Yanran Ma1, Botao Fa2, Xin Yuan1, Yue Zhang1, Zhangsheng Yu1. 1. Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. 2. Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China.
Abstract
Background: The identification of the causal SNPs of complex diseases in large-scale genome-wide association analysis is beneficial to the studies of pathogenesis, prevention, diagnosis and treatment of these diseases. However, existing applicable methods for large-scale data suffer from low accuracy. Developing powerful and accurate methods for detecting SNPs associated with complex diseases is highly desired. Results: We propose a score-based two-stage Bayesian network method to identify causal SNPs of complex diseases for case-control designs. This method combines the ideas of constraint-based methods and score-and-search methods to learn the structure of the disease-centered local Bayesian network. Simulation experiments are conducted to compare this new algorithm with several common methods that can achieve the same function. The results show that our method improves the accuracy and stability compared to several common methods. Our method based on Bayesian network theory results in lower false-positive rates when all correct loci are detected. Besides, real-world data application suggests that our algorithm has good performance when handling genome-wide association data. Conclusion: The proposed method is designed to identify the SNPs related to complex diseases, and is more accurate than other methods which can also be adapted to large-scale genome-wide analysis studies data.
Background: The identification of the causal SNPs of complex diseases in large-scale genome-wide association analysis is beneficial to the studies of pathogenesis, prevention, diagnosis and treatment of these diseases. However, existing applicable methods for large-scale data suffer from low accuracy. Developing powerful and accurate methods for detecting SNPs associated with complex diseases is highly desired. Results: We propose a score-based two-stage Bayesian network method to identify causal SNPs of complex diseases for case-control designs. This method combines the ideas of constraint-based methods and score-and-search methods to learn the structure of the disease-centered local Bayesian network. Simulation experiments are conducted to compare this new algorithm with several common methods that can achieve the same function. The results show that our method improves the accuracy and stability compared to several common methods. Our method based on Bayesian network theory results in lower false-positive rates when all correct loci are detected. Besides, real-world data application suggests that our algorithm has good performance when handling genome-wide association data. Conclusion: The proposed method is designed to identify the SNPs related to complex diseases, and is more accurate than other methods which can also be adapted to large-scale genome-wide analysis studies data.
Authors: Xiang Wan; Can Yang; Qiang Yang; Hong Xue; Xiaodan Fan; Nelson L S Tang; Weichuan Yu Journal: Am J Hum Genet Date: 2010-09-10 Impact factor: 11.025
Authors: René S Kahn; Iris E Sommer; Robin M Murray; Andreas Meyer-Lindenberg; Daniel R Weinberger; Tyrone D Cannon; Michael O'Donovan; Christoph U Correll; John M Kane; Jim van Os; Thomas R Insel Journal: Nat Rev Dis Primers Date: 2015-11-12 Impact factor: 52.329