Article
Genetics & Heredity
Weijie Guo, Mengyuan Dai, Zhuoling Zhong, San Zhu, Guidong Gong, Mei Chen, Junling Guo, Yaoyao Zhang
Summary: This study used a two-sample Mendelian Randomization (2SMR) study to explore the causal relationship between genetically predicted vitamin D levels and the risk of Uterine Fibroids (UFs). The results indicate that elevated serum vitamin D levels are strongly related to a reduction in the risk of UFs, suggesting a potentially new and effective treatment option.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Hanxiao Chen, Ze Du, Yaoyao Zhang, Mengling Li, Rui Gao, Lang Qin, Hongjing Wang
Summary: Current studies indicate that there is no causal association between vitamin C and the risk of cancer. Further research is needed to discover the potential protective and therapeutic effects of vitamin C on cancer and its underlying mechanisms.
FRONTIERS IN GENETICS
(2022)
Article
Horticulture
D. S. Kishor, Yoonji Noh, Woon-Ho Song, Gung Pyo Lee, Younghoon Park, Jin-Kee Jung, Eun-Jo Shim, Sung-Chur Sim, Sang-Min Chung
Summary: East Asia's Oriental melon serves as an important fruit crop, with SNP genotyping proving useful in detecting genetic diversity and protecting breeders' rights. Through GBS, 5640 SNPs were detected in 48 melon varieties, with 164 successfully validated and used to classify 87 varieties into distinct groups. GWAS analyses revealed 18 significant SNPs associated with morphological traits, including potential candidate genes for sex expression.
SCIENTIA HORTICULTURAE
(2021)
Review
Plant Sciences
Hilde Nybom, Gunars Lacis
Summary: Recent national and international projects have focused on large-scale genotyping of vegetatively propagated crops, aiming to identify true-to-type plant material, detect synonyms, investigate genetic diversity, and create sustainable databases for research and breeding. Different DNA markers and next-generation sequencing methods have their advantages and disadvantages, with large-scale phenotyping methods lagging behind but crucial for understanding commercially important traits. Collaborative projects with broad-scale data collection are likely to produce more reliable results in the analysis of gene action and development of robust DNA markers.
Article
Biochemistry & Molecular Biology
Mesfin Haile, Nayoung Ro, Ho-Cheol Ko, Hyeonseok Oh, Gi-An Lee
Summary: In this study, the genetic basis of carotenoid and capsaicinoid content in Capsicum chinense germplasms was investigated, and significant variability in these traits was observed. Genome-wide association analysis identified several SNPs associated with carotenoids and capsaicinoids, and the function of the associated genes will be further studied. These findings have important implications for selecting pepper varieties with desirable traits and enhancing the nutritional and medicinal properties of pepper.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Do Yoon Hyun, Raveendar Sebastin, Gi-An Lee, Kyung Jun Lee, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, Man-Jung Kang, Seung Bum Lee, Ik Jang, Na-Young Ro, Gyu-Taek Cho
Summary: Melon is an economically important horticultural crop with rich morphological and genetic variability. Utilizing genotyping-by-sequencing (GBS)-derived SNP analysis, this study revealed the genetic structure and diversity among muskmelon, makuwa, and cantaloupes, showing rapid linkage disequilibrium decay in muskmelon varieties. Bayesian phylogenetic tree and haplotype analysis supported the intraspecific relationships among the three melon varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
V. G. Ishwarya Lakshmi, M. Sreedhar, V. JhansiLakshmi, C. Gireesh, Santosha Rathod, Rajaguru Bohar, Santosh Deshpande, R. Laavanya, K. N. S. Usha Kiranmayee, Sreedhar Siddi, S. Vanisri
Summary: This study identified marker-trait associations related to brown planthopper resistance in rice through SNP genotyping data and developed SNP markers for identifying resistant genotypes. The results showed that the Bph17 and Bph32 genes could be validated using gene specific SNPs and transferred to other rice varieties. This has important implications for breeding resistant rice varieties against the brown planthopper.
FRONTIERS IN GENETICS
(2022)
Article
Fisheries
Yu Zhou, Huang-Cui Fu, Ying-Ying Wang, He-Zhong Huang
Summary: In this study, a genome-wide association study (GWAS) was performed using mandarin fish to identify SNPs and candidate genes associated with growth traits. Many of the candidate genes were found to be related to bone differentiation, growth and development, cell division, and neurogenesis.
Article
Nutrition & Dietetics
George Dahma, Radu Neamtu, Razvan Nitu, Adrian Gluhovschi, Felix Bratosin, Mirela Loredana Grigoras, Carmen Silaghi, Cosmin Citu, Igwe Nwobueze Orlu, Sanket Bhattarai, Adelina Geanina Mocanu, Marius Craina, Elena Bernad
Summary: The study explores the effect of vitamin D supplementation on preventing preeclampsia. The findings suggest that pregnant women who supplemented with vitamin D have a lower risk of recurrent preeclampsia and gestational hypertension.
Article
Fisheries
Jie Ding, Yibo Zhang, Jiaying Wang, Cheng Liu, Xinming Gao, Yuanjie Wu, Jinqian Wang, Xiongfei Wu, Junquan Zhu, Weiliang Shen
Summary: This study genetically characterized the hypoxia tolerance in large yellow croaker using a genome-wide association study (GWAS). Four significant single-nucleotide polymorphisms (SNPs) were identified, and ten candidate genes related to hypoxia tolerance were determined. These findings provide new insights into breeding hypoxia-tolerant large yellow croaker.
Article
Chemistry, Multidisciplinary
Mi-Yeon Cha, Ja-Eun Choi, Da-Som Lee, So-Ra Lee, Sang-In Lee, Jong-Ho Park, Jin-Hee Shin, In Soo Suh, Byung Ho Kim, Kyung-Won Hong
Summary: This study confirmed six genetic skin indexes and identified SNP loci associated with facial skin characteristics. Although some previously identified SNPs were not replicated, this study has the potential to contribute to future research on cosmetic-related genes.
APPLIED SCIENCES-BASEL
(2022)
Article
Clinical Neurology
Viktor Grut, Martin Bistrom, Jonatan Salzer, Pernilla Stridh, Anna Lindam, Lucia Alonso-Magdalena, Oluf Andersen, Daniel Jons, Martin Gunnarsson, Magnus Vrethem, Johan Hultdin, Peter Sundstrom
Summary: This study found that high levels of free vitamin D3 at a young age reduce the risk of MS later in life, and also implicate a role for DBP in MS etiology.
EUROPEAN JOURNAL OF NEUROLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Manuel More, Eudosio Veli, Alan Cruz, Juan Pablo Gutierrez, Gustavo Gutierrez, F. Abel Ponce de Leon
Summary: This study aims to identify candidate genomic regions associated with fiber diameter in alpacas using whole genome association analysis. Four candidate regions were identified, and the genetic heritability and selection signature of SNPs were analyzed using different association methods.
Article
Biology
Abdullah Ali H. Alzahrani, Raed A. Alharbi, Mohammed Sarhan A. Alzahrani, Mohammed A. Sindi, Ghalia Shamlan, Faisal A. Alzahrani, Mohammad A. Albanghali, Abdulmajeed Abdulghani A. Sindi
Summary: This study conducted a case-control study on periodontitis and vitamin D levels in the Albaha region of Saudi Arabia, revealing a significant association between periodontitis and deficient or insufficient levels of vitamin D among Saudi adults.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Dev Paudel, Rocheteau Dareus, Julia Rosenwald, Maria Munoz-Amatriain, Esteban F. Rios
Summary: Cowpea, a major crop used for human consumption and livestock feed, has been studied for its genetic basis of flowering time through genome-wide association studies, revealing seven reliable SNP markers and candidate genes associated with flowering time, which could facilitate breeding efforts and knowledge transfer to other legume species.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Maria Pena-Chilet, Gema Roldan, Javier Perez-Florido, Francisco M. Ortuno, Rosario Carmona, Virginia Aquino, Daniel Lopez-Lopez, Carlos Loucera, Jose L. Fernandez-Rueda, Asuncion Gallego, Francisco Garcia-Garcia, Anna Gonzalez-Neira, Guillermo Pita, Rocio Nunez-Torres, Javier Santoyo-Lopez, Carmen Ayuso, Pablo Minguez, Almudena Avila-Fernandez, Marta Corton, Miguel Angel Moreno-Pelayo, Matias Morin, Alvaro Gallego-Martinez, Jose A. Lopez-Escamez, Salud Borrego, Guillermo Antinolo, Jorge Amigo, Josefa Salgado-Garrido, Sara Pasalodos-Sanchez, Beatriz Morte, Angel Carracedo, Angel Alonso, Joaquin Dopazo
Summary: The Collaborative Spanish Variability Server (CSVS) is a database containing genomes and exomes of unrelated Spanish individuals, generated through a crowdsourcing effort. It provides data support for studying disease variants and population genetic variations, with a web interface for querying and conducting pseudo-control studies for diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Mathematical & Computational Biology
Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Cubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, Maria Pena-Chilet, Joaquin Dopazo
Summary: The web interface presents a comprehensive mechanistic model of the SARS-CoV-2 disease map, allowing the inference of human signaling circuits' detailed activity from gene expression experiments. Additionally, it enables the study of potential interventions' effects and has the potential to be an invaluable asset in the search for efficient antiviral treatments.
Review
Oncology
Marisol Huerta, Susana Rosello, Luis Sabater, Ana Ferrer, Noelia Tarazona, Desamparados Roda, Valentina Gambardella, Clara Alfaro-Cervello, Marina Garces-Albir, Andres Cervantes, Maider Ibarrola-Villava
Summary: Pancreatic cancer is a highly challenging and poor prognosis malignancy. Liquid biopsy using circulating tumor DNA (ctDNA) shows great potential as a non-invasive biomarker for early diagnosis, prognosis, and management of the disease, although its sensitivity remains limited and cannot be used as a screening or diagnostic tool.
Editorial Material
Oncology
V. Gambardella, M. Ibarrola-Villaba, N. Tarazona, A. Cervantes
Article
Biochemistry & Molecular Biology
Macarena Lopez-Sanchez, Carlos Loucera, Maria Pena-Chilet, Joaquin Dopazo
Summary: Recent studies have shown the importance of host genetics in the prognosis of COVID-19. This study used a mathematical mechanistic model to identify potential interactions between rare disease genes and the COVID-19 infection process. Out of the analyzed disease genes, 254 genes directly affect the COVID-19 molecular disease mechanism and 207 genes have an indirect effect. These findings suggest the potential for preventive measures in some rare diseases based on the links between disease genes and COVID-19 hallmarks.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Carlos S. Casimiro-Soriguer, Carlos Loucera, Maria Pena-Chilet, Joaquin Dopazo
Summary: The gut microbiome has gained attention for its association with diseases like colorectal cancer and its potential to predict diseases through non-intrusive biomarkers. A meta-analysis of fecal metagenomic samples revealed that an interpretable machine learning approach based on functional profiles showed greater accuracy in predicting colorectal cancer compared to previous proposals. This approach was also effective in identifying samples with adenoma, making it promising for detecting early stages of colorectal cancer and facilitating intervention. Functional profiles provide insights into the molecular mechanisms behind these conditions and have demonstrated superior accuracy compared to taxonomic profiles.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
David Millan-Esteban, Maria Pena-Chilet, Zaida Garcia-Casado, Esperanza Manrique-Silva, Celia Requena, Jose Banuls, Jose Antonio Lopez-Guerrero, Aranzazu Rodriguez-Hernandez, Victor Traves, Joaquin Dopazo, Amaya Viros, Rajiv Kumar, Eduardo Nagore
Summary: The divergent pathway model suggests that cutaneous melanoma can be divided into two groups - one with a propensity for melanocyte proliferation and the other associated with cumulative solar damage. Molecular profiling using sequencing and bioinformatics tools revealed that nevogenic melanomas had mutations in BRAF, while CSD melanomas had mutations in NF1, ROS1, GNA11, and RAC1. This study concludes that nevogenic and CSD melanomas are distinct biological entities with implications for targeted therapies.
Meeting Abstract
Clinical Neurology
Ana M. Perez-Gutierrez, Rosario Carmona, Luis Javier Martinez-Gonzalez, Elena Lopez-Isac, Joaquin Dopazo, Jorge A. Cervilla, Blanca Gutierrez, Esther Molina, Juan Antonio Zarza-Rebollo, Maria Pena-Chilet, Daniel Lopez-Lopez, Javier Perez-Florido, Margarita Rivera
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Oncology
Yasemin C. Cole, Yu-Zhi Zhang, Beatrice Gallo, Adam P. Januszewski, Anca Nastase, David J. Essex, Caroline M. H. Thaung, Victoria M. L. Cohen, Mandeep S. Sagoo, Anne M. Bowcock
Summary: A study on 100 uveal melanomas from the UK revealed that loss of nuclear BAP1 (nBAP1) predicts shorter overall survival. Tumors with BAP1 loss of function mutations frequently exhibited heterogeneous BAP1 staining, and tumors with >= 25% loss of nBAP1 were a more reliable prognostic indicator than chromosome 3 loss (LOH3) or chromosome 8q gain. Majority of BAP1 mutations result in loss of nBAP1 and aberrant expression of cBAP1.
Article
Biochemistry & Molecular Biology
Lorena Olivares-Gonzalez, Sheyla Velasco, Idoia Gallego, Marina Esteban-Medina, Gustavo Puras, Carlos Loucera, Alicia Martinez-Romero, Maria Pena-Chilet, Jose Luis Pedraz, Regina Rodrigo
Summary: This study evaluated the effect of an essential fatty acid (EFA) supplement containing specialized pro-resolving mediators (SPMs) on retinal degeneration and microglia activation in a mouse model of RP. The EFA supplement improved retinal function, reduced inflammation and microglia activation, and reduced oxidative stress markers. These findings suggest that oral supplementation with SPMs such as the EFA supplement could be a potential therapeutic approach for resolving inflammation in RP.
Article
Biochemistry & Molecular Biology
Cankut Cubuk, Carlos Loucera, Maria Pena-Chilet, Joaquin Dopazo
Summary: Reprogramming metabolism is a key feature of cancer, and recent research suggests that metabolites may play a crucial role in regulating signaling pathways. Mechanistic models were used to analyze the metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA), and Gaussian Processes combined with SHapley Additive exPlanations (SHAP) were employed to identify potential causal relationships between metabolite production and signaling pathway regulation. A total of 317 metabolites were found to significantly impact signaling circuits, revealing a complex crosstalk between signaling and metabolic pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Rocio Nunez-Torres, Guillermo Pita, Maria Pena-Chilet, Daniel Lopez-Lopez, Jorge Zamora, Gema Roldan, Belen Herraez, Nuria Alvarez, Maria Rosario Alonso, Joaquin Dopazo, Anna Gonzalez-Neira
Summary: The implementation of pharmacogenetics (PGx) is a significant milestone for achieving safer and more effective therapies in precision medicine. However, the adoption of PGx diagnostics is slow and unequal worldwide, partly due to the lack of ethnic-specific PGx information. Genetic data from 3006 Spanish individuals were analyzed, revealing allele frequencies and putative deleterious variants for main PGx genes. A comparison of high-throughput diagnostic techniques indicated that genotyping with the PGx HT array is the most suitable solution. The integrated information is made available through the Collaborative Spanish Variant Server for the scientific community.
Review
Biology
Alba Loras, Luis G. Gonzalez-Bonet, Julia L. Gutierrez-Arroyo, Conrado Martinez-Cadenas, Maria Angeles Marques-Torrejon
Summary: Glioblastoma multiforme (GBM) is an incurable and highly malignant brain tumor in adults. It contains a cell population called glioma stem cells (GSCs) that contribute to therapy resistance and tumor recurrence. Recent data suggest that neural stem cells (NSCs) in the subventricular zone (SVZ) may be the cells of origin for GBM and are also involved in disease progression and recurrence. Identifying the cellular origin of GBM is crucial for early detection techniques and the development of targeted therapies.
Article
Virology
Carlos Loucera, Rosario Carmona, Marina Esteban-Medina, Gerrit Bostelmann, Dolores Munoyerro-Muniz, Roman Villegas, Maria Pena-Chilet, Joaquin Dopazo
Summary: This study utilized data from the Andalusian Population Health Database to investigate the relationship between prior drug consumption and patient outcomes in COVID-19. It identified 21 drugs associated with better patient survival and effectively controlled covariates.
Article
Genetics & Heredity
Daniel Lopez-Lopez, Gema Roldan, Jose Fernandez-Rueda, Gerrit Bostelmann, Rosario Carmona, Virginia Aquino, Javier Perez-Florido, Francisco Ortuno, Guillermo Pita, Rocio Nunez-Torres, Anna Gonzalez-Neira, Maria Pena-Chilet, Joaquin Dopazo
Summary: SPACNACS is a collaborative database that collects copy number variation data from more than 400 genomes and exomes of unrelated Spanish individuals. It provides detailed information on the local genetic variability and can be used for disease gene discovery and pharmacogenomics research.