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Articles 1 - 30 of 34
Full-Text Articles in Medical Genetics
A Genomic Approach For Accurate Identification Of Closely Related Species With Next-Generation Sequencing Samples, Nour Al Dain Marzouka, Amira Al-Aamri, Fatima Alshamsi, Mariam Khalili, Sarah El Hajj Chehadeh, Meera S. Mohamed, Yassir Mohammed Eltahir, Rafeek Koliyan, Mohamed Moustafa Abdelhalim, Assem Attia, Mira Mousa, Guan Tay, Habiba Alsafar
A Genomic Approach For Accurate Identification Of Closely Related Species With Next-Generation Sequencing Samples, Nour Al Dain Marzouka, Amira Al-Aamri, Fatima Alshamsi, Mariam Khalili, Sarah El Hajj Chehadeh, Meera S. Mohamed, Yassir Mohammed Eltahir, Rafeek Koliyan, Mohamed Moustafa Abdelhalim, Assem Attia, Mira Mousa, Guan Tay, Habiba Alsafar
Research outputs 2022 to 2026
Accurate species identification from Whole Genome Sequencing (WGS) data remains challenging, particularly for closely related species such as sheep (Ovis aries) and goats (Capra hircus). Through analysis of mapping quality metrics and Kraken2 taxonomic classification of 40 WGS sheep and goat samples, we demonstrate that conventional approaches yield ambiguous results, with overlapping alignment rates and inconclusive taxonomic assignments. We present a robust comparative genomic approach that uses species-specific genomic regions to distinguish these species in WGS samples. We define species-specific regions as those exhibiting distinctive coverage patterns: average coverage when samples are aligned to their matching reference genome but absent/low …
Deep Reinforcement Learning–Driven Multi-Omics Integration For Constructing Gtage: A Novel Aging Clock From Igg N-Glycome And Blood Transcriptome, Yao Xia, Syed Mohammed Shamsul Islam, Xingang Li, Abdul Baten, Xuerui Tan, Wei Wang
Deep Reinforcement Learning–Driven Multi-Omics Integration For Constructing Gtage: A Novel Aging Clock From Igg N-Glycome And Blood Transcriptome, Yao Xia, Syed Mohammed Shamsul Islam, Xingang Li, Abdul Baten, Xuerui Tan, Wei Wang
Research outputs 2022 to 2026
Previous studies have demonstrated that the immunoglobulin G (IgG) N-glycome and transcriptome are potential biochemical signatures of chronological and biological ages, and several aging clocks have been developed. By integrating the IgG N-glycome and transcriptome, we propose a novel aging clock, gtAge. We developed a deep reinforcement learning-based multiomics integration method called AlphaSnake. The results showed that AlphaSnake achieved a predicted coefficient of determination (R2) value of 0.853, outperforming the concatenation-based integration method (R2 = 0.820). The gtAge estimated by AlphaSnake explained up to 85.3% of the variance in chronological age, which was higher than that in …
Can Dna Be Glycosylated?, Wei Wang
Can Dna Be Glycosylated?, Wei Wang
Research outputs 2022 to 2026
No abstract provided.
Development And Validation Of An Interpretable Risk Prediction Model For The Early Classification Of Thalassemia, Jin Xin Lai, Jia Wei Tang, Shan Shan Gong, Ming Xiong Qin, Yu Lu Zhang, Quan Fa Liang, Li Yan Li, Zhen Cai, Liang Wang
Development And Validation Of An Interpretable Risk Prediction Model For The Early Classification Of Thalassemia, Jin Xin Lai, Jia Wei Tang, Shan Shan Gong, Ming Xiong Qin, Yu Lu Zhang, Quan Fa Liang, Li Yan Li, Zhen Cai, Liang Wang
Research outputs 2022 to 2026
Thalassemia is an inherited blood disorder. Current diagnostic methods mainly rely on sophisticated equipment and specifically trained technicians. This study aims to identify and genotype thalassemia by applying machine learning (ML) algorithms to routine blood parameters. This study recruited a derivation cohort of 31,311 individuals from four independent hospitals and developed eight machine learning (ML) models for the purpose. The performance of these models was compared using a set of evaluation metrics. An additional cohort of 2000 patients was recruited for external validation to assess the generalization of the models. The results demonstrated that the categorical boosting (CatBoost) model exhibited …
Profiling Of Igg N-Glycosylation For Axial Spondyloarthritis And Other Rheumatic Diseases, Xiaojia Xu, Zhixian Chen, Manshu Song, Zhiduo Hou, Lois Balmer, Chunbin Zhou, Yayi Huang, Haifeng Hou, Wei Wang, Ling Lin
Profiling Of Igg N-Glycosylation For Axial Spondyloarthritis And Other Rheumatic Diseases, Xiaojia Xu, Zhixian Chen, Manshu Song, Zhiduo Hou, Lois Balmer, Chunbin Zhou, Yayi Huang, Haifeng Hou, Wei Wang, Ling Lin
Research outputs 2022 to 2026
Background: Axial spondyloarthritis (axSpA) is an inflammatory rheumatic disease with challenges in diagnosis and disease activity assessment. While alterations in immunoglobulin G (IgG) N-glycosylation have been observed in varied rheumatic diseases, those in axSpA remains unclear. This study aims to explore the role of IgG N-glycan profiles in diagnosis and disease activity of axSpA. Methods: A clinical case-control study was conducted involving patients with axSpA (n = 138), systemic lupus erythematosus (n = 102), rheumatoid arthritis (n = 106), osteoarthritis (n = 33), gout (n = 41) and healthy controls (n = 117). Ultra-performance liquid chromatography was employed to analyze …
Combining Lumipulse P-Tau217 And Aβ42/40 As Confirmatory Tests For Aβ Positivity Prior To Disease-Modifying Therapy, James D. Doecke, Ahmed Chenna, Mintzu Lo, Youssouf Badal, Brandon Yee, Robert Martone, Christos Petropoulos, Christopher J. Fowler, Simon Laws, Stephanie R. Rainey-Smith, Ralph N. Martins, Christopher C. Rowe, Colin L. Masters, John Winslow
Combining Lumipulse P-Tau217 And Aβ42/40 As Confirmatory Tests For Aβ Positivity Prior To Disease-Modifying Therapy, James D. Doecke, Ahmed Chenna, Mintzu Lo, Youssouf Badal, Brandon Yee, Robert Martone, Christos Petropoulos, Christopher J. Fowler, Simon Laws, Stephanie R. Rainey-Smith, Ralph N. Martins, Christopher C. Rowe, Colin L. Masters, John Winslow
Research outputs 2022 to 2026
Introduction: For a blood-based biomarker to be considered a confirmatory test for the detection of abnormal amyloid beta (Aβ) levels, the sensitivity and specificity must be equivalent to that of current cerebrospinal fluid tests. Methods: In the current study we assessed the ability of phosphorylated tau (p-tau)217 and Aβ42/40 from the Lumipulse G p-tau217 and β-amyloid ratio (1-42/1-40) tests, individually and combined, to predict Aβ positron emission tomography status in two sub-cohorts from the Australian Imaging, Biomarkers, and Lifestyle Study of Ageing. Results: Testing an Alzheimer's disease continuum cohort, the area under the curve (AUC), sensitivity, specificity, and accuracy for …
Atopy-Related Immune Profiles Are Subject To Genetic Influence As Evaluated Using School-Aged Twin Pairs, Jonatan Leffler, James F. Read, Danny Mok, Michael Serralha, Anthony Bosco, Patrick G. Holt, Richard Saffery, Deborah H. Strickland
Atopy-Related Immune Profiles Are Subject To Genetic Influence As Evaluated Using School-Aged Twin Pairs, Jonatan Leffler, James F. Read, Danny Mok, Michael Serralha, Anthony Bosco, Patrick G. Holt, Richard Saffery, Deborah H. Strickland
Research outputs 2022 to 2026
The interaction of genetic and environmental contributions to immunological traits and their association with atopic disease remain unclear. Flow cytometry and in vitro cytokine responses were used to characterize immune profiles from 93 school-aged twin pairs. Using an established twin pair analytical strategy, the genetic and environmental influences on immunological traits were evaluated, along with their association with atopy. Our findings suggest strong genetic influence on several traits, particularly B cell abundance. In contrast, cytokine responses from in vitro stimulations appeared mainly shaped by environmental exposures. Regarding associations with atopy, greater abundance of both B cells and basophils were observed …
Risk Factors For Mismatches In The Art Laboratory: An Analysis Of 73,719 Electronic Witnessing Points, Maria Forbrig, Kelli Peirce, Chris Copeland, Jay Natalwala, Vincent Chapple, Yanhe Liu
Risk Factors For Mismatches In The Art Laboratory: An Analysis Of 73,719 Electronic Witnessing Points, Maria Forbrig, Kelli Peirce, Chris Copeland, Jay Natalwala, Vincent Chapple, Yanhe Liu
Research outputs 2022 to 2026
Research question: What are the risk factors for mismatches (involving or not involving biological material) and critical mismatches (CMM; involving biological material) in an assisted reproductive technology laboratory equipped with an electronic witnessing system (EWS)? Design: In total, 73,719 witnessing points were extracted retrospectively from an EWS database, representing 11,210 consecutive treatment cycles performed at Fertility North between January 2016 and July 2023. Results: Overall, 138 (0.19%) mismatches and 16 (0.02%) CMM were identified during the study period. Significant differences were detected in both mismatch (P = 0.003) and CMM (P = 0.038) rates between different time periods of the …
Genomic Characterisation Of The Relationship And Causal Links Between Vascular Calcification, Alzheimer’S Disease, And Cognitive Traits, Emmanuel O. Adewuyi, Simon M. Laws
Genomic Characterisation Of The Relationship And Causal Links Between Vascular Calcification, Alzheimer’S Disease, And Cognitive Traits, Emmanuel O. Adewuyi, Simon M. Laws
Research outputs 2022 to 2026
Background/Objectives: Observational studies suggest a link between vascular calcification and dementia or cognitive decline, but the evidence is conflicting, and the underlying mechanisms are unclear. Here, we investigate the shared genetic and causal relationships of vascular calcification—coronary artery calcification (CAC) and abdominal aortic calcification (AAC)—with Alzheimer’s disease (AD), and five cognitive traits. Methods: We analyse large-scale genome-wide association studies (GWAS) summary statistics, using well-regarded methods, including linkage disequilibrium score regression (LDSC), Mendelian randomisation (MR), pairwise GWAS (GWAS-PW), and gene-based association analysis. Results: Our findings reveal a nominally significant positive genome-wide genetic correlation between CAC and AD, which becomes non-significant after …
Is It Underestimated Or Overestimated?, Zhuoqiao He, Xuerui Tan
Is It Underestimated Or Overestimated?, Zhuoqiao He, Xuerui Tan
Research outputs 2022 to 2026
No abstract provided.
Pulmonary Nodule Malignancy Probability: A Meta-Analysis Of The Brock Model, S. Chen, W. L. Lin, W. T. Liu, L. Y. Zou, Y. Chen, F. Lu
Pulmonary Nodule Malignancy Probability: A Meta-Analysis Of The Brock Model, S. Chen, W. L. Lin, W. T. Liu, L. Y. Zou, Y. Chen, F. Lu
Research outputs 2022 to 2026
Aim: This study aims to quantify the performance of the Brock model through a systematic review and meta-analysis and to clarify its overall accuracy in predicting malignant pulmonary nodules. Materials and Methods: A systematic search was conducted in databases including the Cochrane Library, Excerpta Medica database (EMBASE), MEDLINE, Web of Science, Chinese Biological Medicine Database (CBM), China National Knowledge Infrastructure (CNKI), VIP, and Wanfang from their inception until May 1, 2024, to collect observational cohort studies involving the Brock model. The primary outcome was the pooled area under the receiver operating characteristic curve (ROC) the area under curve (AUC) for …
A Roadmap To Precision Medicine Through Post-Genomic Electronic Medical Records, Kevin M. Mendez, Stacey N. Reinke, Rachel S. Kelly, Qingwen Chen, Mark Su, Michael Mcgeachie, Scott Weiss, David I. Broadhurst, Jessica A. Lasky-Su
A Roadmap To Precision Medicine Through Post-Genomic Electronic Medical Records, Kevin M. Mendez, Stacey N. Reinke, Rachel S. Kelly, Qingwen Chen, Mark Su, Michael Mcgeachie, Scott Weiss, David I. Broadhurst, Jessica A. Lasky-Su
Research outputs 2022 to 2026
The promise of integrating Electronic Medical Records (EMR) and genetic data for precision medicine has largely fallen short due to its omission of environmental context over time. Post-genomic data can bridge this gap by capturing the real-time dynamic relationship between underlying genetics and the environment. This perspective highlights the pivotal role of integrating EMR and post-genomics for personalized health, reflecting on lessons from past efforts, and outlining a roadmap of challenges and opportunities that must be addressed to realize the potential of precision medicine.
Mirnaome-Metabolome Wide Association Study Reveals Effects Of Mirna Regulation In Eosinophilia And Airflow Obstruction In Childhood Asthma, Rinku Sharma, Kevin Mendez, Sofina Begum, Su Chu, Nicole Prince, Julian Hecker, Rachel S. Kelly, Qingwen Chen, Craig E. Wheelock, Juan C. Celedón, Clary Clish, Robert Gertszen, Kelan G. Tantisira, Scott T. Weiss, Jessica Lasky-Su, Michael Mcgeachie
Mirnaome-Metabolome Wide Association Study Reveals Effects Of Mirna Regulation In Eosinophilia And Airflow Obstruction In Childhood Asthma, Rinku Sharma, Kevin Mendez, Sofina Begum, Su Chu, Nicole Prince, Julian Hecker, Rachel S. Kelly, Qingwen Chen, Craig E. Wheelock, Juan C. Celedón, Clary Clish, Robert Gertszen, Kelan G. Tantisira, Scott T. Weiss, Jessica Lasky-Su, Michael Mcgeachie
Research outputs 2022 to 2026
Background: There are important inter-relationships between miRNAs and metabolites: alterations in miRNA expression can be induced by various metabolic stimuli, and miRNAs play a regulatory role in numerous cellular processes, impacting metabolism. While both specific miRNAs and metabolites have been identified for their role in childhood asthma, there has been no global assessment of the combined effect of miRNAs and the metabolome in childhood asthma. Methods: We performed miRNAome-metabolome-wide association studies (‘miR-metabo-WAS’) in two childhood cohorts of asthma to evaluate the contemporaneous and persistent miRNA-metabolite associations: 1) Genetic Epidemiology of Asthma in Costa Rica Study (GACRS) (N = 1121); 2) …
Genome Wide Association Study Reveals Novel Associations With Face Morphology, Aamer Alshehhi, Mira Mousa, Guan K. Tay, Naoufel Werghi, Habiba Alsafar
Genome Wide Association Study Reveals Novel Associations With Face Morphology, Aamer Alshehhi, Mira Mousa, Guan K. Tay, Naoufel Werghi, Habiba Alsafar
Research outputs 2022 to 2026
Genome-wide association studies (GWAS) on the Middle Eastern population, including the United Arab Emirates (UAE), have been relatively limited. The present study aims to investigate genotype-face morphology associations in the UAE population through Genome Wide Association Studies (GWAS). Phenotypic data (44 face measurements) from 172 Emiratis was obtained through three-dimensional (3D) scanning technology and an automatic face landmarking technique. GWAS analysis revealed associations of 19 genetic loci with six face features, 14 of which are novel. The GWAS analysis revealed 11 significant relationships between 44 face parameters and 242 SNPs, exceeding the GWAS significance threshold. These phenotypes were previously associated …
Improving The Clinical Diagnostic Criteria For Genetically Confirmed Adult-Onset Huntington Disease: Considering Nonmotor Presentations, Ciaran M. Considine, Clare M. Eddy, Samuel A. Frank, Sandra K. Kostyk, Mayke Oosterloo, Annie Killoran, Erin Furr Stimming, Matthias Dose, Travis Cruickshank, Thomas D. Bird, Louise Vetter, Astri Arnesen, James Valvano, Herwig W. Lange, Daniel O. Claassen
Improving The Clinical Diagnostic Criteria For Genetically Confirmed Adult-Onset Huntington Disease: Considering Nonmotor Presentations, Ciaran M. Considine, Clare M. Eddy, Samuel A. Frank, Sandra K. Kostyk, Mayke Oosterloo, Annie Killoran, Erin Furr Stimming, Matthias Dose, Travis Cruickshank, Thomas D. Bird, Louise Vetter, Astri Arnesen, James Valvano, Herwig W. Lange, Daniel O. Claassen
Research outputs 2022 to 2026
BackgroundHuntington disease (HD) is a genetic neurodegenerative disorder. Given the focus on motor manifestations, nonmotor symptoms are frequently underappreciated in clinical evaluations, despite frequently contributing to primary functional impairment.Recent FindingsA diagnosis of motor-onset as the definition of manifest symptoms misrepresents the complex nature of HD presentation. Despite recent attempt to integrate nonmotor diagnostic criteria, practical guidelines are necessary to inform clinical diagnosis. We propose an HD diagnostic framework and staging system that prioritizes genetic testing, integrates motor and nonmotor symptom considerations in the determination of clinical disease onset and severity, and acknowledges the secondary role of clinically indicated diagnostic assessments, …
To Discard Or Not To Discard 1pns? A Systematic Review And Meta-Analysis On 291,474 Embryos, T. Lee, F. Qi, K. Peirce, J. Natalwala, V. Chapple, P. J. Mark, K. Sanders, Y. Liu
To Discard Or Not To Discard 1pns? A Systematic Review And Meta-Analysis On 291,474 Embryos, T. Lee, F. Qi, K. Peirce, J. Natalwala, V. Chapple, P. J. Mark, K. Sanders, Y. Liu
Research outputs 2022 to 2026
Unlike embryos that display two pronuclei (2PN), monopronucleated (1PN) embryos are assumed to be haploid and can be routinely discarded. Although there are reports of live births after 1PN embryo transfer, the developmental and clinical prognosis of 1PN embryos has not been systematically evaluated. The aim of this review was to elucidate the developmental, clinical and neonatal outcomes of 1PN embryos compared with 2PN embryos. Twenty-four studies met the inclusion criteria. The blastulation rate was lower in 1PN embryos compared with 2PN embryos [risk ratio (RR) 0.50, 95% CI 0.48–0.51]. The live birth rate was lower in 1PN blastocysts when …
Establishment Of Reference Intervals For Serum Immunoglobulin G N-Glycosylation Features In Healthy Chinese Adults: A Nationwide Survey In The Framework Of Predictive, Preventive, And Personalized Medicine, Changyu Liu, Yinghao Wang, Xingang Li, Xiaojia Xu, Ruirui Xu, Cuihong Tian, Zhixian Chen, Xinxia Lu, Yuejin Li, Meng Wang, Zhaoyang Tang, Xueyu Chen, Guoyong Ding, Xuerui Tan, Dong Li, Haifeng Hou, Wei Wang
Establishment Of Reference Intervals For Serum Immunoglobulin G N-Glycosylation Features In Healthy Chinese Adults: A Nationwide Survey In The Framework Of Predictive, Preventive, And Personalized Medicine, Changyu Liu, Yinghao Wang, Xingang Li, Xiaojia Xu, Ruirui Xu, Cuihong Tian, Zhixian Chen, Xinxia Lu, Yuejin Li, Meng Wang, Zhaoyang Tang, Xueyu Chen, Guoyong Ding, Xuerui Tan, Dong Li, Haifeng Hou, Wei Wang
Research outputs 2022 to 2026
Background: Immunoglobulin G (IgG) N-glycosylation plays a vital role in the pathogenesis of autoimmune disorders, inflammatory diseases, and viral infections. While various models of serum IgG N-glycosylation have been developed to identify individuals at high risk for relevant diseases, reference intervals (RIs) for the levels of IgG N-glycans have not been established yet. Identifying RIs for serum IgG N-glycans closely associated with biological aging and disease risk contributes to predictive, preventive, and personalized medicine (PPPM/3PM), which results in improvement of patients’ outcomes, enhancement of healthcare efficiency, and in reducing burden of chronic diseases. This study is aimed at defining the …
Circulating Lipocalin-2 Across The Adult Lifespan, Carlie Bauer, Cassandra Smith, Sara Vogrin, Andrew S. Palmer, Mary Woessner, Shanie Landen, Macsue Jacques, Elizabeth Byrnes, Nir Eynon, Marc Sim, Joshua R. Lewis, Itamar Levinger
Circulating Lipocalin-2 Across The Adult Lifespan, Carlie Bauer, Cassandra Smith, Sara Vogrin, Andrew S. Palmer, Mary Woessner, Shanie Landen, Macsue Jacques, Elizabeth Byrnes, Nir Eynon, Marc Sim, Joshua R. Lewis, Itamar Levinger
Research outputs 2022 to 2026
Lipocalin-2 (LCN2), a hormone produced by adipocytes, osteoblasts and renal tubular cells, is implicated in age-related diseases, including cardio-metabolic disease. To understand the role LCN2 may play in pathological states, we first need to elucidate the relationship between circulating LCN2 with indices of cardio-metabolic health during “normal” ageing. This study examined the relationship between serum levels of LCN2, age and cardio-metabolic measures across the adult lifespan in males and females. We conducted a pooled cohort analysis including 124 community-dwelling males (n = 52) and females (n = 72) (age 20 - 87 years, median BMI 25.92 (23.04, 29.81) kg/m2). Serum …
Diagnostic Power Of Serum Creatinine/Cystatin C Ratio For Identifying Low Mri-Muscle Volume And Low Grip Strength: Data From 9 731 To 149 707 Uk Biobank Older Adults, Ben Kirk, Chia Ling Kuo, Peiran Liu, Meiruo Xiang, Jesse Zanker, Konstantinos Prokopidis, Marc Sim, Richard H. Fortinsky, George A. Kuchel, Gustavo Duque
Diagnostic Power Of Serum Creatinine/Cystatin C Ratio For Identifying Low Mri-Muscle Volume And Low Grip Strength: Data From 9 731 To 149 707 Uk Biobank Older Adults, Ben Kirk, Chia Ling Kuo, Peiran Liu, Meiruo Xiang, Jesse Zanker, Konstantinos Prokopidis, Marc Sim, Richard H. Fortinsky, George A. Kuchel, Gustavo Duque
Research outputs 2022 to 2026
BACKGROUND: Biomarkers for sarcopenia are lacking. We examined the diagnostic power of serum creatinine to cystatin C ratio for identifying low magnetic resonance imaging-muscle volume and low grip strength in a large observational study of UK Biobank older adults. METHODS: Serum creatinine and cystatin C were measured via immunoassays (Beckman Coulter AU5800 and Siemens Advia 1800, respectively) and grip strength by hydraulic hand dynamometer at baseline visit (2008-2010). magnetic resonance imaging-thigh fat-free muscle volume and DXA-derived appendicular lean mass were measured at imaging visit (2014-2018). Extreme outliers were removed, and covariates (demographic, lifestyle, and clinical factors, as well as time …
Genome-Wide Cross-Disease Analyses Highlight Causality And Shared Biological Pathways Of Type 2 Diabetes With Gastrointestinal Disorders, Emmanuel O. Adewuyi, Tenielle Porter, Eleanor K. O’Brien, Oladapo Olaniru, Giuseppe Verdile, Simon M. Laws
Genome-Wide Cross-Disease Analyses Highlight Causality And Shared Biological Pathways Of Type 2 Diabetes With Gastrointestinal Disorders, Emmanuel O. Adewuyi, Tenielle Porter, Eleanor K. O’Brien, Oladapo Olaniru, Giuseppe Verdile, Simon M. Laws
Research outputs 2022 to 2026
Studies suggest links between diabetes and gastrointestinal (GI) traits; however, their underlying biological mechanisms remain unclear. Here, we comprehensively assess the genetic relationship between type 2 diabetes (T2D) and GI disorders. Our study demonstrates a significant positive global genetic correlation of T2D with peptic ulcer disease (PUD), irritable bowel syndrome (IBS), gastritis-duodenitis, gastroesophageal reflux disease (GERD), and diverticular disease, but not inflammatory bowel disease (IBD). We identify several positive local genetic correlations (negative for T2D – IBD) contributing to T2D’s relationship with GI disorders. Univariable and multivariable Mendelian randomisation analyses suggest causal effects of T2D on PUD and gastritis-duodenitis and …
Complete Genome Sequences Of Toxigenic Clostridioides Difficile Isolated From Australian Feral Horses, Natasza Hain-Saunders, Daniel R. Knight, Mieghan Bruce, Thomas V. Riley
Complete Genome Sequences Of Toxigenic Clostridioides Difficile Isolated From Australian Feral Horses, Natasza Hain-Saunders, Daniel R. Knight, Mieghan Bruce, Thomas V. Riley
Research outputs 2022 to 2026
Recent increases in community-associated Clostridioides difficile infections have highlighted the importance of monitoring toxigenic C. difficile from animal and environmental sources. We provide the complete circularized genomes of two toxigenic C. difficile strains isolated from feral horse faeces. Genome N64 (sequence type 964) consists of a single chromosome of 4,078,791 bp, while genome H251 (sequence type 963) comprises one chromosome (4,304,722 bp) and three plasmids (150,942 bp, 11,534 bp, and 9,074 bp).
Potentially Causal Association Between Immunoglobulin G N-Glycans And Cardiometabolic Diseases: Bidirectional Two-Sample Mendelian Randomization Study, Xiaoni Meng, Di Liu, Meiling Cao, Wei Wang, Youxin Wang
Potentially Causal Association Between Immunoglobulin G N-Glycans And Cardiometabolic Diseases: Bidirectional Two-Sample Mendelian Randomization Study, Xiaoni Meng, Di Liu, Meiling Cao, Wei Wang, Youxin Wang
Research outputs 2022 to 2026
Background: Observational studies support that altered immunoglobulin G (IgG) N-glycosylation and inflammatory factors are associated with cardiometabolic diseases (CMDs); nevertheless, the causality between them remains unclear. Methods: Two-sample Mendelian randomization (MR) analyses were conducted to systematically investigate the bidirectional causality between IgG N-glycans and nine CMDs in both East Asians and Europeans. Results: In the forward MR analysis, the univariable MR analysis presented suggestive causality of 14 and eight genetically instrumented IgG N-glycans with CMDs in East Asians and Europeans, respectively; the multivariable MR analysis showed that ten and 11 pairs of glycan-CMD associations were identified in East Asian and …
Anti-Inflammatory And Anti-(Lymph)Angiogenic Properties Of An Abcb5+ Limbal Mesenchymal Stem Cell Population, Berbang Meshko, Thomas L. A. Volatier, Johanna Mann, Mark A. Kluth, Christoph Ganss, Markus H. Frank, Natasha Y. Frank, Bruce R. Ksander, Claus Cursiefen, Maria Notara
Anti-Inflammatory And Anti-(Lymph)Angiogenic Properties Of An Abcb5+ Limbal Mesenchymal Stem Cell Population, Berbang Meshko, Thomas L. A. Volatier, Johanna Mann, Mark A. Kluth, Christoph Ganss, Markus H. Frank, Natasha Y. Frank, Bruce R. Ksander, Claus Cursiefen, Maria Notara
Research outputs 2022 to 2026
Corneal transparency and avascularity are essential for vision. The avascular cornea transitions into the vascularized conjunctiva at the limbus. Here, we explore a limbal stromal cell sub-population that expresses ABCB5 and has mesenchymal stem cell characteristics. Human primary corneal stromal cells were enriched for ABCB5 by using FACS sorting. ABCB5+ cells expressed the MSC markers CD90, CD73, and CD105. ABCB5+ but not ABCB5− cells from the same donor displayed evidence of pluripotency with a significantly higher colony-forming efficiency and the ability of trilineage differentiation (osteogenic, adipogenic, and chondrogenic). The ABCB5+ cell secretome demonstrated lower levels of the pro-inflammatory protein MIF …
Methylgenotyper: Accurate Estimation Of Snp Genotypes And Genetic Relatedness From Dna Methylation Data, Yi Jiang, Minghan Qu, Minghui Jiang, Xuan Jiang, Shane Fernandez, Tenielle Porter, Simon M. Laws, Colin L. Masters, Huan Guo, Shanshan Cheng, Chaolong Wang
Methylgenotyper: Accurate Estimation Of Snp Genotypes And Genetic Relatedness From Dna Methylation Data, Yi Jiang, Minghan Qu, Minghui Jiang, Xuan Jiang, Shane Fernandez, Tenielle Porter, Simon M. Laws, Colin L. Masters, Huan Guo, Shanshan Cheng, Chaolong Wang
Research outputs 2022 to 2026
Epigenome-wide association studies (EWAS) are susceptible to widespread confounding caused by population structure and genetic relatedness. Nevertheless, kinship estimation is challenging in EWAS without genotyping data. Here, we proposed MethylGenotyper, a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms (SNPs) directly from commercial DNA methylation microarrays. We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm. We conducted extensive simulations to demonstrate the performance of the method. When applying MethylGenotyper to the Infinium EPIC array data …
Bidirectional Two-Sample Mendelian Randomization Study Of Immunoglobulin G N-Glycosylation And Senescence-Associated Secretory Phenotype, Haotian Wang, Di Liu, Xiaoni Meng, Wenxin Sun, Cancan Li, Huimin Lu, Deqiang Zheng, Lijuan Wu, Shengzhi Sun, Youxin Wang
Bidirectional Two-Sample Mendelian Randomization Study Of Immunoglobulin G N-Glycosylation And Senescence-Associated Secretory Phenotype, Haotian Wang, Di Liu, Xiaoni Meng, Wenxin Sun, Cancan Li, Huimin Lu, Deqiang Zheng, Lijuan Wu, Shengzhi Sun, Youxin Wang
Research outputs 2022 to 2026
Observational studies revealed changes in Immunoglobulin G (IgG) N-glycosylation during the aging process. However, it lacks causal insights and remains unclear in which direction causal relationships exist. The two-sample bidirectional Mendelian randomization (MR) design was adopted to explore causal associations between IgG N-glycans and the senescence-associated secretory phenotype (SASP). Inverse variance weighted (IVW) and Wald ratio methods were used as the main analyses, supplemented by sensitivity analyses. Forward MR analyses revealed causal associations between the glycan peak (GP) and SASP, including GP6 (odds ratio [OR] = 0.428, 95% confidence interval [CI] = 0.189–0.969) and GP17 (OR = 0.709, 95%CI = …
Investigating The Genetic Makeup Of The Major Histocompatibility Complex (Mhc) In The United Arab Emirates Population Through Next-Generation Sequencing, Nour A. D. Marzouka, Halima Alnaqbi, Amira Al-Aamri, Guan Tay, Habiba Alsafar
Investigating The Genetic Makeup Of The Major Histocompatibility Complex (Mhc) In The United Arab Emirates Population Through Next-Generation Sequencing, Nour A. D. Marzouka, Halima Alnaqbi, Amira Al-Aamri, Guan Tay, Habiba Alsafar
Research outputs 2022 to 2026
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the …
Application Of Genomics And Epigenetics In Disease And Syndrome Classification, Yanqi Dang, Wei Wang, Aiping Lyu, Lisheng Wang, Guang Ji
Application Of Genomics And Epigenetics In Disease And Syndrome Classification, Yanqi Dang, Wei Wang, Aiping Lyu, Lisheng Wang, Guang Ji
Research outputs 2022 to 2026
No abstract provided.
Variations In The Germinal Center Response Revealed By Genetically Diverse Mouse Strains, Anne Marie Aubin, Daria Vdovenko, Roxanne Collin, Lois Balmer, Lise Coderre, Grant Morahan, Félix Lombard-Vadnais, Sylvie Lesage
Variations In The Germinal Center Response Revealed By Genetically Diverse Mouse Strains, Anne Marie Aubin, Daria Vdovenko, Roxanne Collin, Lois Balmer, Lise Coderre, Grant Morahan, Félix Lombard-Vadnais, Sylvie Lesage
Research outputs 2022 to 2026
The humoral response is complex and involves multiple cellular populations and signaling pathways. Bacterial and viral infections, as well as immunization regimens, can trigger this type of response, promoting the formation of microanatomical cellular structures called germinal centers (GCs). GCs formed in secondary lymphoid organs support the differentiation of high-affinity plasma cells and memory B cells. There is growing evidence that the quality of the humoral response is influenced by genetic variants. Using 12 genetically divergent mouse strains, we assessed the impact of genetics on GC cellular traits. At steady state, in the spleen, lymph nodes and Peyer's patches, we …
Systemic Treatment Of Recessive Dystrophic Epidermolysis Bullosa With Mesenchymal Stromal Cells: A Scoping Review Of The Literature And Conclusions For Future Clinical Research, Elke Niebergall-Roth, Kathrin Dieter, Markus H. Frank, Mark A. Kluth
Systemic Treatment Of Recessive Dystrophic Epidermolysis Bullosa With Mesenchymal Stromal Cells: A Scoping Review Of The Literature And Conclusions For Future Clinical Research, Elke Niebergall-Roth, Kathrin Dieter, Markus H. Frank, Mark A. Kluth
Research outputs 2022 to 2026
Background: The ability of mesenchymal stromal cells (MSCs) to facilitate regenerative responses in inflamed and injured tissues, coupled with preclinical data suggesting potential to restore defective collagen VII at the dermo-epidermal junction, has raised the hope that MSCs may provide an effective disease-modifying therapy for patients suffering from recessive dystrophic epidermolysis bullosa (RDEB). Methods: We present a descriptive analysis of the clinical research on systemic MSC administration to RDEB patients available in PubMed, including six early-phase studies and one case report, involving 59 patients who received 1–3 intravenous infusions of MSCs from various sources. Results: Based on 133 MSC infusions, …
Glycan Clock Of Ageing—Analytical Precision And Time-Dependent Inter- And I-Individual Variability, Borna Rapčan, Manshu Song, Azra Frkatović-Hodžić, Tea Pribić, Jakov Vuk, Anđelo Beletić, Maja Hanić, Julija Jurić, Petra Tominac, Josip Milas, Vedrana Ivić, Sven Viland, Sara Bonet, Branko Šego, Marija Heffer, Wei Wang, Michael P. Snyder, Gordan Lauc
Glycan Clock Of Ageing—Analytical Precision And Time-Dependent Inter- And I-Individual Variability, Borna Rapčan, Manshu Song, Azra Frkatović-Hodžić, Tea Pribić, Jakov Vuk, Anđelo Beletić, Maja Hanić, Julija Jurić, Petra Tominac, Josip Milas, Vedrana Ivić, Sven Viland, Sara Bonet, Branko Šego, Marija Heffer, Wei Wang, Michael P. Snyder, Gordan Lauc
Research outputs 2022 to 2026
Ageing is a complex biological process with variations among individuals, leading to the development of ageing clocks to estimate biological age. Glycans, particularly in immunoglobulin G (IgG), have emerged as potential biomarkers of ageing, with changes in glycosylation patterns correlating with chronological age. For precision analysis, three different plasma pools were analysed over 26 days in tetraplicates, 312 samples in total. In short-term variability analysis, two cohorts were analysed: AstraZeneca MFO cohort of 26 healthy individuals (median age 20) and a cohort of 70 premenopausal Chinese women (median age 22.5) cohort monitored over 3 months. Long-term variability analysis involved two …