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JOURNAL ARTICLE
Jiarui Mi, Qingwei Jiang, Zhengwei Qi, Zhengye Liu, Xiaoyin Bai, Xia Zheng, Jiaguo Wu, Yanfei Fang, Aiming Yang, Haotian Chen
The causal relationships between plasma metabolites and cholelithiasis/cholecystitis risks remain elusive. Using two-sample Mendelian randomization, we found that genetic proxied plasma campesterol level showed negative correlation with the risk of both cholelithiasis and cholecystitis. Furthermore, the increased risk of cholelithiasis is correlating with the increased level of plasma campesterol. Lastly, genetic colocalization study showed that the leading SNP, rs4299376, which residing at the ABCG5/ABCG8 gene loci, was shared by plasma campesterol level and cholelithiasis, indicating that the aberrant transportation of plant sterol/cholesterol from the blood stream to the bile duct/gut lumen might be the key in preventing cholesterol gallstone formation...
February 12, 2024: Human Genomics
#22
JOURNAL ARTICLE
Shymaa E Ayoub, Olfat G Shaker, Mohamed Masoud, Essam A Hassan, Eman M Ezzat, Mona I Ahmed, Randa I Ahmed, Amal A Ibrahim Amin, Fadwa Abd El Reheem, Abeer A Khalefa, Rania H Mahmoud
Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has a high incidence of spread. On January 30, 2020, the World Health Organization proclaimed a public health emergency of worldwide concern. More than 6.9 million deaths and more than 768 million confirmed cases had been reported worldwide as of June 18, 2023. This study included 51 patients and 50 age- and sex-matched healthy subjects. The present study aimed to identify the expression levels of lncRNA CASC2 and miRNA-21-5p (also known as miRNA-21) in COVID-19 patients and their relation to the clinicopathological characteristics of the disease...
February 12, 2024: Human Genomics
#23
Renuka Harit, Sajal De, Piyoosh Kumar Singh, Deepika Kashyap, Manish Kumar, Dibakar Sahu, Chander Prakash Yadav, Mradul Mohan, Vineeta Singh, Ram Singh Tomar, Kailash C Pandey, Kapil Vashisht
No abstract text is available yet for this article.
February 8, 2024: Human Genomics
#24
JOURNAL ARTICLE
M I Farrim, A Gomes, D Milenkovic, R Menezes
BACKGROUND: Diabetes is a spectrum of metabolic diseases affecting millions of people worldwide. The loss of pancreatic β-cell mass by either autoimmune destruction or apoptosis, in type 1-diabetes (T1D) and type 2-diabetes (T2D), respectively, represents a pathophysiological process leading to insulin deficiency. Therefore, therapeutic strategies focusing on restoring β-cell mass and β-cell insulin secretory capacity may impact disease management. This study took advantage of powerful integrative bioinformatic tools to scrutinize publicly available diabetes-associated gene expression data to unveil novel potential molecular targets associated with β-cell dysfunction...
February 8, 2024: Human Genomics
#25
JOURNAL ARTICLE
Evridiki-Pandora G Tsare, Maria I Klapa, Nicholas K Moschonas
BACKGROUND: It is valuable to analyze the genome-wide association studies (GWAS) data for a complex disease phenotype in the context of the protein-protein interaction (PPI) network, as the related pathophysiology results from the function of interacting polyprotein pathways. The analysis may include the design and curation of a phenotype-specific GWAS meta-database incorporating genotypic and eQTL data linking to PPI and other biological datasets, and the development of systematic workflows for PPI network-based data integration toward protein and pathway prioritization...
February 8, 2024: Human Genomics
#26
JOURNAL ARTICLE
Yabing Li, Brijen Miyani, Russell A Faust, Randy E David, Irene Xagoraraki
BACKGROUND: Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing. RESULTS: During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated...
February 6, 2024: Human Genomics
#27
JOURNAL ARTICLE
Lirui Dai, Liang Lyu, Peizhi Zhou, Shu Jiang
Many researchers have explored the potential association between one neurosurgical disease and coronavirus disease 2019 (COVID-19), but few systematically analyzed the association and causality between COVID-19 and various neurosurgical diseases. A Mendelian randomization analysis was conducted to evaluate the causal association between COVID-19 (including critically ill COVID-19, hospitalized COVID-19, and respiratory syndrome coronavirus 2 (SARS-CoV-2) infection) and 30 neurosurgical diseases within European populations...
February 5, 2024: Human Genomics
#28
JOURNAL ARTICLE
Pelin Ünal, Ye Lu, Bas Bueno-de-Mesquita, Casper H J van Eijck, Renata Talar-Wojnarowska, Andrea Szentesi, Maria Gazouli, Edita Kreivenaite, Francesca Tavano, Ewa Małecka-Wojciesko, Bálint Erőss, Martin Oliverius, Stefania Bunduc, Mateus Nóbrega Aoki, Ludmila Vodickova, Ugo Boggi, Matteo Giaccherini, Jurate Kondrackiene, Roger Chammas, Orazio Palmieri, George E Theodoropoulos, Maarten F Bijlsma, Daniela Basso, Beatrice Mohelnikova-Duchonova, Pavel Soucek, Jakob R Izbicki, Vytautas Kiudelis, Giuseppe Vanella, Paolo Giorgio Arcidiacono, Barbara Włodarczyk, Thilo Hackert, Ben Schöttker, Faik G Uzunoglu, Franco Bambi, Mara Goetz, Viktor Hlavac, Hermann Brenner, Francesco Perri, Silvia Carrara, Stefano Landi, Péter Hegyi, Frederike Dijk, Evaristo Maiello, Giovanni Capretti, Sabrina Gloria Giulia Testoni, Maria Chiara Petrone, Hannah Stocker, Stefano Ermini, Livia Archibugi, Manuel Gentiluomo, Giulia Martina Cavestro, Raffaele Pezzilli, Gregorio Di Franco, Anna Caterina Milanetto, Cosimo Sperti, John P Neoptolemos, Luca Morelli, Klara Vokacova, Claudio Pasquali, Rita T Lawlor, Francesca Bazzocchi, Juozas Kupcinskas, Gabriele Capurso, Daniele Campa, Federico Canzian
Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk...
February 2, 2024: Human Genomics
#29
JOURNAL ARTICLE
Johanna I Kiiski, Mikko Neuvonen, Mika Kurkela, Päivi Hirvensalo, Kreetta Hämäläinen, E Katriina Tarkiainen, Johanna Sistonen, Mari Korhonen, Sofia Khan, Arto Orpana, Anne M Filppula, Marko Lehtonen, Mikko Niemi
BACKGROUND: Individual assessment of CYP enzyme activities can be challenging. Recently, the potato alkaloid solanidine was suggested as a biomarker for CYP2D6 activity. Here, we aimed to characterize the sensitivity and specificity of solanidine as a CYP2D6 biomarker among Finnish volunteers with known CYP2D6 genotypes. RESULTS: Using non-targeted metabolomics analysis, we identified 9152 metabolite features in the fasting plasma samples of 356 healthy volunteers...
February 1, 2024: Human Genomics
#30
JOURNAL ARTICLE
Cristina Mejías-Molina, Anna Pico-Tomàs, Sandra Martínez-Puchol, Marta Itarte, Helena Torrell, Núria Canela, Carles M Borrego, Lluís Corominas, Marta Rusiñol, Sílvia Bofill-Mas
BACKGROUND: Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments...
February 1, 2024: Human Genomics
#31
JOURNAL ARTICLE
Xue Zhang, Qian Chen, Junnan Li, Xin Luo, Jianyun Luo, Jian Li, Ziye Zeng, Yan Wu, Hua Zhang, Yanling Dong
Expanded carrier screening (ECS) based on next-generation sequencing has been the subject of few studies to estimate the effectiveness of ECS in the Chinese population. A total of 3737 individuals from Southwest China or the general Chinese population, including 1048 pairs and 1641 individuals, were analysed by ECS for 155 monogenetic diseases. An ECS panel was used to detect 147 genes and 10,449 variants in 145 autosomal recessive and 10 X-linked recessive disorders. A total of 43.27% (1617/3737) were found to be carriers of at least one of the 155 monogenetic diseases...
January 31, 2024: Human Genomics
#32
JOURNAL ARTICLE
Renuka Harit, Sajal De, Piyoosh Kumar Singh, Deepika Kashyap, Manish Kumar, Dibakar Sahu, Chander Prakash Yadav, Mradul Mohan, Vineeta Singh, Ram Singh Tomar, Kailash C Pandey, Kapil Vashisht
The present study investigated two single nucleotide polymorphisms (SNPs)-rs479200 and rs516651 in the host EGLN1/PHD2 gene for their association with COVID-19 severity. A retrospective cohort of 158 COVID-19 patients from the Indian population (March 2020 to June 2021) was enrolled. Notably, the frequency of C allele (0.664) was twofold higher than T allele (0.336) in severe COVID-19 patients. Here, we report a novel finding that the C allele of rs479200 in the EGLN1 gene imparts a high risk of severe COVID-19 (odds ratio-6...
January 30, 2024: Human Genomics
#33
JOURNAL ARTICLE
Azza Ramadan, Anan S Jarab, Ahmad Z Al Meslamani
BACKGROUND: Community pharmacists must be well-equipped to advance pharmacogenomics services. Nevertheless, limited data is available regarding pharmacists' knowledge and attitudes toward pharmacogenomics testing. The present study aimed to evaluate community pharmacists' knowledge and attitudes toward pharmacogenomics testing in the UAE. METHODS: In this cross-sectional study, a validated, online, self-administered survey, was randomly distributed to community pharmacists across the United Arab Emirates (UAE)...
January 30, 2024: Human Genomics
#34
JOURNAL ARTICLE
Syed Irtiza Ali, Obaid Yusuf Khan, Nadir Naveed, Hussain Ahmad, Najma Patel, Afsheen Arif
BACKGROUND: Congenital heart defects (CHDs) are the heart structural malformations present at birth. Septal defects account for 40% of CHD, including atrial, ventricular and atrioventricular septal defects. In Pakistan, the prevalence of CHD is 3.4 in 1000, and a study estimated that 60,000 babies are born with CHD annually. Methylenetetrahydrofolate reductase (MTHFR), a chief enzyme, involved in the folate metabolism. The missense mutation, C677T (rs1801133), exists in MTHFR gene, results in a MTHFR thermolabile variant having low enzymatic activity...
January 29, 2024: Human Genomics
#35
JOURNAL ARTICLE
Huijun Lei, Jiaheng Li, Bojin Zhao, Si Hoi Kou, Fengxia Xiao, Tianhui Chen, San Ming Wang
BACKGROUND: Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs...
January 29, 2024: Human Genomics
#36
REVIEW
Kalliopi K Gkouskou, Maria G Grammatikopoulou, Evgenia Lazou, Theodora Vasilogiannakopoulou, Despina Sanoudou, Aristides G Eliopoulos
This review discusses the landscape of personalized prevention and management of obesity from a nutrigenetics perspective. Focusing on macronutrient tailoring, we discuss the impact of genetic variation on responses to carbohydrate, lipid, protein, and fiber consumption. Our bioinformatic analysis of genomic variants guiding macronutrient intake revealed enrichment of pathways associated with circadian rhythm, melatonin metabolism, cholesterol and lipoprotein remodeling and PPAR signaling as potential targets of macronutrients for the management of obesity in relevant genetic backgrounds...
January 29, 2024: Human Genomics
#37
JOURNAL ARTICLE
Sachin Mulmi Shrestha, Xin Fang, Hui Ye, Lihua Ren, Qinghua Ji, Ruihua Shi
INTRODUCTION: Circular RNAs (CircRNA) have emerged as an interest of research in recent years due to its regulatory role in various kinds of cancers of human body. Esophageal squamous cell carcinoma (ESCC) is one of the major disease subtype in Asian countries, including China. CircRNAs are formed by back-splicing covalently joined 3'- and 5'- ends rather than canonical splicing and are found to have binding affinity with miRNAs that conjointly contribute to oncogenesis. MATERIALS AND METHODS: 4 pairs of normal, cancer adjacent tissues and cancer tissues were analyzed by high-throughput RNA sequencing and 84 differentially upregulated circRNAs were detected in cancer tissues...
January 10, 2024: Human Genomics
#38
JOURNAL ARTICLE
Lubna Q Khasawneh, Habiba Alsafar, Hiba Alblooshi, Mushal Allam, George P Patrinos, Bassam R Ali
BACKGROUND: Clopidogrel is a widely prescribed prodrug that requires activation via specific pharmacogenes to exert its anti-platelet function. Genetic variations in the genes encoding its transporter, metabolizing enzymes, and target receptor lead to variability in its activation and platelet inhibition and, consequently, its efficacy. This variability increases the risk of secondary cardiovascular events, and therefore, some variations have been utilized as genetic biomarkers when prescribing clopidogrel...
January 3, 2024: Human Genomics
#39
EDITORIAL
Vasilis Vasiliou
No abstract text is available yet for this article.
January 2, 2024: Human Genomics
#40
JOURNAL ARTICLE
Yuantao Zou, Xingliang Tan, Gangjun Yuan, Yi Tang, Yanjun Wang, Cong Yang, Sihao Luo, Zhiming Wu, Kai Yao
BACKGROUND: The effect of SPP1 in squamous cell carcinoma of the penis (PSCC) remained unknown. We attempted to clarify the function of the SPP1 gene in PSCC. METHOD: Eight paired penile cancer specimens (including penile cancer tissue, paracancerous tissue, and positive lymph node tissue) subjected to whole transcriptome sequencing were analysed to identify differentially expressed genes. We used immunohistochemistry to detect the expression of SPP1 protein and immune cell related proteins in penile cancer tissue...
December 19, 2023: Human Genomics
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