Article
Endocrinology & Metabolism
Min Wang, Kun Mei, Ce Chao, Dongmei Di, Yongxiang Qian, Bin Wang, Xiaoying Zhang
Summary: Mendelian randomization analysis clarified the potential association between rheumatoid arthritis (RA) and heart failure (HF), indicating that genetic susceptibility to RA may increase the risk of HF.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Pharmacology & Pharmacy
Frank Eektimmerman, Jesse J. J. Swen, Alfons A. A. den Broeder, Johanna M. W. Hazes, Fina S. S. Kurreeman, Suzanne M. M. Verstappen, Nisha Nair, Andrzej Pawlik, Mike T. T. Nurmohamed, Vita Dolzan, Stefan Bohringer, Cornelia F. F. Allaart, Henk-Jan Guchelaar
Summary: This nested case-control genome-wide association study identified seven suggestive genetic variants associated with methotrexate-induced liver injury (MTX-DILI), located in the intronic protein-coding regions of FTCDNL1, BCOR, FGF14, RBMS3, and PFDN4/DOK5 genes. However, further investigation is needed to validate these results.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Multidisciplinary Sciences
Helen R. Gosselt, Costanza L. Vallerga, Pooja R. Mandaviya, Erik Lubberts, Johanna M. W. Hazes, Robert de Jonge, Sandra G. Heil
Summary: The study did not identify genome-wide significant differences as biomarkers for Methotrexate (MTX) therapy response, necessitating meta-analyses.
Article
Rheumatology
Yuya Shirai, Yoshimitsu Nakanishi, Akari Suzuki, Hachirou Konaka, Rika Nishikawa, Kyuto Sonehara, Shinichi Namba, Hiroaki Tanaka, Tatsuo Masuda, Moto Yaga, Shingo Satoh, Mayuko Izumi, Yumiko Mizuno, Tatsunori Jo, Yuichi Maeda, Takuro Nii, Eri Oguro-Igashira, Takayuki Morisaki, Yoichiro Kamatani, Shingo Nakayamada, Chikako Nishigori, Yoshiya Tanaka, Yoshito Takeda, Kazuhiko Yamamoto, Atsushi Kumanogoh, Yukinori Okada
Summary: Our study used multi-trait and cross-population genome-wide association study (GWAS) meta-analysis to identify genetic correlations and shared components between autoimmune and allergic diseases. We found that there are genetic similarities and shared loci between these diseases, and enrichment analyses highlighted common pathways and cell types involved.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Biotechnology & Applied Microbiology
Mimi Wang, Jingyun Wu, Shufeng Lei, Xingbo Mo
Summary: This study identified RNAm-SNPs related to rheumatoid arthritis (RA) and suggested that they may affect the expression levels of corresponding genes and proteins.
Article
Genetics & Heredity
Huijing Huang, Xinyi Dong, Kaimin Mao, Wanwan Pan, Bin'en Nie, Lindi Jiang
Summary: In this study, gene signatures between rheumatoid arthritis (RA) and osteoarthritis (OA) joints were identified using the Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE153015. Differentially expressed genes (DEGs) were screened and functional enrichment analysis revealed associations with T cell activation or chemokine activity. Protein-protein interaction (PPI) network analysis identified key modules and hub genes for each group. The novel DEGs and functional pathways discovered in this study may provide new insights into the molecular mechanisms and therapeutic strategies of RA and OA.
FRONTIERS IN GENETICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Xinyue Wang, Xiaoqian Jiang, Jaideep Vaidya
Summary: The paper proposes two algorithms for generating synthetic SNPs that are indistinguishable from real SNPs. Through game theoretic analysis, it demonstrates the possibility of incentivizing honest behavior by the server. Extensive experiments show that the proposed method can ensure efficient and trustworthy outsourcing of logistic regression for GWAS.
JOURNAL OF BIOMEDICAL INFORMATICS
(2021)
Article
Multidisciplinary Sciences
Xiaoyu Liang, Xuewei Cao, Qiuying Sha, Shuanglin Zhang
Summary: The article introduces a novel multivariate method for phenome-wide association studies (PheWAS) and demonstrates its superiority through extensive simulation studies and real-life application. The proposed method involves hierarchical clustering, clustering linear combination, and false discovery rate control steps.
Review
Plant Sciences
Laura Tibbs Cortes, Zhiwu Zhang, Jianming Yu
Summary: Genome-wide association studies (GWAS) have become a powerful tool for investigating complex traits, with the development of the mixed model framework reducing false positives. Advances in technology have led to the development of methods to increase computational speed or improve statistical power in GWAS.
Article
Rheumatology
Jing Ni, Peng Wang, Kang-Jia Yin, Xiao-Ke Yang, Han Cen, Cong Sui, Guo-Cui Wu, Hai-Feng Pan
Summary: Our study identified 47 significant candidate genes for RA through a cross-tissue and single-tissue transcriptome-wide association study, with 13 genes located outside of previously reported significant loci. Enrichment analyses showed shared genetic determinants among autoimmune thyroid disease, asthma, type I diabetes mellitus, and RA.
Article
Multidisciplinary Sciences
Ludivine Obry, Cyril Dalmasso
Summary: In this study, we evaluated recent weighted multiple testing procedures for genome wide association studies (GWAS) through a simulation study. We also introduced a new efficient procedure called wBHa, which prioritizes the detection of genetic variants with low minor allel frequencies while maximizing overall detection power. Our results demonstrated that wBHa outperformed other procedures in detecting rare variants while maintaining good overall power.
Review
Biochemistry & Molecular Biology
Imane Lalami, Carole Abo, Bruno Borghese, Charles Chapron, Daniel Vaiman
Summary: This review discusses the genetics of endometriosis, a common feminine disease with a genetic heritability estimated at around 50%. Large GWAS studies have identified some genes and loci associated with the disease, but a significant portion of the heritability remains unexplained. Additional efforts such as exome sequencing may be needed to fully elucidate the genetic factors of endometriosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Medicine, General & Internal
Lisa Bastarache, Joshua C. Denny, Dan M. Roden
Summary: This article discusses the concept and methodology of phenome-wide association studies, which aim to identify associations between genetic variations and phenotypic traits using a dataset.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2022)
Article
Multidisciplinary Sciences
Abbas Saad Alatrany, Wasiq Khan, Abir Hussain, Dhiya Al-Jumeily
Summary: The increasing incidence of Alzheimer's disease (AD) poses socioeconomic challenges. In this study, a hybrid feature selection approach and neural network models are used to predict AD. The approach outperformed existing methods with 99% accuracy and f1-score, providing impactful outcomes for other chronic diseases.
Article
Multidisciplinary Sciences
Jack W. O'Sullivan, John P. A. Ioannidis
Summary: This study compared SNVs from earlier and later GWAS and found a replication rate of 85.0% in subsequent studies, with a lower replication rate for binary phenotypes compared to quantitative phenotypes. The study also identified a decrease in SNV effect size for binary phenotypes, but an increase for quantitative phenotypes, and developed a model that could predict SNV replication effectively.
SCIENTIFIC REPORTS
(2021)
Article
Endocrinology & Metabolism
Li Liu, Yan Wen, Lei Zhang, Peng Xu, Xiao Liang, Yanan Du, Ping Li, Awen He, QianRui Fan, Jingcan Hao, Wenyu Wang, Xiong Guo, Hui Shen, Qing Tian, Feng Zhang, Hong-Wen Deng
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2018)
Article
Psychiatry
Yan Wen, Feng Zhang, Xiancang Ma, Qianrui Fan, Wenyu Wang, Jiawen Xu, Feng Zhu, Jingcan Hao, Awen He, Li Liu, Xiao Liang, Yanan Du, Ping Li, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo
SCHIZOPHRENIA BULLETIN
(2019)
Article
Cell & Tissue Engineering
A. He, Y. Ning, Y. Wen, Y. Cai, K. Xu, J. Han, L. Liu, Y. Du, X. Liang, P. Li, Q. Fan, J. Hao, X. Wang, X. Guo, T. Ma, F. Zhang
BONE & JOINT RESEARCH
(2018)
Article
Endocrinology & Metabolism
Xiao Liang, CuiYan Wu, Hongmou Zhao, Li Liu, Yanan Du, Ping Li, Yan Wen, Yan Zhao, Miao Ding, Bolun Cheng, Shiqiang Cheng, Mei Ma, Lu Zhang, Xiong Guo, Hui Shen, Qing Tian, Feng Zhang, Hong-Wen Deng
Article
Behavioral Sciences
Huimei Huang, Shiqiang Cheng, Miao Ding, Yan Wen, Mei Ma, Lu Zhang, Ping Li, Bolun Cheng, Xiao Liang, Li Liu, Yanan Du, Yan Zhao, Om Prakash Kafle, Bei Han, Feng Zhang
Article
Endocrinology & Metabolism
Xiao Liang, Yanan Du, Yan Wen, Li Liu, Ping Li, Yan Zhao, Miao Ding, Bolun Cheng, Shiqiang Cheng, Mei Ma, Lu Zhang, Hui Shen, Qing Tian, Xiong Guo, Feng Zhang, Hong-Wen Deng
CALCIFIED TISSUE INTERNATIONAL
(2019)
Article
Endocrinology & Metabolism
M. Ma, D. -G. Huang, X. Liang, L. Zhang, S. Cheng, B. Cheng, X. Qi, P. Li, Y. Du, L. Liu, Y. Zhao, M. Ding, Y. Wen, X. Guo, F. Zhang
OSTEOPOROSIS INTERNATIONAL
(2019)
Article
Cell Biology
Xiao Liang, Sen Wang, Li Liu, Yanan Du, Bolun Cheng, Yan Wen, Yan Zhao, Miao Ding, Shiqiang Cheng, Mei Ma, Lu Zhang, Xin Qi, Ping Li, Xiong Guo, Feng Zhang
Article
Biochemistry & Molecular Biology
Bolun Cheng, Xiao Liang, Yan Wen, Ping Li, Lu Zhang, Mei Ma, Shiqiang Cheng, Yanan Du, Li Liu, Miao Ding, Yan Zhao, Feng Zhang
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Article
Orthopedics
Ping Li, Cuiyan Wu, Xiong Guo, Yan Wen, Li Liu, Xiao Liang, Yanan Du, Lu Zhang, Mei Ma, Shiqiang Cheng, Bolun Cheng, Sen Wang, Feng Zhang
Summary: This study aimed to uncover insights into the epigenetic modifications for Kashin-Beck disease (KBD) by integrating multiple datasets, leading to the identification of genetic control (GC) genes of DNA methylation for KBD. The results suggest that these GC genes may contribute to the erosion of cartilage in KBD, aiding in understanding the epigenetic alteration of the disease.
Article
Genetics & Heredity
Ping Li, Xi Wang, Xiong Guo, Yan Wen, Li Liu, Xiao Liang, Yanan Du, Cuiyan Wu, Sen Wang, Feng Zhang
ANNALS OF HUMAN GENETICS
(2020)
Article
Endocrinology & Metabolism
Junlong Wu, Yanan Du, Jidong Song, Xiaoqian Dang, Kunzheng Wang, Yan Wen, Feng Zhang, Ruiyu Liu
Article
Clinical Neurology
Xin Qi, Fanglin Guan, Yan Wen, Ping Li, Mei Ma, Shiqiang Cheng, Lu Zhang, Chujun Liang, Bolun Cheng, Feng Zhang
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2020)
Article
Biochemical Research Methods
Shiqiang Cheng, Bei Han, Miao Ding, Yan Wen, Mei Ma, Lu Zhang, Xin Qi, Bolun Cheng, Ping Li, Om Prakash Kafle, Xiao Liang, Li Liu, Yanan Du, Yan Zhao, Feng Zhang
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Rheumatology
Ping Li, Yujie Ning, Xiong Guo, Yan Wen, Bolun Cheng, Mei Ma, Lu Zhang, Shiqiang Cheng, Sen Wang, Feng Zhang
ARTHRITIS RESEARCH & THERAPY
(2019)