Article
Multidisciplinary Sciences
Veronica J. Vieland, Sang-Cheol Seok
Summary: The study aims to explore the performance of TE-PPLD in the context of small to moderate sample sizes, comparing it with Cox Proportional Hazards analysis. The results will help inform the future application in the DMD study, demonstrating the advantages of TE-PPLD and the original PPLD over regression-based GWAS approaches in this context.
Review
Multidisciplinary Sciences
David O. Enoma, Janet Bishung, Theresa Abiodun, Olubanke Ogunlana, Victor Chukwudi Osamor
Summary: This article discusses the applications and future trends of machine learning algorithms in genome-wide association studies (GWAS) to better understand the effects of population genetic variants. The study found that algorithms such as classification, regression, ensemble, and neural networks have been applied to GWAS and their application areas are comprehensively discussed.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2022)
Article
Genetics & Heredity
Jin Zhang, Min Chen, Yangjun Wen, Yin Zhang, Yunan Lu, Shengmeng Wang, Juncong Chen
Summary: The newly developed FastRR algorithm under the MLM framework shows superior power in detecting and estimating the effects of multiple genetic markers on traits, providing a more accurate and stable approach for both large and small QTN detection. Compared with existing methods, FastRR algorithm also offers the advantage of high computing speed in high dimensional genomic datasets.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Xuehang Xiong, Jianxin Li, Pingping Su, Haiyang Duan, Li Sun, Shuhao Xu, Yan Sun, Haidong Zhao, Xiaoyang Chen, Dong Ding, Xuehai Zhang, Jihua Tang
Summary: Through comparative analysis of GWAS models, this study identified 140 quantitative trait nucleotides (QTNs) associated with maize chlorophyll content, involving 481 genes and explaining 0.29-10.28% of phenotypic variation. The GRMZM2G110408 (ZmCCS3) gene was identified by multiple models and in multiple environments, and its encoded protein likely contributes to chlorophyll biosynthesis. These findings are important for ideotype-based breeding of new maize varieties with high photosynthetic efficiency.
Article
Plant Sciences
Liqiang He, Yao Sui, Yanru Che, Huixian Wang, Khalid Y. Rashid, Sylvie Cloutier, Frank M. You
Summary: This study evaluated the resistance of 445 flax accessions to pasmo, a disease caused by the fungus Septoria linicola. Genetic analysis identified numerous QTNs associated with pasmo resistance, providing potential targets for improving resistance in flax breeding programs. Additionally, the study discovered candidate genes and gene-environment interactions that contribute to pasmo resistance in flax.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Guogen Zhang, Zhiyuan Bi, Jing Jiang, Jingbing Lu, Keyang Li, Di Bai, Xinchen Wang, Xueyu Zhao, Min Li, Xiuqin Zhao, Wensheng Wang, Jianlong Xu, Zhikang Li, Fan Zhang, Yingyao Shi
Summary: By utilizing genome-wide association and epistasis analysis (GWAES), the genetic basis of rice saline-alkali tolerance was studied. A total of 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified, explaining a significant portion of the phenotypic variation of saline-alkali tolerance. Most of these QTNs were located in genomic regions associated with saline-alkali tolerance or known genes. The finding of candidate genes and favorable haplotypes provides valuable information for genetic improvement of rice saline-alkali tolerance.
FRONTIERS IN PLANT SCIENCE
(2023)
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
Biochemical Research Methods
Shanwen Sun, Benzhi Dong, Quan Zou
Summary: Genome-wide association studies (GWAS) have made significant progress in discovering genetic variants underlying complex human diseases and agriculturally important traits over the last decade. However, challenges such as detecting epistasis, SNPs with small effects, and distinguishing causal variants still exist. Advancements in statistical modeling and machine learning are driving improvements in GWAS analyses, while state-of-the-art tools are being developed to enhance signal detection and prioritize SNPs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Mingyang Quan, Xin Liu, Qingzhang Du, Liang Xiao, Wenjie Lu, Yuanyuan Fang, Peng Li, Li Ji, Deqiang Zhang
Summary: This study utilized a systems genetics approach to investigate the genetic architecture and regulatory pathways of photosynthesis and wood properties in Populus tomentosa, revealing coordinated regulatory networks for these two processes. A total of 222 significant single-nucleotide polymorphisms and 74 epistatic interactions were detected, providing insights into the transcriptional regulatory networks of candidate genes coordinating photosynthesis and wood properties. Furthermore, heterologous expression experiments demonstrated the regulatory roles of two pleiotropic genes in balancing photosynthesis and wood formation, which could aid in genetic breeding and molecular design in trees.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Yu Zhong Peng, Yanmei Lin, Yiran Huang, Ying Li, Guangsheng Luo, Jianping Liao
Summary: The study introduces a novel method named GEP-EpiSeeker, based on Gene Expression Programming algorithm, for identifying epistatic interactions in Genome-wide Association Studies. Experimental results demonstrate that GEP-EpiSeeker outperforms comparative methods in detecting epistasis.
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
Biochemical Research Methods
Gizem Caylak, Oznur Tastan, A. Ercument Cicek
Summary: Potpourri is a tool for detecting interacting SNP pairs, diversifying the selected SNPs' genomic regions and investigating their co-occurrence patterns. It can input and prioritize SNPs in regulatory or coding regions for testing. The program identifies and returns a list of prioritized SNP pairs for epistasis testing.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Plant Sciences
Liqiang He, Huixian Wang, Yao Sui, Yuanyuan Miao, Cheng Jin, Jie Luo
Summary: In this study, GWAS was conducted using amino acid content and high-quality SNPs of rice accessions, and different methods were compared. The results showed that the use of the 3VmrMLM method could identify the most QTNs and stable QTLs, and candidate genes were found to be involved in important metabolic pathways. Additionally, this method could detect QTN-by-environment interactions for five FAA levels. These findings are important for molecular breeding of rice and understanding FAA accumulation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Caroline Ariyoshi, Gustavo Cesar Sant'ana, Mariane Silva Felicio, Gustavo Hiroshi Sera, Livia Maria Nogueira, Lucas Mateus Rivero Rodrigues, Rafaelle Vecchia Ferreira, Bruna Silvestre Rodrigues da Silva, Mario Lucio Vilela de Resende, Suzete Aparecida Lanza Destefano, Douglas Silva Domingues, Luiz Filipe Protasio Pereira
Summary: Bacteria halo blight, caused by Pseudomonas syringae pv. garcae, is a significant disease in coffee plants, particularly in mountain regions and mild climate areas. This study focused on identifying genetic factors associated with resistance to this disease in Ethiopian accessions of Coffea arabica. The research utilized population structure analysis and genome-wide association study (GWAS) to identify quantitative trait nucleotides (QTNs) linked to resistance. The findings provide valuable insights into the genetic control of resistance to bacteria halo blight in Coffea arabica and contribute to the understanding of the domestication history of this species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Muhammad Ikram, Ruiqiang Lai, Yanshi Xia, Ronghua Li, Weicai Zhao, Kadambot H. M. Siddique, Jianjun Chen, Peiguo Guo
Summary: This study identified novel stable QTNs and candidate genes associated with plant height in tobacco through measuring plant height of 94 tobacco accessions and conducting a genome-wide association study. The findings provide important information for investigating the genetic basis and molecular breeding of tobacco.
Article
Biochemistry & Molecular Biology
Marta Marquie, Fernando Garcia-Gutierrez, Adelina Orellana, Laura Montrreal, Itziar de Rojas, Pablo Garcia-Gonzalez, Raquel Puerta, Claudia Olive, Amanda Cano, Isabel Hernandez, Maitee Rosende-Roca, Liliana Vargas, Juan Pablo Tartari, Ester Esteban-De Antonio, Urszula Bojaryn, Mario Ricciardi, Diana M. Ariton, Vanesa Pytel, Montserrat Alegret, Gemma Ortega, Ana Espinosa, Alba Perez-Cordon, Angela Sanabria, Nathalia Munoz, Nuria Lleonart, Nuria Aguilera, Ainhoa Garcia-Sanchez, Emilio Alarcon-Martin, Lluis Tarraga, Agustin Ruiz, Merce Boada, Sergi Valero
Summary: This study found that the association between Alzheimer's disease biomarkers and neuropsychiatric symptoms has a significant impact on the conversion to dementia in patients with mild cognitive impairment. A total of 500 individuals with MCI were followed-up yearly, and it was found that certain AT(N) profiles and the presence of depression and apathy were associated with a higher risk of conversion. The additive combination of AT(N) profile with depression exacerbates the risk of conversion, and a synergic effect of prodromal AD profile with depressive symptoms is evidenced.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Pablo Garcia-Gonzalez, Itziar de Rojas, Sonia Moreno-Grau, Laura Montrreal, Raquel Puerta, Emilio Alarcon-Martin, Ines Quintela, Adela Orellana, Victor Andrade, Pamela V. Martino Adami, Stefanie Heilmann-Heimbach, Pilar Gomez-Garre, Maria Teresa Perinan, Ignacio Alvarez, Monica Diez-Fairen, Raul Nunez Llaves, Claudia Olive Roig, Guillermo Garcia-Ribas, Manuel Menendez-Gonzalez, Carmen Martinez, Miquel Aguilar, Mariateresa Buongiorno, Emilio Franco-Macias, Maria Eugenia Saez, Amanda Cano, Maria J. Bullido, Luis Miguel Real, Eloy Rodriguez-Rodriguez, Jose Luis Royo, Victoria Alvarez, Pau Pastor, Gerard Pinol-Ripoll, Pablo Mir, Miguel Calero Lara, Miguel Medina Padilla, Pascual Sanchez-Juan, Angel Carracedo, Sergi Valero, Isabel Hernandez, Lluis Tarraga, Alfredo Ramirez, Merce Boada, Agustin Ruiz
Summary: Mosaic loss of chromosome Y (mLOY) is a common somatic event associated with Alzheimer's disease (AD) and can be age-confounded in genome-wide association studies. This study used Mendelian randomisation to construct an age-independent mLOY polygenic risk score (mloy-PRS) and found that higher genetic risk for mLOY was associated with faster progression to AD in men with mild cognitive impairment. The study suggests that mLOY is involved in AD pathogenesis and shows associations with cerebrospinal fluid biomarkers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Itziar de Rojas, Laura del Barrio, Isabel Hernandez, Laura Montrreal, Pablo Garcia-Gonzalez, Marta Marquie, Sergi Valero, Amanda Cano, Adelina Orellana, Merce Boada, Santos Manes, Agustin Ruiz
Summary: Cholesterol efflux capacity (CEC), which is closely related to Alzheimer's disease and other clinical conditions, is determined by APOE genotype and plasma metabolome profile. In this study, it was found that plasma 3-hydroxybutyrate and male sex were strongly correlated with CEC. Most NMR particles associated with CEC were not correlated with APOE genotype. The study confirmed the impact of APOE genotype on plasma lipoprotein particles and omega-3 fatty acids independently of plasma cholesterol level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Infectious Diseases
M. Santos, A. Corma-Gomez, M. Fernandez-Fuertes, A. Gonzalez-Serna, P. Rincon, L. M. Real, J. A. Pineda, J. Macias
Summary: This study investigated the prevalence and causes of significant liver damage among 619 people living with HIV. The results showed that 18.2% of the patients had significant liver damage, with 35.7% attributed to nonviral liver damage, mainly metabolic associated steatohepatitis. The study concluded that the burden of liver damage remains high among people living with HIV after HIV/HCV coinfection microelimination.
JOURNAL OF INFECTION
(2023)
Article
Neurosciences
Javier Villadiego, Juan Garcia-Arriaza, Reposo Ramirez-Lorca, Roberto Garcia-Swinburn, Daniel Cabello-Rivera, Alicia E. Rosales-Nieves, Maria I. Alvarez-Vergara, Fernando Cala-Fernandez, Ernesto Garcia-Roldan, Juan L. Lopez-Ogayar, Carmen Zamora, David Astorgano, Guillermo Albericio, Patricia Perez, Ana M. Munoz-Cabello, Alberto Pascual, Mariano Esteban, Jose Lopez-Barneo, Juan Jose Toledo-Aral
Summary: In this study using a transgenic mouse model, it was found that SARS-CoV-2 primarily replicates in neurons in the brain, causing neuronal loss, glial activation, and vascular damage. However, vaccination with the MVA-CoV2-S vaccine provided full protection against cerebral infection and associated damage, even after reinfection.
NATURE NEUROSCIENCE
(2023)
Review
Pharmacology & Pharmacy
Amanda Cano, Alvaro Munoz-Morales, Elena Sanchez-Lopez, Miren Ettcheto, Eliana B. Souto, Antonio Camins, Merce Boada, Agustin Ruiz
Summary: Neurodegenerative diseases have unknown etiology in many cases and lack effective treatments. The blood-brain barrier poses a challenge for drug delivery. Exosomes, secreted vesicles, have emerged as promising therapeutic tools due to their natural origin and molecular similarities. They are particularly promising for targeting neurodegenerative diseases due to the difficulty of accessing the brain and the complexity of the diseases.
Article
Biochemistry & Molecular Biology
Francisco Mayo, Lourdes Gonzalez-Vinceiro, Laura Hiraldo-Gonzalez, Claudia Calle-Castillejo, Sara Morales-Alvarez, Reposo Ramirez-Lorca, Miriam Echevarria
Summary: Aquaporin-4 (AQP4) is a water channel that is abundant in the central nervous system and plays a key role in maintaining water balance. While its expression and function in adults are well-established, little is known about its expression and localization during postnatal development. This study examined the expression of AQP4 mRNA and protein in the brain and spinal cord of mice at different stages of postnatal development. The results revealed changes in the expression and localization of AQP4 during early development, suggesting a potential role for AQP4 in early cell differentiation and myelination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Amanda Cano, Ester Esteban-de-Antonio, Mireia Bernuz, Raquel Puerta, Pablo Garcia-Gonzalez, Itziar de Rojas, Claudia Olive, Alba Perez-Cordon, Laura Montrreal, Raul Nunez-Llaves, Oscar Sotolongo-Grau, Emilio Alarcon-Martin, Sergi Valero, Montserrat Alegret, Elvira Martin, Pamela V. Martino-Adami, Miren Ettcheto, Antonio Camins, Assumpta Vivas, Marta Gomez-Chiari, Miguel angel Tejero, Adelina Orellana, Lluis Tarraga, Marta Marquie, Alfredo Ramirez, Merce Marti, Maria Isabel Pividori, Merce Boada, Agustin Ruiz
Summary: Alzheimer's disease (AD) is commonly preceded by a prodromal phase characterized by high levels of A beta and p-tau-mediated neuronal injury and mild cognitive impairment (MCI). Differential diagnosis of MCI causes in these prodromal stages is a challenge for clinicians. Blood biomarkers, particularly plasma extracellular vesicles (pEVs), are emerging as potential tools for early AD detection.
JOURNAL OF NANOBIOTECHNOLOGY
(2023)
Article
Neurosciences
Marta Marquie, Ainhoa Garcia-Sanchez, Emilio Alarcon-Martin, Joan Martinez, Miguel Castilla-Marti, Luis Castilla-Marti, Adelina Orellana, Laura Montrreal, Itziar de Rojas, Pablo Garcia-Gonzalez, Raquel Puerta, Claudia Olive, Amanda Cano, Isabel Hernandez, Maitee Rosende-Roca, Liliana Vargas, Juan Pablo Tartari, Ester Esteban-De Antonio, Urszula Bojaryn, Mario Ricciardi, Diana M. Ariton, Vanesa Pytel, Montserrat Alegret, Gemma Ortega, Ana Espinosa, Alba Perez-Cordon, Angela Sanabria, Nathalia Munoz, Nuria Lleonart, Nuria Aguilera, Lluis Tarraga, Sergi Valero, Agustin Ruiz, Merce Boada
Summary: This study aimed to investigate the association between macular vessel density measured by optical coherence tomography angiography (OCT-A) and the AT(N) classification based on cerebrospinal fluid (CSF) biomarkers in individuals with mild cognitive impairment (MCI). The results showed that there was no association between macular vessel density measures and the AT(N) classification in MCI patients.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Medicine, General & Internal
Jiao Luo, Jesper Qvist Thomassen, Celine Bellenguez, Benjamin Grenier-Boley, Itziar de Rojas, Atahualpa Castillo, Kayenat Parveen, Fahri Kuecuekali, Aude Nicolas, Oliver Peters, Anja Schneider, Martin Dichgans, Dan Rujescu, Norbert Scherbaum, Deckert Juergen, Steffi Riedel-Heller, Lucrezia Hausner, Laura Molina Porcel, Emrah Duezel, Timo Grimmer, Jens Wiltfang, Stefanie Heilmann-Heimbach, Susanne Moebus, Thomas Tegos, Nikolaos Scarmeas, Jordi Clarimon, Fermin Moreno, Jordi Perez-Tur, Maria J. Bullido, Pau Pastor, Raquel Sanchez-Valle, Victoria Alvarez, Merce Boada, Pablo Garcia-Gonzalez, Raquel Puerta, Pablo Mir, Luis M. Real, Gerard Pinol-Ripoll, Jose Maria Garcia-Alberca, Jose Luis Royo, Eloy Rodriguez-Rodriguez, Hilkka Soininen, Teemu Kuulasmaa, Alexandre de Mendonca, Shima Mehrabian, Jakub Hort, Martin Vyhnalek, Sven van der Lee, Caroline Graff, Goran Papenberg, Vilmantas Giedraitis, Anne Boland, Delphine Bacq-Daian, Jean-Francois Deleuze, Gael Nicolas, Carole Dufouil, Florence Pasquier, Olivier Hanon, Stephanie Debette, Edna Gruenblatt, Julius Popp, Luisa Benussi, Daniela Galimberti, Beatrice Arosio, Patrizia Mecocci, Vincenzo Solfrizzi, Lucilla Parnetti, Alessio Squassina, Lucio Tremolizzo, Barbara Borroni, Benedetta Nacmias, Sandro Sorbi, Paolo Caffarra, Davide Seripa, Innocenzo Rainero, Antonio Daniele, Carlo Masullo, Gianfranco Spalletta, Julie Williams, Philippe Amouyel, Frank Jessen, Patrick Kehoe, Tsolaki Magda, Giacomina Rossi, Pascual Sanchez-Juan, Kristel Sleegers, Martin Ingelsson, Ole A. Andreassen, Mikko Hiltunen, Cornelia Van Duijn, Rebecca Sims, Wiesje van der Flier, Agustin Ruiz, Alfredo Ramirez, Jean-Charles Lambert, Ruth Frikke-Schmidt
Summary: This genetic association study identifies novel genetic associations between high HDL cholesterol concentrations and high systolic blood pressure with increased risk of AD, potentially inspiring new drug targeting and improved prevention implementation.
Article
Medicine, General & Internal
Javier Martinez-Sanz, Jorge Diaz-alvarez, Marta Rosas, Raquel Ron, Jose Antonio Iribarren, Enrique Bernal, Felix Gutierrez, Andres Ruiz Sancho, Noemi Cabello, Julian Olalla, Santiago Moreno, Sergio Serrano-Villar
Summary: The study suggests that a low CD4/CD8 ratio during HIV treatment is associated with immunosenescence. Data analysis shows that patients with a CD4/CD8 ratio less than 0.3 in the second year of ART have an increased risk of developing SNAEs in the next five years.
Article
Multidisciplinary Sciences
Luis Miguel Real, Maria E. Saez, Anais Corma-Gomez, Antonio Gonzalez-Perez, Christian Thorball, Rocio Ruiz, Maria Reyes Jimenez-Leon, Alejandro Gonzalez-Serna, Carmen Gasca-Capote, Maria Jose Bravo, Jose Luis Royo, Alberto Perez-Gomez, Maria Ines Camacho-Sojo, Isabel Gallego, Joana Vitalle, Sara Bachiller, Alicia Gutierrez-Valencia, Francisco Vidal, Jacques Fellay, Mathias Lichterfeld, Ezequiel Ruiz-Mateos, Swiss HIV Cohort Study
Summary: Some HIV controllers experience immunologic progression with CD4(+) T cell decline. Genetic factors associated with CD4(+) T cell decline in HIV controllers were identified. Specific genetic factors were found to be associated with the long-term non-progressor HIV spontaneous control phenotype.
