keyword
https://read.qxmd.com/read/38496462/an-integrative-multi-context-mendelian-randomization-method-for-identifying-risk-genes-across-human-tissues
#21
Yihao Lu, Ke Xu, Bowei Kang, Brandon L Pierce, Fan Yang, Lin S Chen
Mendelian randomization (MR) provides valuable assessments of the causal effect of exposure on outcome, yet the application of conventional MR methods for mapping risk genes encounters new challenges. One of the issues is the limited availability of expression quantitative trait loci (eQTLs) as instrumental variables (IVs), hampering the estimation of sparse causal effects. Additionally, the often context/tissue-specific eQTL effects challenge the MR assumption of consistent IV effects across eQTL and GWAS data...
March 7, 2024: medRxiv
https://read.qxmd.com/read/38495498/illuminating-shared-genetic-associations-between-oesophageal-carcinoma-and-pulmonary-carcinoma-risk
#22
JOURNAL ARTICLE
Dengfeng Zhang, Jing Li, Tianxing Lu, Fangchao Zhao, Pengfei Guo, Zhirong Li, Xiaoliang Duan, Yishuai Li, Shujun Li, Jianhang Li
Background: Lung cancer and oesophageal cancer are prevalent malignancies with rising incidence and mortality worldwide. While some environmental and behavioural risk factors for these cancers are established, the contribution of genetic factors to their pathogenesis remains incompletely defined. This study aimed to interrogate the intricate genetic relationship between lung cancer and oesophageal cancer and their potential comorbidity. Methods: We utilised linkage disequilibrium score regression (LDSC) to analyse the genetic correlation between oesophageal carcinoma and lung carcinoma...
2024: Journal of Cancer
https://read.qxmd.com/read/38493154/integrative-cross-omics-and-cross-context-analysis-elucidates-molecular-links-underlying-genetic-effects-on-complex-traits
#23
JOURNAL ARTICLE
Yihao Lu, Meritxell Oliva, Brandon L Pierce, Jin Liu, Lin S Chen
Genetic effects on functionally related 'omic' traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propose X-ING (Cross-INtegrative Genomics) for cross-omics and cross-context integrative analysis. X-ING takes as input multiple matrices of association statistics, each obtained from different omics data types across multiple cellular contexts. It models the latent binary association status of each statistic, captures the major association patterns among omics data types and contexts, and outputs the posterior mean and probability for each input statistic...
March 16, 2024: Nature Communications
https://read.qxmd.com/read/38491773/subset-based-method-for-cross-tissue-transcriptome-wide-association-studies-improves-power-and-interpretability
#24
JOURNAL ARTICLE
Xinyu Guo, Nilanjan Chatterjee, Diptavo Dutta
Integrating results from genome-wide association studies (GWAS) and studies of molecular phenotypes like gene expressions, can improve our understanding of the biological functions of trait-associated variants, and can help prioritize candidate genes for downstream analysis. Using reference expression quantitative trait loci (eQTL) studies, several methods have been proposed to identify gene-trait associations, primarily based on gene expression imputation. To increase the statistical power by leveraging substantial eQTL-sharing across tissues, meta-analysis methods aggregating such gene-based test results across multiple tissues or contexts have been developed as well...
March 14, 2024: HGG advances
https://read.qxmd.com/read/38486454/dissecting-the-molecular-basis-of-spike-traits-by-integrating-gene-regulatory-network-and-genetic-variation-in-wheat
#25
JOURNAL ARTICLE
Guo Ai, Chao He, Siteng Bi, Ziru Zhou, Ankui Liu, Xin Hu, Yanyan Liu, Liujie Jin, JiaCheng Zhou, Heping Zhang, Dengxiang Du, Hao Chen, Xin Gong, Sulaiman Saeed, Handong Su, Caixia Lan, Wei Chen, Qiang Li, Hailiang Mao, Lin Li, Hao Liu, Dijun Chen, Kerstin Kaufmann, Khaled F Alazab, Wenhao Yan
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes affecting the spike traits. Here, we systematically identify genes involved in spike trait formation by integrating the information of genomic variation and gene regulatory network (GRN) controlling young spike development in wheat...
March 14, 2024: Plant communications
https://read.qxmd.com/read/38484702/diet-composition-impacts-eqtl-discovery-across-multiple-tissues-in-baboons
#26
JOURNAL ARTICLE
Rachel M Petersen, Amanda J Lea
Understanding how genetic variation impacts gene expression is a major goal of genomics; however, only a fraction of disease-associated loci have been demonstrated to impact gene expression when cells are in an unperturbed "steady state." In this issue of Cell Genomics, Lin et al.1 investigate how exposure to a particular cellular context (i.e., a high-cholesterol, high-fat diet) can enhance our ability to identify new regulatory variants through longitudinal sampling of three tissue types in the baboon...
March 13, 2024: Cell Genom
https://read.qxmd.com/read/38480585/genetic-factors-underlying-host-resistance-to-rhipicephalus-microplus-tick-infestation-in-braford-cattle-a-systems-biology-perspective
#27
JOURNAL ARTICLE
Wanessa A Carvalho, Emanuelle B Gaspar, Robert Domingues, Luciana C A Regitano, Fernando F Cardoso
Approximately 80% of the world's cattle are raised in regions with a high risk of tick-borne diseases, resulting in significant economic losses due to parasitism by Rhipicephalus (Boophilus) microplus. However, the lack of a systemic biology approach hampers a comprehensive understanding of tick-host interactions that mediate tick resistance phenotypes. Here, we conducted a genome-wide association study (GWAS) of 2933 Braford cattle and found 340 single-nucleotide polymorphisms (SNPs) associated with tick counts...
March 13, 2024: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://read.qxmd.com/read/38478511/the-impact-of-genetically-controlled-splicing-on-exon-inclusion-and-protein-structure
#28
JOURNAL ARTICLE
Jonah Einson, Mariia Minaeva, Faiza Rafi, Tuuli Lappalainen
Common variants affecting mRNA splicing are typically identified though splicing quantitative trait locus (sQTL) mapping and have been shown to be enriched for GWAS signals by a similar degree to eQTLs. However, the specific splicing changes induced by these variants have been difficult to characterize, making it more complicated to analyze the effect size and direction of sQTLs, and to determine downstream splicing effects on protein structure. In this study, we catalogue sQTLs using exon percent spliced in (PSI) scores as a quantitative phenotype...
2024: PloS One
https://read.qxmd.com/read/38476469/association-of-antidiabetic-drug-target-genes-with-inflammatory-bowel-disease-a-mendelian-randomization-study
#29
JOURNAL ARTICLE
Xiangli Qing, Lin Wang, Shuangshuang Fang, Yanran Ban, Zhuotai Zhong, Weiqi Sun, Chenhui Zhang, Tao Zhang, Yang Yang, Wei Wei
BACKGROUND: An unmet medical need for the treatment of inflammatory bowel disease (IBD) exists. A part of antidiabetic drugs had potential effects on IBD in various observational research. OBJECTIVE: To investigate the potential of antidiabetic drugs on IBD. METHODS: We undertook a summary-data-based Mendelian randomization (SMR) using the expression quantitative trait loci (eQTL) expressed in the blood or colon and a two sample Mendelian randomization (TSMR) utilizing single nucleotide polymorphism (SNP) of antidiabetic drug target genes mediated by blood glucose traits...
2024: Journal of Inflammation Research
https://read.qxmd.com/read/38464248/adelle-a-global-testing-method-for-trans-eqtl-mapping
#30
Takintayo Akinbiyi, Mary Sara McPeek, Mark Abney
Understanding the genetic regulatory mechanisms of gene expression is a challenging and ongoing problem. Genetic variants that are associated with expression levels are readily identified when they are proximal to the gene (i.e., cis-eQTLs), but SNPs distant from the gene whose expression levels they are associated with (i.e., trans-eQTLs) have been much more difficult to discover, even though they account for a majority of the heritability in gene expression levels. A major impediment to the identification of more trans-eQTLs is the lack of statistical methods that are powerful enough to overcome the obstacles of small effect sizes and large multiple testing burden of trans-eQTL mapping...
February 26, 2024: bioRxiv
https://read.qxmd.com/read/38464142/complex-traits-heritability-is-highly-clustered-in-the-eqtl-bipartite-network
#31
Katherine Stone, John Platig, John Quackenbush, Maud Fagny
Single Nucleotide Polymorphisms (SNPs) associated with traits typically explain a small part of the trait genetic heritability- with the remainder thought to be distributed throughout the genome. Such SNPs are likely to alter expression levels of biologically relevant genes. Expression Quantitative Trait Locus (eQTL) networks analysis has helped to functionally characterize such variants. We systematically analyze the distribution of SNP heritability for ten traits across 29 tissue-specific eQTL networks. We find that heritability is clustered in a small number or tissue-specific, functionally relevant SNP-gene modules and that the greatest occurs in local "hubs" that are both the cornerstone of the network's modules and tissue-specific regulatory elements...
March 1, 2024: bioRxiv
https://read.qxmd.com/read/38464086/prioritizing-metabolic-gene-regulators-through-multi-omic-network-integration-in-maize
#32
Fabio Gomez-Cano, Jonas Rodriguez, Peng Zhou, Yi-Hsuan Chu, Erika Magnusson, Lina Gomez-Cano, Arjun Krishnan, Nathan M Springer, Natalia de Leon, Erich Grotewold
Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks...
February 27, 2024: bioRxiv
https://read.qxmd.com/read/38464039/withdrawn-the-effect-of-ischemia-on-expression-quantitative-trait-loci-eqtl-in-human-myocardium-and-insights-into-myocardial-injury-etiology
#33
Azam Yazdani, Sameeksha Tiwari, Mahyar Heydarpour
To understand the pathological processes of myocardial ischemia in humans, we performed RNA sequencing of the left ventricle (LV) tissue samples in 118 patients undergoing aortic valve replacement surgery at baseline and after cold cardioplegic arrest/ischemia, single-cell RNA sequencing was additionally performed in four patients. We characterized the genetic basis of interindividual variation in the transcriptome of human LV in baseline and post-ischemia conditions by the identification of local expression quantitative trait loci (cis-eQTL)...
February 20, 2024: Research Square
https://read.qxmd.com/read/38461317/incorporating-genetic-similarity-of-auxiliary-samples-into-egene-identification-under-the-transfer-learning-framework
#34
JOURNAL ARTICLE
Shuo Zhang, Zhou Jiang, Ping Zeng
BACKGROUND: The term eGene has been applied to define a gene whose expression level is affected by at least one independent expression quantitative trait locus (eQTL). It is both theoretically and empirically important to identify eQTLs and eGenes in genomic studies. However, standard eGene detection methods generally focus on individual cis-variants and cannot efficiently leverage useful knowledge acquired from auxiliary samples into target studies. METHODS: We propose a multilocus-based eGene identification method called TLegene by integrating shared genetic similarity information available from auxiliary studies under the statistical framework of transfer learning...
March 9, 2024: Journal of Translational Medicine
https://read.qxmd.com/read/38459946/singleq-a-comprehensive-database-of-single-cell-expression-quantitative-trait-loci-sc-eqtls-cross-human-tissues
#35
JOURNAL ARTICLE
Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M Gracie Gordon, Chun Jimmie Ye, Joseph E Powell, Mulin Jun Li, Shuquan Rao
Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner...
March 9, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38459044/multivariate-canonical-correlation-analysis-identifies-additional-genetic-variants-for-chronic-kidney-disease
#36
JOURNAL ARTICLE
Amy J Osborne, Agnieszka Bierzynska, Elizabeth Colby, Uwe Andag, Philip A Kalra, Olivier Radresa, Philipp Skroblin, Maarten W Taal, Gavin I Welsh, Moin A Saleem, Colin Campbell
Chronic kidney diseases (CKD) have genetic associations with kidney function. Univariate genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), two complementary kidney function markers. However, it is unknown whether additional SNPs for kidney function can be identified by multivariate statistical analysis. To address this, we applied canonical correlation analysis (CCA), a multivariate method, to two individual-level CKD genotype datasets, and metaCCA to two published GWAS summary statistics datasets...
March 9, 2024: NPJ Systems Biology and Applications
https://read.qxmd.com/read/38459032/non-coding-autoimmune-risk-variant-defines-role-for-icos-in-t-peripheral-helper-cell-development
#37
JOURNAL ARTICLE
Taehyeung Kim, Marta MartĂ­nez-Bonet, Qiang Wang, Nicolaj Hackert, Jeffrey A Sparks, Yuriy Baglaenko, Byunghee Koh, Roxane Darbousset, Raquel Laza-Briviesca, Xiaoting Chen, Vitor R C Aguiar, Darren J Chiu, Harm-Jan Westra, Maria Gutierrez-Arcelus, Matthew T Weirauch, Soumya Raychaudhuri, Deepak A Rao, Peter A Nigrovic
Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors...
March 9, 2024: Nature Communications
https://read.qxmd.com/read/38457400/the-primary-ciliary-dyskinesia-related-genetic-risk-score-is-associated-with-susceptibility-to-adult-onset-asthma
#38
JOURNAL ARTICLE
Rie Shigemasa, Hironori Masuko, Hisayuki Oshima, Kentaro Hyodo, Haruna Kitazawa, Jun Kanazawa, Yohei Yatagai, Hiroaki Iijima, Takashi Naito, Takefumi Saito, Satoshi Konno, Tomomitsu Hirota, Mayumi Tamari, Tohru Sakamoto, Nobuyuki Hizawa
BACKGROUND: Disturbance of mucociliary clearance is an important factor in the pathogenesis of asthma. We hypothesized that common variants in genes responsible for ciliary function may contribute to the development of asthma with certain phenotypes. METHODS: Three independent adult Japanese populations (including a total of 1,158 patients with asthma and 2,203 non-asthmatic healthy participants) were studied. First, based on the ClinVar database (https://www.ncbi...
2024: PloS One
https://read.qxmd.com/read/38457382/sedentary-behavior-physical-activity-sleep-duration-and-obesity-risk-mendelian-randomization-study
#39
JOURNAL ARTICLE
Siqing Chen, Lili Yang, Yuting Yang, Wenmini Shi, Matthew Stults-Kolehmainen, Qiao Yuan, Chenchen Wang, Jing Ye
BACKGROUND: Observational studies have suggested associations between sedentary behaviors (SB), physical activity (PA), sleep duration (SD), and obesity, but the causal relationships remain unclear. METHODS: We used Mendelian randomization (MR) with genetic variation as instrumental variables (IVs) to assess the causality between SB/PA/SD and obesity. Genetic variants associated with SB/PA/SD were obtained from Genome-wide association study (GWAS), and obesity data came from FinnGen...
2024: PloS One
https://read.qxmd.com/read/38454350/genome-wide-association-studies-highlight-novel-risk-loci-for-septal-defects-and-left-sided-congenital-heart-defects
#40
JOURNAL ARTICLE
Martin Broberg, Minna Ampuja, Samuel Jones, Tiina Ojala, Otto Rahkonen, Riikka Kivelä, James Priest, Aarno Palotie, Hanna M Ollila, Emmi Helle
BACKGROUND: Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk, we performed a genome wide association study (GWAS) of CHDs in general and specific CHD subgroups using the FinnGen Release 10 (R10) (N > 393,000), followed by functional fine-mapping through eQTL and co-localization analyses using the GTEx database...
March 7, 2024: BMC Genomics
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