SNPkit: An efficient approach to systematic evaluation of candidate single nucleotide polymorphisms in public databases

被引:18
作者
Hao, K
Niu, T
Sangokoya, C
Li, J
Xu, X
机构
[1] Harvard Univ, Sch Publ Hlth, Program Populat Genet, Boston, MA 02115 USA
[2] Stanford Univ, Stanford, CA 94305 USA
[3] Beijing Med Univ, Beijing 100083, Peoples R China
[4] Harvard Univ, Brigham & Womens Hosp, Sch Med, Boston, MA 02115 USA
关键词
D O I
10.2144/02334st06
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
There is widespread interest in devising genotyping method for SNPs that are ro- bust, inexpensive, and simple to perform. Although several high-throughput SNP genotyping technologies have been developed, including the oligonucleotide ligation assay, real-time PCR, and mass spectrometry, the issues of simplicity and cost-effectiveness have not been adequately addressed. Here we describe the application of a novel computer software package, SNPkit, which designs SNP genotyping assays based on a classical approach for discriminating alleles, restriction enzyme digestion. SNPkit can be used in genotyping assays for almost any SNPs including those that do not alter "natural" restriction sites. Using this, method, 164 SNPs have been evaluated in DNA samples from 48 immortalized cell lines of randomly selected Chinese subjects. Sixty-two (37.8%) of the SNPs appeared to be common (frequencies of the minor alleles are greater than or equal to 5%) and were subsequently applied to a larger population-based sample. Overall, by using SNPkit, we have been able to validate and genotype accurately a large fraction of publicly available SNPs without sophisticated instrumentation.
引用
收藏
页码:822 / +
页数:6
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