title: SWGDT: A sliding window-based genotype dependence testing tool for genome-wide susceptibility gene scan.
abstract: Genome-wide association studies (GWAS) are a powerful tool for pathogenetic studies of complex diseases. The rich genetic information of GWAS data is mostly not fully utilized. In this study, we developed a sliding window-based genotype dependence testing tool SWGDT. SWGDT can be applied to GWAS data for genome-wide susceptibility gene scan utilizing known causal gene information. To evaluate the performance of SWGDT, a real GWAS dataset of Kashin-Beck disease (KBD) was analyzed. Immunohistochemistry was also performed to validate the relevance of identified gene with KBD. SWGDT analysis of KBD GWAS data identified a novel candidate gene TACR1 for KBD. Immunohistochemistry observed that the expression level of TACR1 protein in KBD articular cartilage was significantly higher than that in healthy articular cartilage. The real GWAS data analysis results illustrate the performance of SWGDT for genome-wide susceptibility gene scan. SWGDT can help to identify novel disease genes that may be missed by GWAS.
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wen
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Jingcan
authors.initials: J
authors.lastname: Hao
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Xiong
authors.initials: X
authors.lastname: Guo
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Cuiyan
authors.initials: C
authors.lastname: Wu
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Sen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China.
authors.forename: Tielin
authors.initials: T
authors.lastname: Yang
authors.affiliation: Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Shen
authors.affiliation: Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, PR China.
authors.forename: Xiangding
authors.initials: X
authors.lastname: Chen
authors.affiliation: Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, PR China.
authors.forename: Lijun
authors.initials: L
authors.lastname: Tan
authors.affiliation: Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Tian
authors.affiliation: Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA.
authors.forename: Hong-Wen
authors.initials: HW
authors.lastname: Deng
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China. Electronic address: fzhxjtu@mail.xjtu.edu.cn.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
mesh_terms: D002358:Cartilage, Articular; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D057767:Kashin-Beck Disease / Q000235:genetics*; D013223:Statistics as Topic
keywords: Genome-wide association studies; Genotype independence analysis; SWGDT; Sliding window