Article
Biotechnology & Applied Microbiology
Mo Li, Yi Hu, Baihui Zhao, Luan Chen, Hailiang Huang, Cong Huai, Xiaoqing Zhang, Jinghong Zhang, Wei Zhou, Lu Shen, Qi Zhen, Bao Li, Wenjun Wang, Lin He, Shengying Qin
Summary: A two-stage study identified genetic markers associated with TB susceptibility in 616 TB patients and 709 healthy controls. The study confirmed 6 nominally significant SNPs and a HLA-II allele as predisposing factors for TB. The research provides insight into the genetic variants linked to TB susceptibility and sheds light on tuberculosis pathogenesis.
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.
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
Medical Laboratory Technology
Lisa A. Lansdon, Maxime Cadieux-Dion, John C. Herriges, Jeffrey Johnston, Byunggil Yoo, Joseph T. Alaimo, Isabelle Thiffault, Neil Miller, Ana S. A. Cohen, Elena A. Repnikova, Lei Zhang, Midhat S. Farooqi, Emily G. Farrow, Carol J. Saunders
Summary: The study validated the clinical effectiveness of the laboratory's migration from GRCh37 to GRCh38, and identified some important differences between the two genome versions, including discrepancies leading to protein coding sequence variants and discrepancies resolved in coding regions.
CLINICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Kleanthi Lakiotaki, Zaharias Papadovasilakis, Vincenzo Lagani, Stefanos Fafalios, Paulos Charonyktakis, Michail Tsagris, Ioannis Tsamardinos
Summary: This article introduces an automated machine learning approach customized for genomic data, which can provide reliable predictive and diagnostic models and discover genetic variants with higher predictive performance. The approach can also compute individual risk prediction scores, generalize to new, unseen data, and better differentiate causal variants from other highly correlated variants.
Article
Clinical Neurology
Manuela M. X. Tan, Michael A. Lawton, Edwin Jabbari, Regina H. Reynolds, Hirotaka Iwaki, Cornelis Blauwendraat, Sofia Kanavou, Miriam Pollard, Leon Hubbard, Naveed Malek, Katherine A. Grosset, Sarah L. Marrinan, Nin Bajaj, Roger A. Barker, David J. Burn, Catherine Bresner, Thomas Foltynie, Nicholas W. Wood, Caroline H. Williams-Gray, John Hardy, Michael A. Nalls, Andrew B. Singleton, Nigel M. Williams, Yoav Ben-Shlomo, Michele T. M. Hu, Donald G. Grosset, Maryam Shoai, Huw R. Morris
Summary: The study found that genetic variants associated with Parkinson's disease risk are not linked to disease progression. The APOE epsilon 4 tagging variant was significantly associated with cognitive progression, while ATP8B2 gene showed a nominal association with motor progression. The new method shows promise in improving the measurement of symptom progression in PD.
MOVEMENT DISORDERS
(2021)
Review
Cell Biology
Carina Mauersberger, Heribert Schunkert, Hendrik B. Sager
Summary: While the importance of inflammation in atherosclerosis is recognized, the exact molecular processes remain unclear. Modern genetics, specifically genome-wide association studies, have revealed many loci related to inflammatory processes in coronary artery disease, but translating these findings into specific molecular mechanisms is still challenging.
Article
Biology
Francesc Coll, Theodore Gouliouris, Sebastian Bruchmann, Jody Phelan, Kathy E. Raven, Taane G. Clark, Julian Parkhill, Sharon J. Peacock
Summary: PowerBacGWAS is a computational pipeline that performs power calculations for bacterial genome-wide association studies using existing genomic data. This tool implements two alternative approaches for power calculations and can determine sample sizes required to detect causal variants of different minor allele frequencies, effect sizes, and phenotype heritability. It can also be applied to other bacterial populations to determine statistically significant associations or detectable associations with a given sample size.
COMMUNICATIONS BIOLOGY
(2022)
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cardiac & Cardiovascular Systems
Tejas P. Singh, Matt A. Field, Matthew J. Bown, Gregory T. Jones, Jonathan Golledge
Summary: This study systematically reviewed previous AAA GWAS and identified 33 SNPs associated with AAA diagnosis at genome-wide significance. However, the association between SNPs and AAA growth was not adequately examined. Previous GWAS have various design limitations, such as inconsistent case and control ascertainment and limited phenotyping of the AAAs.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Physiology
Roddy Walsh, Sean J. Jurgens, Jeanette Erdmann, Connie R. Bezzina
Summary: Genome-wide association studies (GWAS) have identified common genetic variants associated with traits and diseases, providing insights into genetic architecture, correlations across traits and diseases, and potential clinical applications. The utilization of GWAS in cardiovascular diseases and associated phenotypic traits has been facilitated by multicenter registry studies and large biobank data sets. However, challenges still exist in this field and need to be addressed.
PHYSIOLOGICAL REVIEWS
(2023)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Genetics & Heredity
Michal Marczyk, Agnieszka Macioszek, Joanna Tobiasz, Joanna Polanska, Joanna Zyla
Summary: The study evaluated the impact of different integration methods and linkage disequilibrium correction on multiple GSA algorithms, with CERNO and MAGENTA combined with Stouffer method showing the most efficiency. LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. The best performance was observed when using Fisher or Stouffer integration with LD correction.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Jie Gao, Xin Hu, Chunyan Gao, Guang Chen, Hui Feng, Zhen Jia, Peimin Zhao, Haiyang Yu, Huaiwen Li, Zedong Geng, Jingbo Fu, Jun Zhang, Yikeng Cheng, Bo Yang, Zhanghan Pang, Daoquan Xiang, Jizeng Jia, Handong Su, Hailiang Mao, Caixia Lan, Wei Chen, Wenhao Yan, Lifeng Gao, Wanneng Yang, Qiang Li
Summary: This study used a non-invasive and high-throughput phenotyping platform to monitor a diverse wheat panel and investigate the genetic controls of growth and yield-related traits. By conducting whole genome re-sequencing and a genome-wide association analysis, the study identified numerous marker-trait associations and quantitative trait loci (QTLs) that contribute to wheat growth and yield production. The temporal dynamics of these QTLs were also revealed. This research provides insights into optimizing wheat growth and yield, and offers the potential for high-throughput early selection to accelerate breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Neurosciences
Shu-Yu Liang, Zuo-Teng Wang, Lan Tan, Jin-Tai Yu
Summary: This article introduces the function and dysfunction of microtubule-associated protein tau in the central nervous system and discusses its role in neurodegenerative diseases, tau phosphorylation-related enzymes and proteins, and its relationship with cell dysfunction. The study of tau neurotoxicity provides new directions for the treatment of tauopathies.
MOLECULAR NEUROBIOLOGY
(2022)
Review
Neurosciences
Yi Zhang, Kai-Min Wu, Liu Yang, Qiang Dong, Jin-Tai Yu
Summary: In this article, emerging knowledge on tauopathies from clinical, pathological, genetic, and experimental studies is synthesized to accelerate the development of therapeutics for these diseases. The focus is on depicting pathological characteristics, identifying biomarkers, elucidating the underlying pathogenesis for early diagnosis, and the development of disease-modifying therapies.
MOLECULAR NEURODEGENERATION
(2022)
Article
Environmental Sciences
He-Ying Hu, Ya-Hui Ma, Yue-Ting Deng, Ya-Nan Ou, Wei Cheng, Jian-Feng Feng, Lan Tan, Jin-Tai Yu
Summary: This study found an association between residential greenness and dementia incidence, indicating that increasing greenspace can reduce the risk of dementia. The protective effect of greenness may be mediated through the reduction of particulate air pollution.
ENVIRONMENTAL RESEARCH
(2023)
Article
Clinical Neurology
Rong-Ze Wang, Shu-Yi Huang, Hong-Qi Li, Yu-Xiang Yang, Shi-Dong Chen, Jin-Tai Yu
Summary: Using a Mendelian randomization approach, this study found that genetically determined levels of lipids in small LDL were associated with the risk of stroke, especially large-artery atherosclerotic stroke. Higher cholesterol levels in high-density lipoprotein (HDL-C) were associated with the risk of intracerebral haemorrhage. However, no significant association was found between genetic predisposition to circulating metabolites and magnetic resonance imaging markers of cerebral small vessel disease and microstructural injury.
EUROPEAN JOURNAL OF NEUROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Qiaolifan Aerqin, Zuo-Teng Wang, Kai-Min Wu, Xiao-Yu He, Qiang Dong, Jin-Tai Yu
Summary: This review summarizes the progress made in the discovery of reliable Alzheimer's disease (AD) biomarkers using genomics, transcriptomics, proteomics, and metabolomics. The importance of these biomarkers in the diagnosis and treatment of AD is discussed.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Medicine, General & Internal
Hui-Fu Wang, Wei Zhang, Edmund T. Rolls, Yuzhu Li, Linbo Wang, Ya-Hui Ma, Jujiao Kang, Jianfeng Feng, Jin-Tai Yu, Wei Cheng
Summary: This study investigated the association of hearing performance with cognitive function, brain structure, and cerebrospinal fluid (CSF) proteins. The findings revealed that poor hearing performance was related to worse cognitive function, brain atrophy, and tau pathology.
Review
Clinical Neurology
Na Zhang, Ke-Liang Chen, Yu-Yuan Huang, Shu-Fen Chen, Qiang Dong, Lan Tan, Jin-Tai Yu
CLINICAL NEUROLOGY AND NEUROSURGERY
(2023)
Article
Neurosciences
Zuo-Teng Wang, Yan Fu, Shi-Dong Chen, Yu-Yuan Huang, Ya-Hui Ma, Yan-Jiang Wang, Lan Tan, Jin-Tai Yu
Summary: This study is the first to identify significant associations between TREM1 rs2062323 and AD risk. The rs2062323T may be involved in AD by regulating the expression of TREM1, TREML1, TREM2, and sTREM2. The TREM family is expected to be a potential therapeutic target for AD.
CNS NEUROSCIENCE & THERAPEUTICS
(2023)
Article
Clinical Neurology
Yan Fu, Yan Sun, Zhi-Bo Wang, Dan-Dan Zhang, Lan Tan, Jian-Feng Feng, Wei Cheng, Jin-Tai Yu
Summary: This study used the American Heart Association's Life's Simple 7 (LS7) metric to define cardiovascular and brain health and found that ideal LS7 cardiovascular health factors are associated with both macrostructural and microstructural markers of brain health. The results suggest that better LS7 profiles are linked to better brain health.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yan Sun, Yu Guo, Hong-Qi Li, Lan Tan, Jian-Feng Feng, Wei Cheng, Jin-Tai Yu
Summary: White matter hyperintensities (WMH) are strongly associated with stroke, dementia, and early mortality. This study investigated the relationship between WMH and circulating metabolites in a large sample of individuals from the UK Biobank. The results showed that several metabolites, including high-density lipoprotein (HDL), fatty acids, and glycoprotein acetyls, were associated with WMH. Age and sex also had a significant influence on these associations. The findings suggest that specific metabolomic features accompany WMH and may provide insights into the implications of WMH in different populations.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Geriatrics & Gerontology
Yu He, Shu-Yi Huang, Hui-Fu Wang, Wei Zhang, Yue-Ting Deng, Ya-Ru Zhang, Qiang Dong, Jian-Feng Feng, Wei Cheng, Jin-Tai Yu
Summary: Cohort studies have shown inconsistent associations between omega-3 polyunsaturated fatty acids (n-3 PUFA) or fish oil and dementia risk. This study included a large number of participants and found that higher plasma levels of PUFA and fish oil supplementation were associated with a lower risk of developing dementia.
Article
Biochemistry & Molecular Biology
Shu-Yi Huang, Ya-Ru Zhang, Liu Yang, Yu-Zhu Li, Bang-Sheng Wu, Shi-Dong Chen, Jian-Feng Feng, Qiang Dong, Wei Cheng, Jin-Tai Yu
Summary: Identifying circulating metabolites associated with dementia, cognition, and brain volume could provide new insights into the pathogenesis of dementia. This cohort study found 26 metabolites associated with incident dementia, including specific associations with Alzheimer's disease (AD) and vascular dementia (VD). Circulating levels of certain lipoproteins were found to be associated with the risk of AD and AD phenotypes, while another lipoprotein was associated with the risk of VD.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ji-Yun Cheng, Yue-Ting Deng, Jin-Tai Yu
Summary: Through a more robust analysis, we found potential associations between circulating levels of amino acids and the risk of neurodegenerative diseases. Increase in circulating levels of Glutamine (Gln) was associated with lower risk of Alzheimer's disease (AD), while increase in circulating levels of Leucine (Leu) was associated with lower risk of Parkinson's disease (PD). Replication tests further confirmed the potential association between circulating Gln levels and AD risk.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Neurosciences
Wei-Shi Liu, Ya-Ru Zhang, Yi-Jun Ge, Hui-Fu Wang, Wei Cheng, Jin-Tai Yu
Summary: This study identified the association between TREM2, temporal lobe, and AD using genetic and transcriptomic data, and explored the complex associations among inflammation, brain structure, and neurodegenerative disorders, particularly AD.
MOLECULAR NEUROBIOLOGY
(2023)
Review
Neurosciences
Hai-Shan Jiao, Peng Yuan, Jin-Tai Yu
Summary: Mutations in the TMEM106B gene are risk factors for various neurodegenerative diseases. Previous understanding of the underlying mechanism focused on the impairment of lysosome biogenesis caused by TMEM106B loss-of-function. However, mutations in TMEM106B increase its expression level, thus the molecular process linking these mutations to the apparent disruption in TMEM106B function remains mysterious.
MOLECULAR NEURODEGENERATION
(2023)