Single nucleotide polymorphism (SNP)-set analysis in genome-wide association studies (GWASs)has become a hot topic.Most existing SNP-set analystic methods are designed and work well according to the different natures ...Single nucleotide polymorphism (SNP)-set analysis in genome-wide association studies (GWASs)has become a hot topic.Most existing SNP-set analystic methods are designed and work well according to the different natures of common or rare variants and associated diseases.But the information that the disease associated variants are common or rare cannot be gained in advance.Therefore,in this research,we proposed a new and powerful weighted function method without distinguishing common or rare variants to select tagging SNP-set.We applied our selection method to sequence kernel associa- tion test (SKAT)and compared the power with some existing methods.The simulation results showed that our method has higher power not only than SKAT in un-weighted case,but also than SKAT in other weighted functions.Moreover,the power is improved significantly when the minor allele frequency (MAF)of causal SNP is relatively small.展开更多
基金the National Natural Science Foundation of China(61572522&11371230),Science and technology project of Huangdao District,Qingdao City,Shandong Province(2014-1-43),Shandong Provincial Natural Science Foundation(ZR2015AQ001)Research Funds for Joint Innovative Center for Safe and Effective Mining Technology and Equipment of Coal Resources by Shandong Province and SDUST(2014TDJH102).
文摘Single nucleotide polymorphism (SNP)-set analysis in genome-wide association studies (GWASs)has become a hot topic.Most existing SNP-set analystic methods are designed and work well according to the different natures of common or rare variants and associated diseases.But the information that the disease associated variants are common or rare cannot be gained in advance.Therefore,in this research,we proposed a new and powerful weighted function method without distinguishing common or rare variants to select tagging SNP-set.We applied our selection method to sequence kernel associa- tion test (SKAT)and compared the power with some existing methods.The simulation results showed that our method has higher power not only than SKAT in un-weighted case,but also than SKAT in other weighted functions.Moreover,the power is improved significantly when the minor allele frequency (MAF)of causal SNP is relatively small.
