中国恒河猴（猕猴）高通量单核苷酸多态性发现及长期非进展性感染猴免疫缺陷病毒（SIVmac）候选基因的寻找
High-throughput single-nucleotide polymorphism discovery and the search for candidate genes for long-term SIVmac nonprogression in Chinese rhesus macaques (Macaca mulatta).
作者信息
Trask J Satkoski, Garnica W T, Malhi R S, Kanthaswamy S, Smith D G
机构信息
Department of Anthropology, University of California, Davis, 95616, USA.
出版信息
J Med Primatol. 2011 Aug;40(4):224-32. doi: 10.1111/j.1600-0684.2011.00486.x.
BACKGROUND
Genetic differences between Indian and Chinese rhesus macaques contribute to the phenotypic variance of clinical trials, including infection with SIVmac. The completion of the rhesus genome has facilitated the discovery of several thousand markers.
METHODS
We developed a genome-wide SNP map for rhesus macaques containing 3869 validated markers with an average distance of 0.88 Mb and used the program VarLD to identify genomic areas with significant differences in linkage disequilibrium (LD) between Indian-derived and Chinese rhesus macaques.
RESULTS
Forty-one statistically significant differences in LD between Chinese and Indian-origin rhesus were detected on chromosomes 1, 4, 5 and 11. The region of greatest LD difference was located on the proximal end of chromosome one, which also contained the genes ELAVL4, MAST2 and HIVEP3.
CONCLUSION
These genomic areas provide entry to more detailed studies of gene function. This method is also applicable to the study of differences in biomarkers between regional populations of other species.
背景
印度恒河猴和中国恒河猴之间的基因差异导致了包括感染猴免疫缺陷病毒（SIVmac）在内的临床试验的表型差异。恒河猴基因组的完成促进了数千个标记的发现。
方法
我们为恒河猴开发了一个全基因组单核苷酸多态性（SNP）图谱，其中包含3869个经过验证的标记，平均间距为0.88兆碱基对（Mb），并使用VarLD程序来识别印度来源和中国恒河猴之间连锁不平衡（LD）存在显著差异的基因组区域。
结果
在1号、4号、5号和11号染色体上检测到中国和印度起源的恒河猴之间在LD方面有41个具有统计学意义的差异。LD差异最大的区域位于1号染色体的近端，该区域还包含ELAVL4、MAST2和HIVEP3基因。
结论
这些基因组区域为更详细的基因功能研究提供了切入点。该方法也适用于研究其他物种区域群体之间生物标志物的差异。
Zotero 插件