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
Qingqin S. Li, Randall L. Morrison, Gustavo Turecki, Wayne C. Drevets
Summary: Epigenetic mechanisms play a significant role in the etiology of major depressive disorder (MDD), as indicated by a meta-analysis study. The study identified differentially methylated positions (DMPs) and differentially methylated regions (DMRs) associated with MDD, highlighting the involvement of pathways related to neuronal synaptic plasticity, calcium signaling, and inflammation.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Aliza P. Wingo, Yue Liu, Ekaterina S. Gerasimov, Jake Gockley, Benjamin A. Logsdon, Duc M. Duong, Eric B. Dammer, Chloe Robins, Thomas G. Beach, Eric M. Reiman, Michael P. Epstein, Philip L. De Jager, James J. Lah, David A. Bennett, Nicholas T. Seyfried, Allan I. Levey, Thomas S. Wingo
Summary: This study identified 11 genes that may play a role in Alzheimer's disease (AD) by affecting brain protein abundance, through a proteome-wide association study. Eight of these genes are new AD risk genes not identified before by AD GWAS, providing new insights into AD pathogenesis. This research offers promising targets for further mechanistic and therapeutic studies on AD.
Article
Clinical Neurology
Jaeyoon Chung, Anjali Das, Xinyu Sun, Debora R. Sobreira, Yuk Yee Leung, Catherine Igartua, Sahar Mozaffari, Yi-Fan Chou, Sam Thiagalingam, Jesse Mez, Xiaoling Zhang, Gyungah R. Jun, Thor D. Stein, Brian W. Kunkle, Eden R. Martin, Margaret A. Pericak-Vance, Richard Mayeux, Jonathan L. Haines, Gerard D. Schellenberg, Marcelo A. Nobrega, Kathryn L. Lunetta, Jayant M. Pinto, Li-San Wang, Carole Ober, Lindsay A. Farrer
Summary: Variants in the MGMT gene are associated with the development of Alzheimer's disease (AD), particularly in women. Multi-omics analyses suggest that this association may be mediated by the regulation of MGMT expression.
ALZHEIMERS & DEMENTIA
(2023)
Article
Multidisciplinary Sciences
Abbas Dehghan, Rui Climaco Pinto, Ibrahim Karaman, Jian Huang, Brenan R. Durainayagam, Mohsen Ghanbari, Areesha Nazeer, Qi Zhong, Sonia Liggi, Luke Whiley, Rima Mustafa, Miia Kivipelto, Alina Solomon, Tiia Ngandu, Takahisa Kanekiyo, Tomonori Aikawa, Carola I. Radulescu, Samuel J. Barnes, Goncalo Graca, Elena Chekmeneva, Stephane Camuzeaux, Matthew R. Lewis, Manuja R. Kaluarachchi, M. Arfan Ikram, Elaine Holmes, Ioanna Tzoulaki, Paul M. Matthews, Julian L. Griffin, Paul Elliott
Summary: Genome-wide association studies have identified genetic loci associated with the risk of Alzheimer's disease (AD). In this study, we used metabolomics to investigate the molecular mechanisms underlying these associations. We found an association between lactosylceramides and AD-related single-nucleotide polymorphisms in the ABCA7 gene. We also observed altered concentrations of certain lipids in brain tissue from knockout mice, suggesting that these lipid abnormalities may contribute to the risk of AD.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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.
Article
Biochemistry & Molecular Biology
Mingming Lu, Yadong Zhang, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jingfa Xiao
Summary: Transcriptome-wide association studies have led to a better understanding of genetic variants in regulating diseases and traits. However, there is a lack of databases curating public TWAS information. To fill this gap, TWAS Atlas is introduced as an integrated knowledgebase with 401,266 gene-trait associations from 200 publications, providing a user-friendly web interface for browsing, searching, and downloading relevant information.
NUCLEIC ACIDS RESEARCH
(2023)
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
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
Medicine, General & Internal
Mart Kals, Kevin Kunzmann, Livia Parodi, Farid Radmanesh, Lindsay Wilson, Saef Izzy, Christopher D. Anderson, Ava M. Puccio, David O. Okonkwo, Nancy Temkin, Ewout W. Steyerberg, Murray B. Stein, Geoff T. Manley, Andrew I. R. Maas, Sylvia Richardson, Ramon Diaz-Arrastia, Aarno Palotie, Samuli Ripatti, Jonathan Rosand, David K. Menon
Summary: This study is the first genome-and transcriptome-wide association studies of genetic effects on outcome in traumatic brain injury (TBI). While no genetic variants with genome-wide significance were found, the overall heritability estimate is consistent with the hypothesis that common genetic variation substantially contributes to inter-individual variability in TBI outcome.
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
Multidisciplinary Sciences
Matteo Sesia, Stephen Bates, Emmanuel Candes, Jonathan Marchini, Chiara Sabatti
Summary: The study introduces a comprehensive statistical framework for analyzing data from genome-wide association studies of polygenic traits, demonstrating validity and effectiveness through simulations and applications to the UK Biobank data. The method outperforms state-of-the-art alternatives and is supported by comparisons with other studies, offering researchers fast software for analyzing Biobank-scale datasets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Nutrition & Dietetics
Jing-yi Sun, Haihua Zhang, Yan Zhang, Longcai Wang, Bao-liang Sun, Feng Gao, Guiyou Liu
Summary: This study provides genetic evidence that increased serum calcium levels do not improve bone mineral density in the general population. Elevated serum calcium levels in generally healthy populations, especially in adults older than 60 years, may even reduce bone mineral density. Results are consistent with recent Mendelian randomization findings.
CLINICAL NUTRITION
(2021)
Article
Medicine, Research & Experimental
Haijie Liu, Yan Zhang, Haihua Zhang, Longcai Wang, Tao Wang, Zhifa Han, Liyong Wu, Guiyou Liu
Summary: The study found a negative trend between genetically increased plasma vitamin C levels and Parkinson's disease age at onset (AAO), although there was no significant association with PD occurrence. This suggests that vitamin C may have an impact on the AAO of PD, but further research is needed to confirm this.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Review
Chemistry, Multidisciplinary
Siyu Wei, Junxian Tao, Jing Xu, Xingyu Chen, Zhaoyang Wang, Nan Zhang, Lijiao Zuo, Zhe Jia, Haiyan Chen, Hongmei Sun, Yubo Yan, Mingming Zhang, Hongchao Lv, Fanwu Kong, Lian Duan, Ye Ma, Mingzhi Liao, Liangde Xu, Rennan Feng, Guiyou Liu, Yongshuai Jiang
Summary: EWAS has been utilized for a decade to analyze DNA methylation variation in complex diseases, and has gradually become a hot topic of current studies. The progress of EWAS research, contributions to clinical applications, achievements in typical diseases, challenges encountered, and bold predictions for future development are all discussed.
Article
Genetics & Heredity
Haijie Liu, Yan Zhang, Yang Hu, Haihua Zhang, Tao Wang, Zhifa Han, Shan Gao, Longcai Wang, Guiyou Liu
Summary: The study found that there may be no causal association between plasma vitamin C levels and the risk of Alzheimer's disease in people of European descent. However, a potential relationship between plasma vitamin C levels and the AD proxy phenotype was observed.
GENES AND NUTRITION
(2021)
Article
Clinical Neurology
Haijie Liu, Yang Hu, Yan Zhang, Haihua Zhang, Shan Gao, Longcai Wang, Tao Wang, Zhifa Han, Bao-liang Sun, Guiyou Liu
Summary: Mendelian randomization studies have explored the causal association of risk factors with Alzheimer's disease using large-scale genetic datasets, revealing significant impacts of educational attainment on AD risk but genetic heterogeneity across different datasets. This highlights the importance of interpreting and further investigating findings from different types of datasets to better understand the relationship between education and AD risk.
ALZHEIMERS RESEARCH & THERAPY
(2022)
Letter
Clinical Neurology
Yang Hu, Yan Zhang, Haihua Zhang, Shan Gao, Longcai Wang, Tao Wang, Zhifa Han, Guiyou Liu
ALZHEIMERS & DEMENTIA
(2022)
Article
Endocrinology & Metabolism
Jiali Xu, Gary B. Rajah, Houdi Zhang, Cong Han, Xuxuan Shen, Bin Li, Zhengxing Zou, Wenbo Zhao, Changhong Ren, Guiyou Liu, Yuchuan Ding, Qi Yang, Sijie Li, Xunming Ji
Summary: This study used high-resolution magnetic resonance imaging to investigate the characteristics of patients with moyamoya disease and anterior intracerebral hemorrhage. The results showed that the length of lenticulostriate arteries was shorter and the lumen area of the terminal internal carotid artery was larger in the hemorrhagic group compared to the ischemic group and asymptomatic group. Multivariate analysis revealed that these features were significantly associated with anterior intracerebral hemorrhage. Additionally, the coexistence of reduced lenticulostriate arteries and relatively preserved lumen area of the terminal internal carotid artery may serve as a potential predictor of anterior intracerebral hemorrhage in moyamoya disease patients.
JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM
(2022)
Article
Biochemistry & Molecular Biology
Yang Hu, Yan Zhang, Haihua Zhang, Shan Gao, Longcai Wang, Tao Wang, Zhifa Han, Bao-Liang Sun, Guiyou Liu
Summary: This study used large-scale genome-wide association studies (GWAS) to investigate the causal relationship between educational attainment, cognitive performance, intelligence, and Alzheimer's disease (AD) through univariable and multivariable Mendelian-randomization (MR) analyses. The findings highlight the protective role of cognitive performance in AD, independently of educational attainment and intelligence.
MOLECULAR PSYCHIATRY
(2022)
Letter
Multidisciplinary Sciences
Shizheng Qiu, Yang Hu, Quan Zou, Guiyou Liu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Haiyan Chen, Jing Xu, Siyu Wei, Zhe Jia, Chen Sun, Jingxuan Kang, Xuying Guo, Nan Zhang, Junxian Tao, Yu Dong, Chen Zhang, Yingnan Ma, Wenhua Lv, Hongsheng Tian, Shuo Bi, Hongchao Lv, Chen Huang, Fanwu Kong, Guoping Tang, Yongshuai Jiang, Mingming Zhang
Summary: The Rheumatoid Arthritis Bioinformatics Center (RABC) is a comprehensive multi-omics data resource platform developed to collect and classify scattered data on rheumatoid arthritis. It provides various categories of data and features a user-friendly interface and visualization module.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Zhifa Han, Huiyuan Hu, Peiran Yang, Baicun Li, Guiyou Liu, Junling Pang, Hongmei Zhao, Jing Wang, Chen Wang
Summary: The study demonstrates that a high blood eosinophil count is an independent causal mediator of COPD risk, FEV1/FVC decline, and COPD-related hospitalization. Furthermore, the onset of COPD and the decrease in FEV1/FVC ratio lead to an increase in blood neutrophil count.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Nutrition & Dietetics
Yan Zhang, Haijie Liu, Haihua Zhang, Zhifa Han, Tao Wang, Longcai Wang, Guiyou Liu
Summary: Vitamin D plays an important role in regulating calcium. Mendelian randomization studies have shown a causal association between circulating total 25-hydroxyvitamin D (25(OH)D) level and the risk of multiple sclerosis (MS). However, the causal association of 25(OH)D subtypes and calcium with MS risk remains unclear.
EUROPEAN JOURNAL OF CLINICAL NUTRITION
(2023)
Article
Virology
Shizheng Qiu, Keyang Zheng, Yang Hu, Guiyou Liu
Summary: Observational studies have shown that vitamin D supplementation reduces the risk of COVID-19 infection. This study investigated the genetic correlation and causal relationship between genetically determined vitamin D and COVID-19, and identified overlapping susceptibility loci. The results indicated that genetically determined vitamin D is associated with COVID-19, and increased serum 25 hydroxyvitamin D concentration may benefit the prevention and treatment of COVID-19.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Letter
Multidisciplinary Sciences
Guiyou Liu, Wenbo Zhao, Haihua Zhang, Tao Wang, Zhifa Han, Xunming Ji
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Letter
Clinical Neurology
Yang Hu, Haihua Zhang, Bian Liu, Shan Gao, Tao Wang, Zhifa Han, Xunming Ji, Guiyou Liu
Article
Geriatrics & Gerontology
Sarah N. Kraeutner, Cristina Rubino, Jennifer K. Ferris, Shie Rinat, Lauren Penko, Larissa Chiu, Brian Greeley, Christina B. Jones, Beverley C. Larssen, Lara A. Boyd
Summary: This study examined the age-related changes in brain function and baseline brain structure that support motor skill acquisition. The findings showed that older adults experienced decreases in functional connectivity during motor skill acquisition, while younger adults experienced increases. Additionally, regardless of age group, lower baseline microstructure in a frontoparietal tract was associated with slower motor skill acquisition.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Karen Nuytemans, Farid Rajabli, Melissa Jean-Francois, Jiji Thulaseedhara Kurup, Larry D. Adams, Takiyah D. Starks, Patrice L. Whitehead, Brian W. Kunkle, Allison Caban-Holt, Jonathan L. Haines, Michael L. Cuccaro, Jeffery M. Vance, Goldie S. Byrd, Gary W. Beecham, Christiane Reitz, Margaret A. Pericak-Vance
Summary: This study conducted genetic research on African American AD families and identified a significant linkage signal associated with AD, highlighting the importance of diverse population-level genetic data in understanding the genetic determinants of AD.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Kazuya Suwabe, Ryuta Kuwamizu, Kazuki Hyodo, Toru Yoshikawa, Takeshi Otsuki, Asako Zempo-Miyaki, Michael A. Yassa, Hideaki Soya
Summary: Physical exercise has a positive impact on hippocampal memory decline with aging. Recent studies have shown that even light exercise can improve memory and this improvement is mediated by the ascending arousal system. This study aimed to investigate the effects of light-intensity exercise on hippocampal memory function in healthy older adults and found that pupil dilation during exercise played a role in the memory improvement.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Ajay Sood, Ana Werneck Capuano, Robert Smith Wilson, Lisa Laverne Barnes, Alifiya Kapasi, David Alan Bennett, Zoe Arvanitakis
Summary: The objective of this study was to explore the impact of metformin on cognition and brain pathology. The results showed that metformin users had slower decline in global cognition, episodic memory, and semantic memory compared to non-users. However, the relationship between metformin use and certain brain pathology remains uncertain.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Brian N. Lee, Junwen Wang, Molly A. Hall, Dokyoon Kim, Shana D. Stites, Li Shen
Summary: Alzheimer's disease (AD) is a neurodegenerative disorder characterized by memory and functional impairments. This study analyzed participants from the Alzheimer's Disease Neuroimaging Initiative and found differential associations between cerebral spinal fluid (CSF)/neuroimaging biomarkers and cognitive/functional outcomes, as well as variations between sexes. These findings suggest that sex differences may play a role in the development of AD.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Madeline R. Hale, Rebecca Langhough, Lianlian Du, Bruce P. Hermann, Carol A. Van Hulle, Margherita Carboni, Gwendlyn Kollmorgenj, Kristin E. Basche, Davide Bruno, Leah Sanson-Miles, Erin M. Jonaitis, Nathaniel A. Chin, Ozioma C. Okonkwo, Barbara B. Bendlin, Cynthia M. Carlsson, Henrik Zetterberg, Kaj Blennow, Tobey J. Betthauser, Sterling C. Johnson, Kimberly D. Mueller
Summary: This study demonstrates a relationship between cerebrospinal fluid biomarkers and the ability to recall proper names in the preclinical phase of Alzheimer's disease.
NEUROBIOLOGY OF AGING
(2024)
Article
Geriatrics & Gerontology
Thomas T. Austin, Christian L. Thomas, Ben Warren
Summary: This study investigated the effects of age on the robustness and resilience of auditory system using the desert locust. The researchers found that gene expression changes were mainly influenced by age rather than noise exposure. Both young and aged locusts were able to recover their auditory nerve function within 48 hours of noise exposure, but the recovery of transduction current magnitude was impaired in aged locusts. Key genes responsible for robustness to noise exposure in young locusts and potential candidates for compensatory mechanisms in auditory neurons of aged locusts were identified.
NEUROBIOLOGY OF AGING
(2024)
