Use the keywords feature with a free QxMD account.
Use Read by QxMD to access full text via your institution or open access sources.
Read also provides personalized recommendations to keep you up to date in your field.
Existing User
Sign InNew to Read
Sign Up#21
JOURNAL ARTICLE
Lulu Shang, Wei Zhao, Yi Zhe Wang, Zheng Li, Jerome J Choi, Minjung Kho, Thomas H Mosley, Sharon L R Kardia, Jennifer A Smith, Xiang Zhou
Identifying genetic variants that are associated with variation in DNA methylation, an analysis commonly referred to as methylation quantitative trait locus (meQTL) mapping, is an important first step towards understanding the genetic architecture underlying epigenetic variation. Most existing meQTL mapping studies have focused on individuals of European ancestry and are underrepresented in other populations, with a particular absence of large studies in populations with African ancestry. We fill this critical knowledge gap by performing a large-scale cis-meQTL mapping study in 961 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA) study...
May 11, 2023: Nature Communications
#22
JOURNAL ARTICLE
Fengjun Wu, Hongjiao Wu, Wenqian Hu, Zhi Zhang, Xuemei Zhang
OBJECTIVES: WD repeat-containing protein 74 (WDR74) has been linked with the development of lung cancer. This study aims to investigate the relationship between WDR74 rs11231247 and non-small cell lung cancer (NSCLC) susceptibility and the prognosis of NSCLC patients. METHODS: UALCAN, MethPrimer, ensembl and Pancan meQTL databases were used for bioinformatics analysis. The case-control study included 462 NSCLC patients and 462 health controls. WDR74 rs11231247 genotype was determined by PCR-RFLP...
January 21, 2023: Pathology, Research and Practice
#23
JOURNAL ARTICLE
Lu-Lu Yu, Bi-Wen Hu, Han-Xue Huang, Bing Yu, Qi Xiao, Qiao-Li Lv, Chen-Hui Luo, Cheng-Xian Guo, Jin-Gao Li, Xiao-Xue Xie, Ji-Ye Yin
BACKGROUND: Radiotherapy (RT) is the standard treatment for nasopharyngeal carcinoma (NPC). However, due to individual differences in radiosensitivity, biomarkers are needed to tailored radiotherapy to cancer patients. However, comprehensive genome-wide radiogenomic studies on them are still lacking. The aim of this study was to identify genetic variants associated with radiotherapy response in patients with NPC. METHODS: This was a large‑scale genome-wide association analysis (GWAS) including a total of 981 patients...
January 9, 2023: Journal of Translational Medicine
#24
JOURNAL ARTICLE
Rachel G Miller, Josyf C Mychaleckyj, Suna Onengut-Gumuscu, Trevor J Orchard, Tina Costacou
INTRODUCTION: DNA methylation (DNAme) has been cross-sectionally associated with type 2 diabetes and hemoglobin A1c (HbA1c) in the general population. However, longitudinal data and data in type 1 diabetes are currently very limited. Thus, we performed an epigenome-wide association study (EWAS) in an observational type 1 diabetes cohort to identify loci with DNAme associated with concurrent and future HbA1cs, as well as other clinical risk factors, over 28 years. RESEARCH DESIGN AND METHODS: Whole blood DNAme in 683 597 CpGs was analyzed in the Pittsburgh Epidemiology of Diabetes Complications study of childhood onset (<17 years) type 1 diabetes (n=411)...
January 2023: BMJ Open Diabetes Research & Care
#25
JOURNAL ARTICLE
Yaqi Li, Chunmei Gong, Yuanfei Xu, Xiongshun Liang, Xiaoping Chen, Wenxu Hong, Junxia Yan
BACKGROUND: Diabetic retinopathy (DR) is a common and serious microvascular complication of diabetes mellitus (DM), but its pathological mechanism, especially the formation mechanism of new blood vessels remains unclear. Thrombospondin-1 ( THBS1 ) is a potent endogenous inhibitor of angiogenesis and it was found over expressed in DR in our previous study. Our study aimed to determine whether overexpression of THBS1 is associated with its promoter methylation level, and whether methylation of THBS1 is regulated by genetic variants in DR...
2022: Frontiers in Endocrinology
#26
JOURNAL ARTICLE
Erping Long, Jinhu Yin, Karen M Funderburk, Mai Xu, James Feng, Alexander Kane, Tongwu Zhang, Timothy Myers, Alyxandra Golden, Rohit Thakur, Hyunkyung Kong, Lea Jessop, Eun Young Kim, Kristine Jones, Raj Chari, Mitchell J Machiela, Kai Yu, Mark M Iles, Maria Teresa Landi, Matthew H Law, Stephen J Chanock, Kevin M Brown, Jiyeon Choi
The most recent genome-wide association study (GWAS) of cutaneous melanoma identified 54 risk-associated loci, but functional variants and their target genes for most have not been established. Here, we performed massively parallel reporter assays (MPRAs) by using malignant melanoma and normal melanocyte cells and further integrated multi-layer annotation to systematically prioritize functional variants and susceptibility genes from these GWAS loci. Of 1,992 risk-associated variants tested in MPRAs, we identified 285 from 42 loci (78% of the known loci) displaying significant allelic transcriptional activities in either cell type (FDR < 1%)...
November 18, 2022: American Journal of Human Genetics
#27
JOURNAL ARTICLE
Guoping Tang, Chen Sun, Hongchao Lv, Mingming Zhang, Yongshuai Jiang, Jing Xu
Rheumatoid arthritis (RA) is highly heritable, and previous studies have suggested that genetic variation may affect susceptibility to RA by altering epigenetic modifications (e.g., DNA methylation). Here, we examined how genetic variation influences DNA methylation (DNAm) in RA by integrating individual genetic variation and DNAm data. Epigenome-wide meQTL (methylation quantitative trait loci) analysis was performed on 354 RA patients and 335 controls, scanning 30,101,744 relationships between 62 SNPs and 485,512 DNA methylation sites...
November 7, 2022: FEBS Open Bio
#28
JOURNAL ARTICLE
Kimberly C Paul, Cynthia Kusters, Melissa Furlong, Keren Zhang, Yu Yu, Aline Duarte Folle, Irish Del Rosario, Adrienne Keener, Jeff Bronstein, Janet S Sinsheimer, Steve Horvath, Beate Ritz
Although Parkinson's Disease (PD) is typically described in terms of motor symptoms, depression is a common feature. We explored whether depression influences blood-based genome-wide DNA methylation (DNAm) in 692 subjects from a population-based PD case-control study, using both a history of clinically diagnosed depression and current depressive symptoms measured by the geriatric depression scale (GDS). While PD patients in general had more immune activation and more accelerated epigenetic immune system aging than controls, the patients experiencing current depressive symptoms (GDS≥5) showed even higher levels of both markers than patients without current depressive symptoms (GDS<5)...
December 2022: Brain, behavior, & immunity health
#29
JOURNAL ARTICLE
Junyi Xin, Dongying Gu, Silu Chen, Shuai Ben, Huiqin Li, Zhengdong Zhang, Mulong Du, Meilin Wang
Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains unestablished. Here, we systematically evaluated genetic effects at the genome-wide level on cancer survival that included overall survival (OS) and cancer-specific survival (CSS), leveraging data deposited in the UK Biobank cohort of a total of 19 628 incident patients across 17 cancer types...
August 10, 2022: Nucleic Acids Research
#30
JOURNAL ARTICLE
Patrick Coit, Xiavan Roopnarinesingh, Lourdes Ortiz-Fernández, Kathleen McKinnon-Maksimowicz, Emily E Lewis, Joan T Merrill, W Joseph McCune, Jonathan D Wren, Amr H Sawalha
OBJECTIVES: Lupus T cells demonstrate aberrant DNA methylation patterns dominated by hypomethylation of interferon-regulated genes. The objective of this study was to identify additional lupus-associated DNA methylation changes and determine the genetic contribution to epigenetic changes characteristic of lupus. METHODS: Genome-wide DNA methylation was assessed in naïve CD4+ T cells from 74 patients with lupus and 74 age-matched, sex-matched and race-matched healthy controls...
October 2022: Annals of the Rheumatic Diseases
#31
JOURNAL ARTICLE
Michelle L Roberts, Theodore Kotchen, Xiaoqing Pan, Yingchuan Li, Chun Yang, Pengyuan Liu, Tao Wang, Purushottam Laud, Thomas H Chelius, Yannick Munyura, David L Mattson, Yong Liu, Allen W Cowley, Srividya Kidambi, Mingyu Liang
Epigenetics may reflect the interactions between DNA and environment and lifestyle and DNA methylation marks have been implicated in the development and progression of hypertension. In an African American (AA) cohort of hypertensives and normotensives (n = 281), we have recently discovered up to 72 methylation regions (MRs) in whole blood DNA that were significantly associated with 24-h BP phenotypes (False Discovery Rate (FDR) < 0.05) via reduced representation bisulfite sequencing (RRBS). One-time clinic BP measurements were not associated with MRs...
May 2022: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
#32
JOURNAL ARTICLE
Michela Traglia, Margaux Bout, Lauren A Weiss
Phenotypic differences across sexes are pervasive, but the genetic architecture of sex differences within and across phenotypes is mostly unknown. In this study, we aimed to improve detection power for sex-differentially contributing SNPs previously demonstrated to be enriched in disease association, and we investigate their functions in health, pathophysiology, and genetic function. We leveraged GIANT and UK Biobank summary statistics and defined a set of 2,320 independent SNPs having sexually dimorphic effects within and across biometric traits (MAF > 0...
May 2022: PLoS Genetics
#33
JOURNAL ARTICLE
Boyang Li, Bradley E Aouizerat, Youshu Cheng, Kathryn Anastos, Amy C Justice, Hongyu Zhao, Ke Xu
Here we report three epigenome-wide association studies (EWAS) of DNA methylation on self-reported race, global genetic ancestry, and local genetic ancestry in admixed Americans from three sets of samples, including internal and external replications (Ntotal = 1224). Our EWAS on local ancestry (LA) identified the largest number of ancestry-associated DNA methylation sites and also featured the highest replication rate. Furthermore, by incorporating ancestry origins of genetic variations, we identified 36 methylation quantitative trait loci (meQTL) clumps for LA-associated CpGs that cannot be captured by a model that assumes identical genetic effects across ancestry origins...
April 29, 2022: Communications Biology
#34
JOURNAL ARTICLE
Hong Pan, Pei Fang Tan, Ives Y Lim, Jason Huan, Ai Ling Teh, Li Chen, Min Gong, Felicia Tin, Sartaj Ahmad Mir, Kothandaraman Narasimhan, Jerry K Y Chan, Kok Hian Tan, Michael S Kobor, Peter J Meikle, Markus R Wenk, Yap Seng Chong, Johan G Eriksson, Peter D Gluckman, Neerja Karnani
Asians are underrepresented across many omics databases, thereby limiting the potential of precision medicine in nearly 60% of the global population. As such, there is a pressing need for multi-omics derived quantitative trait loci (QTLs) to fill the knowledge gap of complex traits in populations of Asian ancestry. Here we provide the first blood-based multi-omics analysis of Asian pregnant women, constituting high-resolution genotyping (N = 1079), DNA methylation (N = 915) and transcriptome profiling (N = 238)...
April 21, 2022: Human Molecular Genetics
#35
JOURNAL ARTICLE
Basharat Bhat, Gregory T Jones
Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results...
2022: Methods in Molecular Biology
#36
JOURNAL ARTICLE
José Jaime Martínez-Magaña, Sandra Hernandez, Ana Rosa Garcia, Valeria Cardoso-Barajas, Emmanuel Sarmiento, Beatriz Camarena, Alejandro Caballero, Laura Gonzalez, Jorge Ameth Villatoro-Velazquez, Maria Elena Medina-Mora, Marycarmen Bustos-Gamiño, Clara Fleiz-Bautista, Carlos Alfonso Tovilla-Zarate, Isela Esther Juárez-Rojop, Humberto Nicolini, Alma Delia Genis-Mendoza
Alterations in eating behavior characterized eating disorders (ED). The genetic factors shared between ED diagnoses have been underexplored. The present study performed a genome-wide association study in individuals with disordered eating behaviors in the Mexican population, blood methylation quantitative trait loci (blood-meQTL), summary data-based Mendelian randomization (SMR) analysis, and in silico function prediction by different algorithms. The analysis included a total of 1803 individuals. We performed a genome-wide association study and blood-meQTL analysis by logistic and linear regression...
January 17, 2022: Nutrients
#37
JOURNAL ARTICLE
Ram Ajore, Abhishek Niroula, Maroulio Pertesi, Caterina Cafaro, Malte Thodberg, Molly Went, Erik L Bao, Laura Duran-Lozano, Aitzkoa Lopez de Lapuente Portilla, Thorunn Olafsdottir, Nerea Ugidos-Damboriena, Olafur Magnusson, Mehmet Samur, Caleb A Lareau, Gisli H Halldorsson, Gudmar Thorleifsson, Gudmundur L Norddahl, Kristbjorg Gunnarsdottir, Asta Försti, Hartmut Goldschmidt, Kari Hemminki, Frits van Rhee, Scott Kimber, Adam S Sperling, Martin Kaiser, Kenneth Anderson, Ingileif Jonsdottir, Nikhil Munshi, Thorunn Rafnar, Anders Waage, Niels Weinhold, Unnur Thorsteinsdottir, Vijay G Sankaran, Kari Stefansson, Richard Houlston, Björn Nilsson
Thousands of non-coding variants have been associated with increased risk of human diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an integrative study combining massively parallel reporter assays (MPRA), expression analyses (eQTL, meQTL, PCHiC) and chromatin accessibility analyses in primary cells (caQTL), we investigate 1,039 variants associated with multiple myeloma (MM). We demonstrate that MM susceptibility is mediated by gene-regulatory changes in plasma cells and B-cells, and identify putative causal variants at six risk loci (SMARCD3, WAC, ELL2, CDCA7L, CEP120, and PREX1)...
January 10, 2022: Nature Communications
#38
JOURNAL ARTICLE
Johann S Hawe, Rory Wilson, Katharina T Schmid, Li Zhou, Lakshmi Narayanan Lakshmanan, Benjamin C Lehne, Brigitte Kühnel, William R Scott, Matthias Wielscher, Yik Weng Yew, Clemens Baumbach, Dominic P Lee, Eirini Marouli, Manon Bernard, Liliane Pfeiffer, Pamela R Matías-García, Matias I Autio, Stephane Bourgeois, Christian Herder, Ville Karhunen, Thomas Meitinger, Holger Prokisch, Wolfgang Rathmann, Michael Roden, Sylvain Sebert, Jean Shin, Konstantin Strauch, Weihua Zhang, Wilson L W Tan, Stefanie M Hauck, Juliane Merl-Pham, Harald Grallert, Eudes G V Barbosa, Thomas Illig, Annette Peters, Tomas Paus, Zdenka Pausova, Panos Deloukas, Roger S Y Foo, Marjo-Riitta Jarvelin, Jaspal S Kooner, Marie Loh, Matthias Heinig, Christian Gieger, Melanie Waldenberger, John C Chambers
We determined the relationships between DNA sequence variation and DNA methylation using blood samples from 3,799 Europeans and 3,195 South Asians. We identify 11,165,559 SNP-CpG associations (methylation quantitative trait loci (meQTL), P < 10-14 ), including 467,915 meQTL that operate in trans. The meQTL are enriched for functionally relevant characteristics, including shared chromatin state, High-throuhgput chromosome conformation interaction, and association with gene expression, metabolic variation and clinical traits...
January 3, 2022: Nature Genetics
#39
JOURNAL ARTICLE
Marcus M Soliai, Atsushi Kato, Britney A Helling, Catherine T Stanhope, James E Norton, Katherine A Naughton, Aiko I Klinger, Emma E Thompson, Selene M Clay, Soyeon Kim, Juan C Celedón, James E Gern, Daniel J Jackson, Matthew C Altman, Robert C Kern, Bruce K Tan, Robert P Schleimer, Dan L Nicolae, Jayant M Pinto, Carole Ober
BACKGROUND: Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes. To address these limitations, we used an upper airway epithelial cell (AEC) culture model to assess transcriptional and epigenetic responses to rhinovirus (RV), an asthma-promoting pathogen, and provide context-specific functional annotations to variants discovered in GWASs of asthma...
October 10, 2021: Genome Medicine
#40
JOURNAL ARTICLE
Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
BACKGROUND: Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays' probe design cannot fully consider the vast human genetic diversity, leading to genetic artifacts. Distinguishing genuine from artifactual genetic influence is of particular relevance in the study of DNA methylation heritability and methylation quantitative trait loci. But despite its importance, current strategies to account for genetic artifacts are lagging due to a limited mechanistic understanding on how such artifacts operate...
September 21, 2021: Genome Biology
Make the most of Read.
Download the mobile app.
Download the mobile app.
Fetching more papers... 
