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Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip
Ramayo Caldas, Yuliaxis (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Castelló, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Pena, Romi N
Alves, Estefania
Mercadé, Anna Maria (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Souza, Carla A
Fernández, Ana I
Perez-Enciso, Miguel
Folch, Josep Maria (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)

Date: 2010
Abstract: Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips. We used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species. Our results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; publishedVersion
Published in: BMC genomics, Vol. 11 (10 2010) , p. 593, ISSN 1471-2164

PMID: 20969757
DOI: 10.1186/1471-2164-11-593


10 p, 788.3 KB

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Articles > Research articles
Articles > Published articles

 Record created 2017-12-20, last modified 2019-11-05



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