initials: JY
authors.lastname: Kim
authors.forename: Charisse Flerida A
authors.initials: CF
authors.lastname: Pasaje
authors.forename: Jin Sol
authors.initials: JS
authors.lastname: Lee
authors.forename: Hyoung Doo
authors.initials: HD
authors.lastname: Shin
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D056915:DNA Copy Number Variations; D017353:Gene Deletion; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide