Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

BMC Genomics

Research Article

Frank Panitz¹  Christian Bendixen¹  Bujie Zhan¹  João Fadista¹  Bo Thomsen¹  Jakob Hedegaard² 

[1] 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;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;Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, DK-8200, Aarhus N, Denmark;

关键词: Copy Number Variation;    Comparative Genomic Hybridization;    Single Nucleotide Polymorphism Array;    Copy Number Variation Region;    Heterozygous SNPs;   

DOI  :  10.1186/1471-2164-12-557

 received in 2011-06-23, accepted in 2011-11-14,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundIntegration 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.ResultsWe 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Zhan et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.