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JOURNAL ARTICLE
Renu Verma, Kesia Esther da Silva, Neesha Rockwood, Roeland E Wasmann, Nombuso Yende, Taeksun Song, Eugene Kim, Paolo Denti, Robert J Wilkinson, Jason R Andrews
RATIONALE: Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking. OBJECTIVES: To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing...
March 5, 2024: American Journal of Respiratory and Critical Care Medicine
#2
JOURNAL ARTICLE
Minghui Bao, Haotong Li, Yan Zhang, Jianping Li
The relationship between fine particulate matter (PM2.5) and blood pressure (BP) is a controversial issue. We conducted a two-sample Mendelian randomization (MR) analysis and identified 58 genome-wide significant single-nucleotide polymorphisms associated with PM2.5 as instrument variables. Inverse-variance weighted (IVW) was used as the primary analysis approach. MR-Egger, weighted median, simple model, and weighted model methods were selected for quality control. We found a significant negative causal association of higher genetically predicted PM2...
April 22, 2024: International Journal of Environmental Health Research
#3
JOURNAL ARTICLE
Yu Xin, Tao Yuan, Jun Wang
BACKGROUND: Atopic dermatitis ranks among the prevalent skin disorders. Research has indicated a potential association with brain cancer. Yet, establishing a direct causal relationship between atopic dermatitis and brain cancer continues to be challenging. MATERIALS AND METHODS: We extracted single nucleotide polymorphisms (SNPs) significantly associated with atopic dermatitis (sample size = 382 254) at a genome-wide level from a large Finnish Genome-Wide Association Study (GWAS) dataset (n cases = 15 208, n controls = 367 046)...
April 2024: Skin Research and Technology
#4
JOURNAL ARTICLE
Yunfeng Yu, Keke Tong, Gang Hu, Xinyu Yang, Jingyi Wu, Siyang Bai, Rong Yu
OBJECTIVE: The impact of hepatitis B virus (HBV) on the risk of type 2 diabetes (T2D) remains a controversial topic. This study aims to analyze the causal relationship between HBV and T2D using Mendelian randomization (MR). METHODS: Single nucleotide polymorphisms on chronic hepatitis B (CHB), liver fibrosis, liver cirrhosis, and T2D were obtained from BioBank Japan Project, European Bioinformatics Institute, and FinnGen. Mendelian randomization was utilized to evaluate exposure-outcome causality...
2024: Frontiers in Microbiology
#5
JOURNAL ARTICLE
Han Wu, Hui Wang, Lixia Sun, Mengchen Liu, Haoran Wang, Xianchang Sun, Wenjuan Zhang
PURPOSE: To study the relationship between the single nucleotide polymorphism (SNP) rs2278426 in the angiopoietin-like protein 8 gene ( ANGPTL8 ) and polycystic ovary syndrome (PCOS). PATIENTS AND METHODS: A total of 122 patients with PCOS and 108 controls were recruited for comparison of glucose, lipid, insulin, sex hormone, and ANGPTL8 levels. Polymerase chain reaction (PCR) and gene sequencing were performed for comparison of the frequency of the CC, CT, and TT rs2278426 genotypes and the rs2278426 allele distributions between the PCOS and control groups and between the obese and non-obese subgroups of the PCOS and control groups...
2024: Diabetes, Metabolic Syndrome and Obesity
#6
JOURNAL ARTICLE
Fulya Yaylacıoğlu Tuncay, Kübra Serbest Ceylanoğlu, Sezen Güntekin Ergün, Güntekin Ergün, Onur Konuk
OBJECTIVES: Forkhead box P3 ( FOXP3 ) gene polymorphisms have been evaluated in many autoimmune diseases, including Graves' disease (GD), in different populations. However, those polymorphisms have not been analyzed in GD or Graves' ophthalmopathy (GO) in the Turkish population. In this study, we aimed to evaluate the frequency of FOXP3 polymorphisms in GD with or without ophthalmopathy in a Turkish population. MATERIALS AND METHODS: The study included 100 patients with GO, 74 patients with GD without ophthalmopathy, and 100 age- and sex-matched healthy controls...
April 19, 2024: Turkish Journal of Ophthalmology
#7
Obie Allen, Brandon J Coombes, Vanessa Pazdernik, Barbara Gisabella, Joshua Hartley, Joanna M Biernacka, Mark A Frye, Matej Markota, Harry Pantazopoulos
BACKGROUND: Many patients with bipolar disorder (BD) do not respond to or have difficulties tolerating lithium and/or other mood stabilizing agents. There is a need for personalized treatments based on biomarkers in guiding treatment options. The calcium voltage-gated channel CACNA1C is a promising candidate for developing personalized treatments. CACNA1C is implicated in BD by genome-wide association studies and several lines of evidence suggest that targeting L-type calcium channels could be an effective treatment strategy...
April 12, 2024: medRxiv
#8
David Martino, Nikki Schultz, Ravinder Kaur, Simon D Haren, Nina Kresoje, Annmarie Hoch, Joann Diray-Arce, Jessica Lasky Su, Ofer Levy, Michael Pichichero
Background Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunisations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripharal immune cells from respiratory infection allergy/asthma prone (IAP) infants were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis...
April 3, 2024: Research Square
#9
JOURNAL ARTICLE
Leticia Camargo Tavares, Esteban Alexander Lopera-Maya, Ferdinando Bonfiglio, Tenghao Zheng, Trishla Sinha, Francine Zanchetta Marques, Alexandra Zhernakova, Serena Sanna, Mauro D'Amato
BACKGROUND & AIMS: Irritable bowel syndrome (IBS) shows genetic predisposition, and large-scale genome-wide association studies (GWAS) are emerging, based on heterogeneous disease definitions. We aimed at investigating the genetic architecture of IBS defined according to gold-standard Rome Criteria. METHODS: We conducted GWAS meta-analyses of Rome III IBS and its subtypes in 24,735 IBS cases and 77,149 asymptomatic controls from two independent European cohorts (UK Biobank and Lifelines)...
April 18, 2024: Cellular and Molecular Gastroenterology and Hepatology
#10
JOURNAL ARTICLE
Nannan Li, Ke Yang, Youjie Zeng, Si Cao, Liang Deng
Previous studies indicated conflicting findings regarding the association between vitamin D and abnormal spermatozoa. Herein, we assessed the causal association between circulating 25-Hydroxyvitamin D (25OHD) levels and the risk of abnormal spermatozoa by utilizing bidirectional Mendelian randomization (MR) analysis. Genome-wide association study summary statistics for 25OHD and abnormal spermatozoa were obtained from publicly accessible databases. Single nucleotide polymorphisms (SNPs) associated with 25OHD and SNPs associated with abnormal spermatozoa were used as instrumental variables (IVs) for forward MR analysis and reverse MR analysis, respectively...
April 19, 2024: Reproductive Toxicology
#11
JOURNAL ARTICLE
Thiago S Oliveira, Hericles M Campos, Rafael M Costa, Raphaela C Georg, Jacqueline A Leite, Rita C Tostes, Elson A Costa, Fernanda Cristina A Santos, Núbia S Lobato, Fernando P Filgueira, Paulo César Ghedini
Estrone (E1) constitutes the primary component in oral conjugated equine estrogens (CEEs) and serves as the principal estrogen precursor in the female circulation in the post-menopause. E1 induces endothelium-dependent vasodilation and activate PI3K/NO/cGMP signaling. To assess whether E1 mitigates vascular dysfunction associated with postmenopause and explore the underlying mechanisms, we examined the vascular effects of E1 in ovariectomized (OVX) rats, a postmenopausal experimental model. Blood pressure was measured using tail-cuff plethysmography, and aortic rings were isolated to assess responses to phenylephrine, acetylcholine (ACh), and sodium nitroprusside...
April 21, 2024: Naunyn-Schmiedeberg's Archives of Pharmacology
#12
JOURNAL ARTICLE
Beatriz Vieira Neto, Valéria Tavares, José Brito da Silva, Joana Liz-Pimenta, Inês Soares Marques, Lurdes Salgado, Luísa Carvalho, Deolinda Pereira, Rui Medeiros
Venous thromboembolism (VTE) is a life-threatening haemostatic disease frequently diagnosed among the cancer population. The Khorana Score is currently the primal risk assessment model to stratify oncological patients according to their susceptibility to VTE, however, it displays a limited performance. Meanwhile, intensive research on VTE pathophysiology in the general population has uncovered a range of single-nucleotide polymorphisms (SNPs) associated with the condition. Nonetheless, their predictive ability concerning cancer-associated thrombosis (CAT) is controversial...
April 20, 2024: Journal of Thrombosis and Thrombolysis
#13
JOURNAL ARTICLE
Xin Qiao, Ning Kong, Shiqing Sun, Xiang Li, Chunyu Jiang, Cong Luo, Lingling Wang, Linsheng Song
The Pacific oyster Crassostrea gigas is rich in taurine, which is crucial for its adaptation to the fluctuating intertidal environment and presents significant potential in improving taurine nutrition and boosting immunity in humans. Cysteine dioxygenase (CDO) is a key enzyme involved in the initial step of taurine biosynthesis and plays a crucial role in regulating taurine content in the body. In the present study, polymorphisms of CDO gene in C. gigas (CgCDO) and their association with taurine content were evaluated in 198 individuals...
April 18, 2024: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
#14
JOURNAL ARTICLE
Dr Aruna Sharma, M S Muthu, Vettriselvi V, Sivakumar Nuvvula, Gayathri T
OBJECTIVE: Enamelin is the largest enamel matrix protein encoded by the ENAM gene. The primary purpose of this study was to identify genetic variants in ENAM exon 10 that can alter susceptibility to early childhood caries (ECC). METHODS: This case-control study included 248 children aged 3-6 years, with 124 children diagnosed with ECC in the case group and 124 children without caries in the control group. Questionnaires were used to record demographic data, socioeconomic status, hygienic practices, and feeding practices, and a 24-hour diet diary was kept...
April 18, 2024: Journal of Oral Biosciences
#15
JOURNAL ARTICLE
Naoko P Kurata, Melanie L J Stiassny, Michael J Hickerson, S Elizabeth Alter
Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects on African riverine fishes. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids...
April 19, 2024: Integrative and Comparative Biology
#16
JOURNAL ARTICLE
Vered Stearns, Opeyemi A Jegede, Victor Tsu-Shih Chang, Todd C Skaar, Jeffrey L Berenberg, Ranveer Nand, Atif Shafqat, Nisha Lassi Jacobs, William Luginbuhl, Paul Gilman, Al B Benson, Judie R Goodman, Gary L Buchschacher, N Lynn Henry, Charles L Loprinzi, Patrick J Flynn, Edith P Mitchell, Michael Jordan Fisch, Joseph A Sparano, Lynne I Wagner
PURPOSE: Aromatase Inhibitor-Associated Musculoskeletal Symptoms (AIMSS) are common and frequently lead to AI discontinuation. Single nucleotide polymorphisms (SNPs) in candidate genes have been associated with AIMSS and AI discontinuation. E1Z11 is a prospective cohort study designed to validate associations between 10 SNPs and AI discontinuation due to AIMSS. PATIENTS AND METHODS: Postmenopausal women with stage I-III hormone receptor-positive breast cancer received anastrozole 1 mg daily and completed patient-reported outcomes (PRO) to assess AIMSS (Stanford Health Assessment Questionnaire; HAQ) at baseline, 3, 6, 9, and 12 months...
April 19, 2024: Clinical Cancer Research
#17
JOURNAL ARTICLE
Weichen Song, Yongyong Shi, Guan Ning Lin
We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS-trait associations with a significance of p < 5 × 10-8 . Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis...
April 19, 2024: ELife
#18
JOURNAL ARTICLE
Anudeep P P, Suchitra Kumari, Saroj Dasmajumdar, Manaswini Mangaraj
BACKGROUND: Matrix metalloproteinase-7 (MMP7) plays multiple roles in different stages of tumor development. Elevated MMP7 activity has been reported in ovarian cancer. Single nucleotide polymorphism (SNP) of promoter sites of the MMP7 gene has been shown to cause alteration in gene expression, hence resulting in changes in susceptibility to various diseases and tumor development. METHODS: The current study evaluated the association of epithelial ovarian cancer risk with MMP7 promoter site -181A>G polymorphism in the population of eastern India...
March 2024: Curēus
#19
JOURNAL ARTICLE
Chunlan Chen, Ying He
BACKGROUND: Sarcopenia is common in patients with autoimmune diseases (ADs); however, the causal associations between ADs and sarcopenia remain unclear. Therefore, this study investigated the causal associations using bi-directional Mendelian randomization analysis. METHODS: Exposure-related single-nucleotide polymorphisms (SNPs) were extracted from genome-wide association studies (GWASs). GWAS statistics for common ADs [Crohn's disease (CD), ulcerative colitis (UC), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), psoriasis (PSO), and multiple sclerosis (MS)] and sarcopenia-related traits [hand grip strength (HGS), appendicular fat-free mass (FFM), and walking pace] were obtained from public datasets...
2024: Frontiers in Genetics
#20
JOURNAL ARTICLE
Sara Monzón, Sarai Varona, Anabel Negredo, Santiago Vidal-Freire, Juan Angel Patiño-Galindo, Natalia Ferressini-Gerpe, Angel Zaballos, Eva Orviz, Oskar Ayerdi, Ana Muñoz-Gómez, Alberto Delgado-Iribarren, Vicente Estrada, Cristina García, Francisca Molero, Patricia Sánchez-Mora, Montserrat Torres, Ana Vázquez, Juan-Carlos Galán, Ignacio Torres, Manuel Causse Del Río, Laura Merino-Diaz, Marcos López, Alicia Galar, Laura Cardeñoso, Almudena Gutiérrez, Cristina Loras, Isabel Escribano, Marta E Alvarez-Argüelles, Leticia Del Río, María Simón, María Angeles Meléndez, Juan Camacho, Laura Herrero, Pilar Jiménez, María Luisa Navarro-Rico, Isabel Jado, Elaina Giannetti, Jens H Kuhn, Mariano Sanchez-Lockhart, Nicholas Di Paola, Jeffrey R Kugelman, Susana Guerra, Adolfo García-Sastre, Isabel Cuesta, Maripaz P Sánchez-Seco, Gustavo Palacios
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. Person-to-person transmission appears higher than for clade I or subclade IIa MPXV, possibly caused by genomic changes in subclade IIb MPXV. Key genomic changes could occur in the genome's low-complexity regions (LCRs), which are challenging to sequence and are often dismissed as uninformative. Here, using a combination of highly sensitive techniques, we determine a high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy...
April 18, 2024: Nature Communications
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