keyword
https://read.qxmd.com/read/38547239/the-causal-effect-of-iron-status-on-risk-of-anxiety-disorders-a-two-sample-mendelian-randomization-study
#1
JOURNAL ARTICLE
Ruiying Yin, Qi Gao, Guangzhen Fu, Qiang Zhao
OBJECTIVES: Observational studies had investigated the association of iron metabolism with anxiety disorders. The conclusions were inconsistent and not available to reveal the causal or reverse-causal association due to the confounding. In this study we estimated the potential causal effect of iron homeostasis markers on anxiety disorders using two-sample Mendelian randomization (MR) analysis. METHODS: Summary data of single nucleotide polymorphisms (SNPs) associated with four iron-related biomarkers were extracted from a recent report about analysis of three genome-wide association study (GWAS), the sample size of which ranged from 131471 to 246139 individuals...
2024: PloS One
https://read.qxmd.com/read/38546716/meta-research-understudied-genes-are-lost-in-a-leaky-pipeline-between-genome-wide-assays-and-reporting-of-results
#2
JOURNAL ARTICLE
Reese Richardson, Heliodoro Tejedor Navarro, Luis A Nunes Amaral, Thomas Stoeger
Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results...
March 28, 2024: ELife
https://read.qxmd.com/read/38546604/genetic-associations-of-primary-angle-closure-disease-a-systematic-review-and-meta-analysis
#3
JOURNAL ARTICLE
Yu Jing Liang, Yu Yao Wang, Shi Song Rong, Zhen Ji Chen, Shu Ying Chen, Jenson A Tham, Poemen P Chan, Jason C Yam, Janey L Wiggs, Chi Pui Pang, Clement C Tham, Li Jia Chen
IMPORTANCE: Effects of genetic variants on primary angle-closure disease remained uncertain. OBJECTIVE: To systematically review the associations of common single-nucleotide variants (SNVs) and rare coding variants with primary angle-closure disease, its subtypes (including primary angle-closure glaucoma, primary angle-closure suspect, and primary angle-closure) and progression. DATA SOURCES: Eligible studies from PubMed, Embase, and Web of Science were retrieved up to April 3, 2023...
March 28, 2024: JAMA Ophthalmology
https://read.qxmd.com/read/38546521/integrative-multi-omics-analysis-identifies-genetic-variants-contributing-to-non-syndromic-cleft-lip-with-or-without-cleft-palate
#4
JOURNAL ARTICLE
Shu Lou, Jing Yang, Gui Rong Zhu, Dan Dan Li, Lan Ma, Lin Wang, Yong Chu Pan
OBJECTIVE: To provide novel insights into the aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) by integrating multi-omics data and exploring susceptibility genes associated with NSCL/P. METHODS: A two-stage genome-wide association study (GWAS) of NSCL/P was performed, involving a total of 1,069 cases and 1,724 controls. Using promoter capture Hi-C (pCHi-C) datasets in human embryonic stem cells (hESC) and chromatin immunoprecipitation sequencing (ChIP-seq) in craniofacial tissues, we filtered out single nucleotide polymorphisms (SNPs) with active cis-regulation and their target genes...
March 28, 2024: Chinese Journal of Dental Research
https://read.qxmd.com/read/38546370/hybridization-mediated-range-expansion-and-climate-change-resilience-in-two-keystone-tree-species-of-boreal-forests
#5
JOURNAL ARTICLE
Piyal Karunarathne, Qiujie Zhou, Martin Lascoux, Pascal Milesi
Current global climate change is expected to affect biodiversity negatively at all scales leading to mass biodiversity loss. Many studies have shown that the distribution of allele frequencies across a species' range is often influenced by specific genetic loci associated with local environmental variables. This association reflects local adaptation and allele changes at those loci could thereby contribute to the evolutionary response to climate change. However, predicting how species will adapt to climate change from this type of data alone remains challenging...
April 2024: Global Change Biology
https://read.qxmd.com/read/38546325/epigenome-augmented-eqtl-hotspots-reveal-genome-wide-transcriptional-programs-in-36-human-tissues
#6
JOURNAL ARTICLE
Huanhuan Liu, Qinwei Chen, Jintao Guo, Ying Zhou, Zhiyu You, Jun Ren, Yuanyuan Zeng, Jing Yang, Jialiang Huang, Qiyuan Li
Expression quantitative trait loci (eQTLs) are used to inform the mechanisms of transcriptional regulation in eukaryotic cells. However, the specificity of genome-wide eQTL identification is limited by stringent control for false discoveries. Here, we described a method based on the non-homogeneous Poisson process to identify 125 489 regions with highly frequent, multiple eQTL associations, or 'eQTL-hotspots', from the public database of 59 human tissues or cell types. We stratified the eQTL-hotspots into two classes with their distinct sequence and epigenomic characteristics...
March 27, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38546281/identification-of-coding-variants-in-10q22-1-associated-with-vitiligo-in-the-chinese-han-population
#7
JOURNAL ARTICLE
Xianfa Tang, Hui Cheng, Lu Cheng, Bo Liang, Mengyun Chen, Xiaodong Zheng, Fengli Xiao
Objective: This study aims to identify causal variants associated with vitiligo in an expanded region of 10q22.1. Materials and Methods: We conducted a fine-scale deep analysis of the expanded 10q22.1 region using in a large genome-wide association studies dataset consisting of 1117 cases and 1701 controls through imputation. We selected five nominal coding single nucleotide polymorphisms (SNPs) located in SLC29A3 and CDH23 and genotyped them in an independent cohort of 2479 cases and 2451 controls in a Chinese Han population cohort using the Sequenom MassArray iPLEX1 system...
March 2024: Genetic Testing and Molecular Biomarkers
https://read.qxmd.com/read/38545844/genomic-regions-and-biological-pathways-associated-with-sex-limited-reproductive-traits-in-bovine-species
#8
JOURNAL ARTICLE
Babatunde S Olasege, Zhen Yin Oh, Muhammad S Tahir, Laercio R Porto-Neto, Ben J Hayes, Marina R S Fortes
Many animal species exhibit sex-limited traits, where certain phenotypes are exclusively expressed in one sex. Yet, the genomic regions that contribute to these sex-limited traits in males and females remain a subject of debate. Reproductive traits are ideal phenotypes to study sexual differences since they are mostly expressed in a sex-limited way. Therefore, this study aims to use local correlation analyses to identify genomic regions and biological pathways significantly associated with male and female sex-limited traits in two distinct cattle breeds (Brahman (BB) and Tropical Composite (TC))...
March 28, 2024: Journal of Animal Science
https://read.qxmd.com/read/38545784/evaluation-of-plasma-biomarkers-for-causal-association-with-peripheral-artery-disease
#9
JOURNAL ARTICLE
Pranav Sharma, Derek Klarin, Benjamin F Voight, Philip S Tsao, Michael G Levin, Scott M Damrauer
BACKGROUND: Hundreds of biomarkers for peripheral artery disease (PAD) have been reported in the literature; however, the observational nature of these studies limits causal inference due to the potential of reverse causality and residual confounding. We sought to evaluate the potential causal impact of putative PAD biomarkers identified in human observational studies through genetic causal inference methods. METHODS: Putative circulating PAD biomarkers were identified from human observational studies through a comprehensive literature search based on terms related to PAD using PubMed, Cochrane, and Embase...
March 28, 2024: Arteriosclerosis, Thrombosis, and Vascular Biology
https://read.qxmd.com/read/38545780/genetic-and-epigenetic-mechanisms-regulating-blood-pressure-and-kidney-dysfunction
#10
REVIEW
Kailash N Pandey
The pioneering work of Dr Lewis K. Dahl established a relationship between kidney, salt, and high blood pressure (BP), which led to the major genetic-based experimental model of hypertension. BP, a heritable quantitative trait affected by numerous biological and environmental stimuli, is a major cause of morbidity and mortality worldwide and is considered to be a primary modifiable factor in renal, cardiovascular, and cerebrovascular diseases. Genome-wide association studies have identified monogenic and polygenic variants affecting BP in humans...
March 28, 2024: Hypertension
https://read.qxmd.com/read/38545396/genome-wide-association-study-for-yield-related-traits-in-faba-bean-vicia-faba-l
#11
JOURNAL ARTICLE
Natalia Gutierrez, Marie Pégard, Ignacio Solis, Dejan Sokolovic, David Lloyd, Catherine Howarth, Ana M Torres
Yield is the most complex trait to improve crop production, and identifying the genetic determinants for high yield is a major issue in breeding new varieties. In faba bean ( Vicia faba L.), quantitative trait loci (QTLs) have previously been detected in studies of biparental mapping populations, but the genes controlling the main trait components remain largely unknown. In this study, we investigated for the first time the genetic control of six faba bean yield-related traits: shattering (SH), pods per plant (PP), seeds per pod (SP), seeds per plant (SPL), 100-seed weight (HSW), and plot yield (PY), using a genome-wide association study (GWAS) on a worldwide collection of 352 homozygous faba bean accessions with the aim of identifying markers associated with them...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38545389/genetic-complexity-of-cassava-brown-streak-disease-insights-from-qpcr-based-viral-titer-analysis-and-genome-wide-association-studies
#12
JOURNAL ARTICLE
Leah Nandudu, Samar Sheat, Stephan Winter, Alex Ogbonna, Robert Kawuki, Jean-Luc Jannink
Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38545121/causal-association-between-psoriasis-vulgaris-and-bullous-pemphigoid-a-two-sample-bidirectional-mendelian-randomization-study
#13
JOURNAL ARTICLE
Aobei Zhang, Zhihui Yang, Tao Huang, Mingyue Wang
BACKGROUND: The association between psoriasis vulgaris and bullous pemphigoid (BP) remains largely unknown. OBJECTIVES: To investigate whether there is a causal effect between psoriasis vulgaris and BP. METHODS: Two-sample bidirectional Mendelian randomization (MR) analyses were conducted using publicly released genome-wide association studies (GWAS) summary statistics. The GWAS summary statistics for BP were downloaded online from FinnGen Biobank Documentation of the R12 release, which includes 219 BP cases and 218,066 controls...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38544801/pcgima-developing-the-web-server-for-human-position-defined-cpg-islands-methylation-analysis
#14
JOURNAL ARTICLE
Ming Xiao, Yi Xiao, Jun Yu, Le Zhang
Introduction: CpG island (CGI) methylation is one of the key epigenomic mechanisms for gene expression regulation and chromosomal integrity. However, classical CGI prediction methods are neither easy to locate those short and position-sensitive CGIs (CpG islets), nor investigate genetic and expression pattern for CGIs under different CpG position- and interval- sensitive parameters in a genome-wide perspective. Therefore, it is urgent for us to develop such a bioinformatic algorithm that not only can locate CpG islets, but also provide CGI methylation site annotation and functional analysis to investigate the regulatory mechanisms for CGI methylation...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38544686/causal-relationship-between-alzheimer-s-disease-and-prostate-cancer-a-bidirectional-mendelian-randomization-analysis
#15
JOURNAL ARTICLE
Rongkang Li, Lei Peng, Dashi Deng, Guangzhi Li, Song Wu
BACKGROUND: Previous observational researchers have found an inverse bidirectional link between Alzheimer's disease (AD) and prostate cancer (PCa); yet, the causative nature of this link remains unclear. To investigate the causal interactions between AD and PCa, a bidirectional Mendelian randomization (MR) analysis was conducted. METHODS: This study comprised two Genome-Wide Association Study (GWAS) summary statistics for AD (17,008 cases and 37,154 controls) and PCa (79,148 cases and 61,106 controls) in individuals of European ancestry...
2024: Frontiers in Endocrinology
https://read.qxmd.com/read/38544498/plasma-metabolites-and-risk-of-myocardial-infarction-a-bidirectional-mendelian-randomization-study
#16
JOURNAL ARTICLE
Dong-Hua Li, Qiang Wu, Jing-Sheng Lan, Shuo Chen, You-Yi Huang, Lan-Jin Wu, Zhi-Qing Qin, Ying Huang, Wan-Zhong Huang, Ting Zeng, Xin Hao, Hua-Bin Su, Qiang Su
BACKGROUND: Myocardial infarction (MI) is a critical cardiovascular event with multifaceted etiology, involving several genetic and environmental factors. It is essential to understand the function of plasma metabolites in the development of MI and unravel its complex pathogenesis. METHODS: This study employed a bidirectional Mendelian randomization (MR) approach to investigate the causal relationships between plasma metabolites and MI risk. We used genetic instruments as proxies for plasma metabolites and MI and conducted MR analyses in both directions to assess the impact of metabolites on MI risk and vice versa...
February 28, 2024: Journal of Geriatric Cardiology: JGC
https://read.qxmd.com/read/38543725/molecular-profile-of-variants-potentially-associated-with-severe-forms-of-covid-19-in-amazonian-indigenous-populations
#17
JOURNAL ARTICLE
Rita de Cássia Calderaro Coelho, Carlliane Lima E Lins Pinto Martins, Lucas Favacho Pastana, Juliana Carla Gomes Rodrigues, Kaio Evandro Cardoso Aguiar, Amanda de Nazaré Cohen-Paes, Laura Patrícia Albarello Gellen, Francisco Cezar Aquino de Moraes, Maria Clara Leite Calderaro, Letícia Almeida de Assunção, Natasha Monte, Esdras Edgar Batista Pereira, André Maurício Ribeiro-Dos-Santos, Ândrea Ribeiro-do-Santos, Rommel Mario Rodriguez Burbano, Sandro José de Souza, João Farias Guerreiro, Paulo Pimentel de Assumpção, Sidney Emanuel Batista Dos Santos, Marianne Rodrigues Fernandes, Ney Pereira Carneiro Dos Santos
Coronavirus disease 2019 (COVID-19) is an infection caused by SARS-CoV-2. Genome-wide association studies (GWASs) have suggested a strong association of genetic factors with the severity of the disease. However, many of these studies have been completed in European populations, and little is known about the genetic variability of indigenous peoples' underlying infection by SARS-CoV-2. The objective of the study is to investigate genetic variants present in the genes AQP3 , ARHGAP27 , ELF5L , IFNAR2 , LIMD1 , OAS1 and UPK1A, selected due to their association with the severity of COVID-19, in a sample of indigenous people from the Brazilian Amazon in order to describe potential new and already studied variants...
February 26, 2024: Viruses
https://read.qxmd.com/read/38543719/cross-species-transmission-potential-of-h4-avian-influenza-viruses-in-china-epidemiological-and-evolutionary-study
#18
JOURNAL ARTICLE
Shuxia Lin, Ye Zhang, Jiaying Yang, Lei Yang, Xiyan Li, Hong Bo, Jia Liu, Min Tan, Wenfei Zhu, Dayan Wang, Yuelong Shu
H4 avian influenza viruses (AIVs) have been widely detected in live poultry markets in China. However, the potential public health impact of H4 AIVs remains largely uncertain. Here, we fully analyzed the distribution and phylogenetic relationship of H4 AIVs in China. We obtained 31 isolates of H4 viruses in China during 2009-2022 through surveillance in poultry-associated environments, such as live poultry markets and poultry farms. Genomic sequence analysis together with publicly available data revealed that frequent reassortment and introduction of H4 AIV from wild birds to poultry may have occurred...
February 24, 2024: Viruses
https://read.qxmd.com/read/38543644/identification-of-viruses-in-molossus-bats-from-the-brazilian-amazon-a-descriptive-metagenomic-analysis
#19
JOURNAL ARTICLE
Lucas Rafael Santana Pinheiro, Érika Dayane Leal Rodrigues, Francisco Amilton Dos Santos Paiva, Ana Cecília Ribeiro Cruz, Daniele Barbosa de Almeida Medeiros, Alexandre do Rosário Casseb, Sandro Patroca da Silva, Livia Medeiros Neves Casseb
Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis...
March 16, 2024: Microorganisms
https://read.qxmd.com/read/38542917/the-causality-between-human-immunoglobulin-g-igg-n-glycosylation-and-aging-a-mendelian-randomization-study
#20
JOURNAL ARTICLE
Wenxin Sun, Xuening Jian, Jie Zhang, Xiaoni Meng, Haotian Wang, Deqiang Zheng, Lijuan Wu, Youxin Wang
BACKGROUND: Immunoglobulin G (IgG) N-glycosylation is considered a potential biomarker for aging and various pathological conditions. However, whether these changes in IgG N-glycosylation are a consequence or a contributor to the aging process remains unclear. This study aims to investigate the causality between IgG N-glycosylation and aging using Mendelian randomization (MR) analysis. METHODS: We utilized genetic variants associated with IgG N-glycosylation traits, the frailty index (FI), and leukocyte telomere length (LTL) from a previous genome-wide association study (GWAS) on individuals of European ancestry...
March 14, 2024: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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