Title: Comparative studies on multivariate tests for joint-SNVs analysis and detection for bipolar disorder susceptibility genes
Authors: Jin-Xiong Lv; Han-Chen Huang; Run-Sheng Chen; Lei Xu
Addresses: Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China ' Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ' Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ' Centre for Cognitive Machines and Computational Health, The School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
Abstract: Instead of the single nucleotide variants (SNVs) analysis, many joint-SNVs analysis methods were proposed to tackle the 'missing heritability problem' in the genome-wide association studies (GWASs). In this paper, we performed a comparative study on five typical methods for joint-SNVs analysis and a recently proposed method called Statistics-space Boundary-based test (S-space BBT). For a fair and comprehensive comparison, we conducted simulation experiments by considering dominant single variant, effect direction, minor allele frequency (MAF), odds ratio (OR) and the linkage disequilibrium (LD). The results indicated that the S-space BBT not only does not swamp the significant SNV but also maintains stronger detection power under different configurations. As a result, we applied the S-space BBT to the dataset of bipolar disorder and obtained a list of biomarkers. Besides, the literature researches were conducted to validate the reliability of the results.
Keywords: GWAS; sequence analysis; joint-SNVs analysis; odds ratio; dominant single variant; effect direction; minor allele frequency; the linkage disequilibrium; S-space boundary-based test; bipolar disorder.
International Journal of Data Mining and Bioinformatics, 2017 Vol.17 No.4, pp.341 - 358
Available online: 05 Aug 2017 *Full-text access for editors Access for subscribers Purchase this article Comment on this article