title: Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping.
abstract: BACKGROUND
  Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes.
  
  
  RESULTS
  We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays.
  
  
  CONCLUSIONS
  Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants.
authors.affiliation: Group of Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.
authors.forename: Bujie
authors.initials: B
authors.lastname: Zhan
authors.forename: João
authors.initials: J
authors.lastname: Fadista
authors.forename: Bo
authors.initials: B
authors.lastname: Thomsen
authors.forename: Jakob
authors.initials: J
authors.lastname: Hedegaard
authors.forename: Frank
authors.initials: F
authors.lastname: Panitz
authors.forename: Christian
authors.initials: C
authors.lastname: Bendixen
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D014644:Genetic Variation; D016678:Genome; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation; D008297:Male; D020641:Polymorphism, Single Nucleotide
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