2010-Magee_et_al - Technical note High fidelity of...

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International Sheep Genomics Consortium and D. E. MacHugh D. A. Magee, S. D. E. Park, E. Scraggs, A. M. Murphy, M. L. Doherty, J. W. Kijas, array-based genotyping platform deoxyribonucleic acid using a high-density single nucleotide polymorphism ) Ovis aries Technical note: High fidelity of whole-genome amplified sheep ( doi: 10.2527/jas.2009-2723 originally published online June 18, 2010 2010, 88:3183-3186. J ANIM SCI http://jas.fass.org/content/88/10/3183 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by guest on October 10, 2011 jas.fass.org Downloaded from
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ABSTRACT: Advances in high-throughput geno- typing technologies have afforded researchers the op- portunity to study ever-increasing numbers of SNP in animal genomes. However, many studies encounter difficulties in obtaining sufficient quantities of high- quality DNA for such analyses, particularly when the source biological material is limited or degraded. The recent development of in vitro whole-genome amplifica- tion approaches has permitted researchers to circum- vent these challenges by increasing the amount of us- able DNA in normally small-quantity samples. Here, we assess the performance of whole-genome amplification products generated from ovine genomic DNA using a high-throughput SNP genotyping platform, the newly developed Illumina ovineSNP50 BeadChip. Our results demonstrate a high genotype call rate for conventional genomic DNA and whole-genome amplified genomic DNA. The data also reveal an exceptionally high con- cordance rate (≥99%) between the genotypes generated from whole-genome amplified products and their con- ventional genomic DNA counterparts. This study sup- ports the use of whole-genome amplification as a viable solution for the analysis of high-density SNP genotypic data using compromised or limited starting material. Key words: BeadChip array, genotyping, Ovis aries , sheep, single nucleotide polymorphism, whole-genome amplified DNA ©2010 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2010. 88:3183–3186 doi:10.2527/jas.2009-2723 INTRODUCTION Single nucleotide polymorphisms are the most com- mon form of DNA sequence variation in mammalian ge- nomes (Kruglyak and Nickerson, 2001). The abundance and pan-genomic distribution of SNP have resulted in their adoption as the marker of choice for mammalian genome-wide association studies. These surveys have been enabled by the availability of high-throughput genotyping platforms, such as genotyping arrays (God- dard and Hayes, 2009). Although genotyping arrays have greatly reduced the amount of DNA required for large-scale genotyping, insufficient quantities of genetic material can hamper investigations, especially when the source biological material is limited or of poor quality or both (e.g., forensic, ancient, and archival samples). To facilitate the analysis of compromised samples, whole- genome amplification (
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This note was uploaded on 01/26/2012 for the course ECON 2272 taught by Professor Gay during the Spring '08 term at Birmingham-Southern College.

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2010-Magee_et_al - Technical note High fidelity of...

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