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dc.contributor.authorBickhart, D.M.en_US
dc.contributor.authorHou, Y.en_US
dc.contributor.authorSchroeder, S.G.en_US
dc.contributor.authorAlkan C.en_US
dc.contributor.authorCardone, M.F.en_US
dc.contributor.authorMatukumalli L.K.en_US
dc.contributor.authorSong J.en_US
dc.contributor.authorSchnabel, R.D.en_US
dc.contributor.authorVentura M.en_US
dc.contributor.authorTaylor J.F.en_US
dc.contributor.authorGarcia J.F.en_US
dc.contributor.authorVan Tassell, C.P.en_US
dc.contributor.authorSonstegard, T.S.en_US
dc.contributor.authorEichler, E. E.en_US
dc.contributor.authorLiu G.E.en_US
dc.date.accessioned2016-02-08T09:47:25Z
dc.date.available2016-02-08T09:47:25Z
dc.date.issued2012en_US
dc.identifier.issn10889051
dc.identifier.urihttp://hdl.handle.net/11693/21516
dc.description.abstractCopy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome - wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ 2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. © 2012 by Cold Spring Harbor Laboratory Press.en_US
dc.language.isoEnglishen_US
dc.source.titleGenome Researchen_US
dc.relation.isversionofhttp://dx.doi.org/10.1101/gr.133967.111en_US
dc.subjectapolipoproteinen_US
dc.subjectfatty acid binding protein 2en_US
dc.subjecttaurineen_US
dc.subjectadaptationen_US
dc.subjectarticleen_US
dc.subjectbeef cattleen_US
dc.subjectbreedingen_US
dc.subjectcattleen_US
dc.subjectchromosome mapen_US
dc.subjectcomparative genomic hybridizationen_US
dc.subjectcopy number variationen_US
dc.subjectfluorescence in situ hybridizationen_US
dc.subjectgene duplicationen_US
dc.subjectgene sequenceen_US
dc.subjectgenome analysisen_US
dc.subjectlipid metabolismen_US
dc.subjectlipid transporten_US
dc.subjectmolecular geneticsen_US
dc.subjectnonhumanen_US
dc.subjectnucleotide sequenceen_US
dc.subjectpedigree analysisen_US
dc.subjectpolymerase chain reactionen_US
dc.subjectpriority journalen_US
dc.subjectpromoter regionen_US
dc.subjectquantitative analysisen_US
dc.subjectquantitative trait locusen_US
dc.subjectsequence analysisen_US
dc.subjectAnimalsen_US
dc.subjectCattleen_US
dc.subjectChromosome Mappingen_US
dc.subjectChromosomes, Mammalianen_US
dc.subjectComparative Genomic Hybridizationen_US
dc.subjectDNA Copy Number Variationsen_US
dc.subjectFatty Acid-Binding Proteinsen_US
dc.subjectFemaleen_US
dc.subjectGene Dosageen_US
dc.subjectGene Duplicationen_US
dc.subjectGenomeen_US
dc.subjectGenomicsen_US
dc.subjectIn Situ Hybridization, Fluorescenceen_US
dc.subjectMaleen_US
dc.subjectPolymerase Chain Reactionen_US
dc.subjectSequence Analysis, DNAen_US
dc.subjectSpecies Specificityen_US
dc.subjectBosen_US
dc.titleCopy number variation of individual cattle genomes using next-generation sequencingen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineering
dc.citation.spage778en_US
dc.citation.epage790en_US
dc.citation.volumeNumber22en_US
dc.citation.issueNumber4en_US
dc.identifier.doi10.1101/gr.133967.111en_US


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