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Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genome-wide association studies (GWASs) have identified multiple intergenic single nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (Hi-C), epigenetic annotation and a series of functional assays...
March 12, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Gen Li, Dereje Jima, Fred A Wright, Andrew B Nobel
BACKGROUND: Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood. Joint analysis of eQTL in multiple tissues has the potential to improve, and expand the scope of, single-tissue analyses. Large-scale collaborative efforts such as the Genotype-Tissue Expression (GTEx) program are currently generating high quality data in a large number of tissues...
March 9, 2018: BMC Bioinformatics
Kai Imkamp, Marijn Berg, Cornelis J Vermeulen, Irene H Heijink, Victor Guryev, Huib Am Kerstjens, Gerard H Koppelman, Maarten van den Berge, Alen Faiz
No abstract text is available yet for this article.
March 6, 2018: Journal of Allergy and Clinical Immunology
Meng-Zhu Lu, Qian-Qian Ang, Xiang Zhang, Lan-Fang Zhang, Xiu-Hua Yao, Hong Lv, Xiao-Dong Zheng, Wen-Sheng Lu
A keloid is the process of skin healing, collagen synthesis and metabolism of the loss of normal control in a sustained hyperactive state, resulting in excessive proliferation of collagen fibers. A large-scale genome-wide association study (GWAS) has identified multiple single nucleotide polymorphisms (SNPs) in the 3q22.3 loci that are associated with keloids in a Japanese population. However, the associations of SNPs in 3q22.3 with keloids were not confirmed in a selected Chinese population by a replication study...
2018: American Journal of Translational Research
Sébastien Thériault, Nathalie Gaudreault, Maxime Lamontagne, Mickael Rosa, Marie-Chloé Boulanger, David Messika-Zeitoun, Marie-Annick Clavel, Romain Capoulade, François Dagenais, Philippe Pibarot, Patrick Mathieu, Yohan Bossé
Calcific aortic valve stenosis (CAVS) is a common and life-threatening heart disease and the current treatment options cannot stop or delay its progression. A GWAS on 1009 cases and 1017 ethnically matched controls was combined with a large-scale eQTL mapping study of human aortic valve tissues (n = 233) to identify susceptibility genes for CAVS. Replication was performed in the UK Biobank, including 1391 cases and 352,195 controls. A transcriptome-wide association study (TWAS) reveals PALMD (palmdelphin) as significantly associated with CAVS...
March 7, 2018: Nature Communications
Angel Cy Mak, Marquitta J White, Walter L Eckalbar, Zachary A Szpiech, Sam S Oh, Maria Pino-Yanes, Donglei Hu, Pagé Goddard, Scott Huntsman, Joshua Galanter, Ann Chen Wu, Blanca E Himes, Soren Germer, Julia M Vogel, Karen L Bunting, Celeste Eng, Sandra Salazar, Kevin L Keys, Jennifer Liberto, Thomas J Nuckton, Thomas A Nguyen, Dara G Torgerson, Pui-Yan Kwok, Albert M Levin, Juan C Celedón, Erick Forno, Hakon Hakonarson, Patrick M Sleiman, Amber Dahlin, Kelan G Tantisira, Scott T Weiss, Denise Serebrisky, Emerita Brigino-Buenaventura, Harold J Farber, Kelley Meade, Michael A Lenoir, Pedro C Avila, Saunak Sen, Shannon M Thyne, William Rodriguez-Cintron, Cheryl A Winkler, Andrés Moreno-Estrada, Karla Sandoval, Jose R Rodriguez-Santana, Rajesh Kumar, L Keoki Williams, Nadav Ahituv, Elad Ziv, Max A Seibold, Robert B Darnell, Noah Zaitlen, Ryan D Hernandez, Esteban G Burchard
Rationale Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. Objective To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. Methods We performed the first whole genome sequencing (WGS) pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. Measurements and Main Results We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (p < 3...
March 6, 2018: American Journal of Respiratory and Critical Care Medicine
Thomas J Hoffmann, Elizabeth Theusch, Tanushree Haldar, Dilrini K Ranatunga, Eric Jorgenson, Marisa W Medina, Mark N Kvale, Pui-Yan Kwok, Catherine Schaefer, Ronald M Krauss, Carlos Iribarren, Neil Risch
A genome-wide association study (GWAS) of 94,674 ancestrally diverse Kaiser Permanente members using 478,866 longitudinal electronic health record (EHR)-derived measurements for untreated serum lipid levels empowered multiple new findings: 121 new SNP associations (46 primary, 15 conditional, and 60 in meta-analysis with Global Lipids Genetic Consortium data); an increase of 33-42% in variance explained with multiple measurements; sex differences in genetic impact (greater impact in females for LDL, HDL, and total cholesterol and the opposite for triglycerides); differences in variance explained among non-Hispanic whites, Latinos, African Americans, and East Asians; genetic dominance and epistatic interaction, with strong evidence for both at the ABO and FUT2 genes for LDL; and tissue-specific enrichment of GWAS-associated SNPs among liver, adipose, and pancreas eQTLs...
March 5, 2018: Nature Genetics
Jiyoun Yeo, Diego A Morales, Tian Chen, Erin L Crawford, Xiaolu Zhang, Thomas M Blomquist, Albert M Levin, Pierre P Massion, Douglas A Arenberg, David E Midthun, Peter J Mazzone, Steven D Nathan, Ronald J Wainz, Patrick Nana-Sinkam, Paige F S Willey, Taylor J Arend, Karanbir Padda, Shuhao Qiu, Alexei Federov, Dawn-Alita R Hernandez, Jeffrey R Hammersley, Youngsook Yoon, Fadi Safi, Sadik A Khuder, James C Willey
BACKGROUND: There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. METHODS: To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0...
March 5, 2018: BMC Pulmonary Medicine
Lu Wang, I King Jordan
A convergence of novel genome analysis technologies is enabling population genomic studies of human transposable elements (TEs). Population surveys of human genome sequences have uncovered thousands of individual TE insertions that segregate as common genetic variants, i.e. TE polymorphisms. These recent TE insertions provide an important source of naturally occurring human genetic variation. Investigators are beginning to leverage population genomic data sets to execute genome-scale association studies for assessing the phenotypic impact of human TE polymorphisms...
March 2, 2018: Current Opinion in Genetics & Development
Helen H Tai, David De Koeyer, Mads Sønderkær, Sanne Hedegaard, Martin Lagüe, Claudia Goyer, Lana Nolan, Charlotte Davidson, Kyle Gardner, Jonathan Neilson, Jamuna Risal Paudel, Agnes Murphy, Benoit Bizimungu, Hui Ying Wang, Xingyao Xiong, Dennis Halterman, Kåre Lehmann Nielsen
Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato ( L.). Genetic mapping of resistance to was done using a diploid population of potato. The major quantitative trait locus (QTL) for resistance was found on chromosome 5. The gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that functioned downstream of The alleles were sequenced and found to encode StCDF1...
March 2018: Plant Genome
Veroniqa Lundbäck, Agne Kulyte, Rona J Strawbridge, Mikael Ryden, Peter Arner, Claude Marcus, Ingrid Dahlman
AIMS/HYPOTHESIS: By genome-wide association meta-analysis, 17 genetic loci associated with fasting serum insulin (FSI), a marker of systemic insulin resistance, have been identified. To define potential culprit genes in these loci, in a cross-sectional study we analysed white adipose tissue (WAT) expression of 120 genes in these loci in relation to systemic and adipose tissue variables, and functionally evaluated genes demonstrating genotype-specific expression in WAT (eQTLs). METHODS: Abdominal subcutaneous adipose tissue biopsies were obtained from 114 women...
February 27, 2018: Diabetologia
Timothy D O'Brien, Peilin Jia, Neil E Caporaso, Maria Teresa Landi, Zhongming Zhao
BACKGROUND: There are two main types of lung cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC has many subtypes, but the two most common are lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). These subtypes are mainly classified by physiological and pathological characteristics, although there is increasing evidence of genetic and molecular differences as well. Although some work has been done at the somatic level to explore the genetic and biological differences among subtypes, little work has been done that interrogates these differences at the germline level to characterize the unique and shared susceptibility genes for each subtype...
February 27, 2018: Genome Medicine
Cui-Ping Yang, Xiaoyan Li, Yong Wu, Qiushuo Shen, Yong Zeng, Qiuxia Xiong, Mengping Wei, Chunhui Chen, Jiewei Liu, Yongxia Huo, Kaiqin Li, Gui Xue, Yong-Gang Yao, Chen Zhang, Ming Li, Yongbin Chen, Xiong-Jian Luo
Recent genome-wide association studies (GWAS) have identified multiple risk loci that show strong associations with schizophrenia. However, pinpointing the potential causal genes at the reported loci remains a major challenge. Here we identify candidate causal genes for schizophrenia using an integrative genomic approach. Sherlock integrative analysis shows that ALMS1, GLT8D1, and CSNK2B are schizophrenia risk genes, which are validated using independent brain expression quantitative trait loci (eQTL) data and integrative analysis method (SMR)...
February 26, 2018: Nature Communications
Dan Zhcou, Dandan Zhang, Xiaohui Sun, Zhiqiang Li, Yaqin Ni, Zhongyan Shan, Hong Li, Chengguo Liu, Shuai Zhang, Yi Liu, Ruizhi Zheng, Feixia Pan, Yimin Zhu, Yongyong Shi, Maode Lai
Although numbers of genome-wide association studies (GWAS) have been performed for serum lipid levels, limited heritability has been explained. Studies showed that combining data from GWAS and expression quantitative trait loci (eQTLs) signals can both enhance the discovery of trait-associated SNPs and gain a better understanding of the mechanism. We performed an annotation-based, multistage genome-wide screening for serum-lipid-level-associated loci in totally 6863 Han Chinese. A serum high-density lipoprotein cholesterol (HDL-C) associated variant rs1880118 (hg19 chr7:g...
February 23, 2018: European Journal of Human Genetics: EJHG
Brandon L Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md Yunus, Muhammad G Kibriya, Lin S Chen, Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i...
February 23, 2018: Nature Communications
Naina Gour, Stephane Lajoie, Ursula Smole, Marquitta White, Donglei Hu, Pagé Goddard, Scott Huntsman, Celeste Eng, Angel Mak, Sam Oh, Jung-Hyun Kim, Annu Sharma, Sophie Plante, Ikhlass Haj Salem, Yvonne Resch, Xiao Xiao, Nu Yao, Anju Singh, Susanne Vrtala, Jamila Chakir, Esteban G Burchard, Andrew P Lane, Marsha Wills-Karp
The key factors underlying the development of allergic diseases-the propensity for a minority of individuals to develop dysfunctional responses to harmless environmental molecules-remain undefined. We report a pathway of immune counter-regulation that suppresses the development of aeroallergy and shrimp-induced anaphylaxis. In mice, signaling through epithelially expressed dectin-1 suppresses the development of type 2 immune responses through inhibition of interleukin-33 (IL-33) secretion and the subsequent recruitment of IL-13-producing innate lymphoid cells...
February 23, 2018: Science Immunology
Benjamin H Mullin, Kun Zhu, Jiake Xu, Suzanne J Brown, Shelby Mullin, Jennifer Tickner, Nathan J Pavlos, Frank Dudbridge, John P Walsh, Scott G Wilson
Osteoporosis is a complex disease with a strong genetic component. Genome-wide association studies (GWAS) have been very successful at identifying common genetic variants associated with bone parameters. A recently published study documented the results of the largest GWAS for bone mineral density (BMD) performed to date (n = 142,487), identifying 307 conditionally independent single-nucleotide polymorphisms (SNPs) as associated with estimated BMD (eBMD) at the genome-wide significance level. The vast majority of these variants are non-coding SNPs...
February 23, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Kunjiang Yu, Xiaodong Wang, Feng Chen, Qi Peng, Song Chen, Hongge Li, Wei Zhang, Sanxiong Fu, Maolong Hu, Weihua Long, Pu Chu, Rongzhan Guan, Jiefu Zhang
The apetalous trait of rapeseed ( Brassica napus , AACC, 2 n = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to Sclerotinia sclerotiorum . Currently, the molecular mechanism underlying the apetalous trait of rapeseed is unclear. In this study, 14 petal regulators genes were chosen as target genes (TGs), and the expression patterns of the 14 TGs in the AH population, containing 189 recombinant inbred lines derived from a cross between apetalous "APL01" and normal "Holly," were analyzed in two environments using qRT-PCR...
2018: Frontiers in Plant Science
Aniek C Bouwman, Hans D Daetwyler, Amanda J Chamberlain, Carla Hurtado Ponce, Mehdi Sargolzaei, Flavio S Schenkel, Goutam Sahana, Armelle Govignon-Gion, Simon Boitard, Marlies Dolezal, Hubert Pausch, Rasmus F Brøndum, Phil J Bowman, Bo Thomsen, Bernt Guldbrandtsen, Mogens S Lund, Bertrand Servin, Dorian J Garrick, James Reecy, Johanna Vilkki, Alessandro Bagnato, Min Wang, Jesse L Hoff, Robert D Schnabel, Jeremy F Taylor, Anna A E Vinkhuyzen, Frank Panitz, Christian Bendixen, Lars-Erik Holm, Birgit Gredler, Chris Hozé, Mekki Boussaha, Marie-Pierre Sanchez, Dominique Rocha, Aurelien Capitan, Thierry Tribout, Anne Barbat, Pascal Croiseau, Cord Drögemüller, Vidhya Jagannathan, Christy Vander Jagt, John J Crowley, Anna Bieber, Deirdre C Purfield, Donagh P Berry, Reiner Emmerling, Kay-Uwe Götz, Mirjam Frischknecht, Ingolf Russ, Johann Sölkner, Curtis P Van Tassell, Ruedi Fries, Paul Stothard, Roel F Veerkamp, Didier Boichard, Mike E Goddard, Ben J Hayes
Stature is affected by many polymorphisms of small effect in humans1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3 . Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8 ) explained at most 13...
February 19, 2018: Nature Genetics
Markus Drag, Mathias B Hansen, Haja N Kadarmideen
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg...
2018: PloS One
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