Journal of Heredity Advance Access first published online on June 30, 2007
This version published online on August 9, 2007
Journal of Heredity, doi:10.1093/jhered/esm044
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Large-Scale SNP Genotyping with Canine Buccal Swab DNA
From the Department of Psychiatry and Institute for Human Genetics, Langley Porter Psychiatric Institute, University of California San Francisco, Box 0984-NGL, San Francisco, CA 94143-0984 (Chang, Terrill, Bautista, and Hamilton); the Genomics Core Facility, University of California San Francisco, San Francisco, CA 94143-0984 (Carlson); and the Center for Neurobiology and Behavior, Psychiatry Department, University of Pennsylvania, Philadelphia, PA 19104-3403 (Dyer and Overall)
Address correspondence to S. P. Hamilton, MD, PhD, at the address above, or e-mail: steveh{at}lppi.ucsf.edu.
The dog is an attractive model for genetic studies of complex disease. With drafts of the canine genome complete, a large number of single-nucleotide polymorphisms (SNPs) that are potentially useful for gene-mapping studies and empirical estimations of canine diversity and linkage disequilibrium (LD) are now available. Unfortunately, most canine SNPs remain uncharacterized, and the amount and quality of DNA available from population-based samples are limited. We assessed how these real-world challenges influence automated SNP genotyping methods such as Illumina's GoldenGate assay. We examined 384 SNPs on canine chromosome 9 and successfully genotyped a minimum of 217 and a maximum of 275 SNPs using buccal swab samples for 181 dogs (86 beagles, 76 border collies, and 15 Australian shepherds). Call rates per SNP and sample averaged 97%, with reproducibility within and between analyses averaging 98%. The majority of these SNPs were polymorphic across all 3 breeds. We observed extensive LD, albeit less than reported for surveys using fewer dogs, consistent between breeds. Analyses of population substructure indicated that beagles are distinct from border collies and Australian shepherds. These results demonstrate the suitability of amplified canine buccal samples for high-throughput multiplex genotyping and confirm extensive LD in the dog.
This work was presented in poster form at the Third International Conference on Advances in Canine and Feline Genomics and Inherited Diseases, Davis, CA, August 2006.
Corresponding Editor: Elaine Ostrander