Chang Melanie Lee, Terrill Rebecca Lee, Bautista Maria M, Carlson Elaine J, Dyer Donna J, Overall Karen L, Hamilton Steven P
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, USA.
J Hered. 2007;98(5):428-37. doi: 10.1093/jhered/esm044. Epub 2007 Jun 30.
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.
狗是复杂疾病基因研究的一个有吸引力的模型。随着犬类基因组草图的完成，现在有大量单核苷酸多态性（SNP）可用于基因图谱研究以及对犬类多样性和连锁不平衡（LD）的实证估计。不幸的是，大多数犬类SNP仍未得到表征，且基于群体样本可获得的DNA数量和质量有限。我们评估了这些现实世界中的挑战如何影响自动化SNP基因分型方法，如Illumina公司的GoldenGate检测法。我们检测了犬类9号染色体上的384个SNP，并使用181只狗（86只比格犬、76只边境牧羊犬和15只澳大利亚牧羊犬）的口腔拭子样本成功对至少217个、最多275个SNP进行了基因分型。每个SNP和样本的检出率平均为97%，分析内部和分析之间的重复性平均为98%。这些SNP中的大多数在所有3个品种中都是多态性的。我们观察到广泛的LD，尽管比使用较少数量狗的调查所报告的要少，且在各品种之间是一致的。群体亚结构分析表明，比格犬与边境牧羊犬和澳大利亚牧羊犬不同。这些结果证明了扩增的犬类口腔样本适用于高通量多重基因分型，并证实了狗中存在广泛的LD。
