Review
Immunology
Christian W. Thorball, Jacques Fellay, Alessandro Borghesi
Summary: GWAS have been used to identify host genetic factors influencing immunity and infection traits, exploring resistance against infection, disease progression, and immune responses. These studies provide important insights into individual and population-level differences in response to infection and immune response mechanisms.
CURRENT OPINION IN IMMUNOLOGY
(2021)
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)
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
Obstetrics & Gynecology
Che Xu, Xiangyan Ruan, Alfred O. Mueck
Summary: Menopause not only marks the end of reproductive life, but also has associations with diseases like hyperlipidemia, atherosclerotic cardiovascular disease, osteoporosis, and breast cancer. Traditional epidemiological studies have shown that heredity plays a significant role in determining the age of natural menopause (ANM). Advances in genomic technology have enabled researchers to conduct genome-wide association studies, revealing that defects in DNA damage repair pathways are the primary genetic mechanism. Further genetic and epidemiological studies, including research on polygenic scores and genetic mechanisms, are needed to investigate the pathogenesis and mechanisms related to menopause and its associated diseases.
REPRODUCTIVE BIOMEDICINE ONLINE
(2023)
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
Biochemical Research Methods
Itziar Irigoien, Bru Cormand, Maria Soler-Artigas, Cristina Sanchez-Mora, Josep-Antoni Ramos-Quiroga, Concepcion Arenas
Summary: With the rise of GWAS, the analysis of large-scale SNP data has become crucial in biomedical research. This paper proposes a new method based on genetic distances between individuals to identify disease-related SNPs in case-control studies. By considering population substructure and avoiding multiple testing issues, the method provides ordered lists of SNPs and serves as a useful tool for researchers to focus their attention in the initial stage.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
David A. Sbarra, Ferris A. Ramadan, Karmel W. Choi, Jorien L. Treur, Daniel F. Levey, Robyn E. Wootton, Murray B. Stein, Joel Gelernter, Yann C. Klimentidis
Summary: This study using Mendelian Randomization (MR) found robust evidence for a bidirectional causal relationship between loneliness and major depression (MD). The findings suggest that reducing loneliness may play a causal role in decreasing the risk for depressive illness, highlighting the importance of efforts to reduce loneliness in preventing and ameliorating MD.
MOLECULAR PSYCHIATRY
(2023)
Review
Biochemistry & Molecular Biology
Frederick J. Boehm, Xiang Zhou
Summary: Genome-wide association studies have provided numerous associations for common diseases and complex traits. Mendelian randomization methods, utilizing SNP associations, help uncover causal relationships between complex traits. The availability of GWAS summary statistics has motivated the development of new Mendelian randomization methods with relaxed causality assumptions, offering opportunities for robust biological discoveries.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Statistics & Probability
Bingxin Zhao, Hongtu Zhu
Summary: The study investigates and addresses the bias phenomenon of cross-trait PRS in numerous GWAS applications and proposes a consistent estimator to correct the bias. Results show that the bias-corrected estimators uncover a moderate degree of genetic overlap between cognitive function and human brain structures.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2022)
Article
Biochemical Research Methods
Jean-Tristan Brandenburg, Lindsay Clark, Gerrit Botha, Sumir Panji, Shakuntala Baichoo, Christopher Fields, Scott Hazelhurst
Summary: The H3AGWAS workflow is a powerful and scalable tool for genome-wide association studies, capable of handling large datasets and facilitating parameter adjustments and result analysis.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Huilong Hong, Mei Li, Yijie Chen, Haorang Wang, Jun Wang, Bingfu Guo, Huawei Gao, Honglei Ren, Ming Yuan, Yingpeng Han, Lijuan Qiu
Summary: This study analyzed the phenotypic diversity and genetic basis of epicotyl length (EL) in soybean using 951 cultivars and landraces from different regions. The study identified 180 QTNs and QEIs associated with EL, and predicted 10 candidate genes that may be involved in seed germination and seedling development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Md Azizul Haque, Mohammad Zahangir Alam, Asif Iqbal, Yun-Mi Lee, Chang-Gwon Dang, Jong-Joo Kim
Summary: Holstein has been the most widely used dairy cattle breed in the Korean Peninsula since its introduction in 1885. A genome-wide association study (GWAS) was conducted to identify the genes associated with body conformation traits in the Korean Holstein population, and 24 significant SNPs were identified. The study provides insights into the genetic basis of body conformation traits and paves the way for future breeding strategies in dairy cattle.
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
Biotechnology & Applied Microbiology
Shan Lin, Cuncun Ke, Lin Liu, Yahui Gao, Lingna Xu, Bo Han, Yaofeng Zhao, Shengli Zhang, Dongxiao Sun
Summary: In this study, 14 candidate genes related to immunoglobulin concentrations in colostrum and serum in dairy cattle were identified through genome-wide association studies (GWASs). These findings provide a basis for further investigation into key genes and mutations affecting immunoglobulin concentrations, as well as important information for genetic improvement of immune traits in dairy cattle.
