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Genome wide association studies

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https://www.readbyqxmd.com/read/29679879/polygenic-risk-score-of-serpina6-serpina1-associates-with-diurnal-and-stress-induced-hpa-axis-activity-in-children
#1
Siddheshwar Utge, Katri Räikkönen, Eero Kajantie, Jari Lipsanen, Sture Andersson, Timo Strandberg, Rebecca M Reynolds, Johan G Eriksson, Jari Lahti
PURPOSE: Corticosteroid-binding globulin (CBG) transports glucocorticoids in blood. Variation in genes SERPINA6 encoding for CBG, SERPINA2 and SERPINA1 (serpin family A member 6, 2, and 1) have been shown to influence morning plasma cortisol and CBG in adults. However, association of this genetic variation with diurnal and stress-induced salivary cortisol remain unknown. This study aims to investigate the effect of genetic variation in SERPINA6/2/1 loci on diurnal and stress-induced salivary cortisol in children...
April 13, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29679657/eleven-loci-with-new-reproducible-genetic-associations-with-allergic-disease-risk
#2
Manuel Ar Ferreira, Judith M Vonk, Hansjörg Baurecht, Ingo Marenholz, Chao Tian, Joshua D Hoffman, Quinta Helmer, Annika Tillander, Vilhelmina Ullemar, Yi Lu, Franz Rüschendorf, David A Hinds, Norbert Hübner, Stephan Weidinger, Patrik Ke Magnusson, Eric Jorgenson, Young-Ae Lee, Dorret I Boomsma, Robert Karlsson, Catarina Almqvist, Gerard H Koppelman, Lavinia Paternoster
BACKGROUND: A recent genome-wide association study (GWAS) identified 99 loci that contain genetic risk variants shared between asthma, hay fever and eczema. Many more risk loci shared between these common allergic diseases remain to be discovered, which could point to new therapeutic opportunities. OBJECTIVE: To identify novel risk loci shared between asthma, hay fever and eczema by applying a gene-based test of association to results from a published GWAS that included data from 360,838 individuals...
April 18, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29678584/genome-wide-profiles-of-metastasis-associated-mrnas-and-micrornas-in-salivary-adenoid-cystic-carcinoma
#3
Shubin Wang, Lei Zhang, Pengwei Shi, Yuanyuan Zhang, Hong Zhou, Xuanping Cao
Salivary adenoid cystic carcinoma (SACC) is often accompanied with poor prognosis due to local recurrence, distant metastasis, and perineural invasion. The mechanism involved in SACC metastasis is not yet fully understood. In this study, we profiled the expression of messenger RNA (mRNA) and microRNA (miRNA) in an SACC cell line, ACC-2, and a highly metastatic SACC cell line, ACC-M, using high-throughput sequencing. We discovered that: (1) differentially expressed (DE) mRNAs and DE miRNAs are potentially involved in SACC metastasis; (2) multiple regulatory interactions between DE miRNAs and DE mRNAs exist; and (3) miR-338-5p/3p target LAMC2 to impair motility and invasion of ACC-M and MDA-MB-231 cells...
April 17, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29677560/effective-discovery-of-rare-variants-by-pooled-target-capture-sequencing-a-comparative-analysis-with-individually-indexed-target-capture-sequencing
#4
Seungjin Ryu, Jeehae Han, Trina M Norden-Krichmar, Nicholas J Schork, Yousin Suh
Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies...
March 30, 2018: Mutation Research
https://www.readbyqxmd.com/read/29677463/a-role-for-collagen-iv-in-cardiovascular-disease
#5
Lasse Bach Steffensen, Lars M Rasmussen
Over the past decade, studies have repeatedly found single nucleotide polymorphisms located in the COL4A1 and COL4A2 genes to be associated with cardiovascular disease (CVD), and the 13q34 locus harboring these genes is one of approximately 160 genome-wide significant risk loci for coronary artery disease. COL4A1 and COL4A2 encode the ⍺1- and ⍺2-chains of collagen IV, a major component of basement membranes in various tissues including arteries. In spite of the growing body of evidence indicating a role for collagen IV in CVD, remarkably few studies aim at directly investigating such a role...
April 20, 2018: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29676954/genome-wide-association-study-identifies-loci-and-candidate-genes-for-internal-organ-weights-in-simmental-beef-cattle
#6
Bingxing An, Jiangwei Xia, Tianpeng Chang, Xiaoqiao Wang, Jian Miao, Lingyang Xu, Lupei Zhang, Xue Gao, Yan Chen, Junya Li, Huijiang Gao
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight (HW), liver weight (LIW), spleen weight (SW), lung weight (LUW) and kidney weight (KW) in 1217 Simmental cattle...
April 20, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29676051/genetic-dissection-of-photosynthetic-efficiency-traits-for-enhancing-seed-yield-in-chickpea
#7
Udita Basu, Deepak Bajaj, Akash Sharma, Naveen Malik, Anurag Daware, Laxmi Narnoliya, Virevol Thakro, Hari D Upadhyaya, Rajendra Kumar, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, QTL mapping and expression profiling. This identified 16 potential SNP loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea...
April 20, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29676044/hla-dq%C3%AE-1-amino-acid-position-87-and-dqb1-0301-are-associated-with-chinese-han-sle
#8
Jingying Sun, Chao Yang, Wenmin Fei, Xuelei Zhang, Yujun Sheng, Xiaodong Zheng, Huayang Tang, Wanling Yang, Sen Yang, Xing Fan, Xuejun Zhang
BACKGROUND: Several susceptibility loci have been identified associated with Chinese Han systemic lupus erythematosus (SLE). METHODS: We carried out imputation of classical HLA alleles, amino acids and Single Nucleotide Polymorphisms (SNPs) across the MHC region in Chinese Han SLE genome-wide association study (GWAS) of mainland and Hong Kong populations for the first time using newly constructed Han-MHC reference panel followed by stepwise conditional analysis...
April 19, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29675612/complement-receptor-1-gene-cr1-intragenic-duplication-and-risk-of-alzheimer-s-disease
#9
Ezgi Kucukkilic, Keeley Brookes, Imelda Barber, Tamar Guetta-Baranes, Kevin Morgan, Edward J Hollox
Single nucleotide variants (SNVs) within and surrounding the complement receptor 1 (CR1) gene show some of the strongest genome-wide association signals with late-onset Alzheimer's disease. Some studies have suggested that this association signal is due to a duplication allele (CR1-B) of a low copy repeat (LCR) within the CR1 gene, which increases the number of complement C3b/C4b-binding sites in the mature receptor. In this study, we develop a triplex paralogue ratio test assay for CR1 LCR copy number allowing large numbers of samples to be typed with a limited amount of DNA...
April 19, 2018: Human Genetics
https://www.readbyqxmd.com/read/29675560/patterns-of-differential-gene-expression-in-a-cellular-model-of-human-islet-development-and-relationship-to-type-2-diabetes-predisposition
#10
Marta Perez-Alcantara, Christian Honoré, Agata Wesolowska-Andersen, Anna L Gloyn, Mark I McCarthy, Mattias Hansson, Nicola L Beer, Martijn van de Bunt
AIMS/HYPOTHESIS: Most type 2 diabetes-associated genetic variants identified via genome-wide association studies (GWASs) appear to act via the pancreatic islet. Observed defects in insulin secretion could result from an impact of these variants on islet development and/or the function of mature islets. Most functional studies have focused on the latter, given limitations regarding access to human fetal islet tissue. Capitalising upon advances in in vitro differentiation, we characterised the transcriptomes of human induced pluripotent stem cell (iPSC) lines differentiated along the pancreatic endocrine lineage, and explored the contribution of altered islet development to the pathogenesis of type 2 diabetes...
April 19, 2018: Diabetologia
https://www.readbyqxmd.com/read/29675137/variation-in-chromosome-number-and-breeding-systems-implications-for-diversification-in-pachycereus-pringlei-cactaceae
#11
Carina Gutiérrez-Flores, José L León-de la Luz, Francisco J García-De León, J Hugo Cota-Sánchez
Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP)...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29675039/the-role-of-cell-adhesion-molecule-genes-regulating-neuroplasticity-in-addiction
#12
REVIEW
Dawn E Muskiewicz, George R Uhl, F Scott Hall
A variety of genetic approaches, including twin studies, linkage studies, and candidate gene studies, has established a firm genetic basis for addiction. However, there has been difficulty identifying the precise genes that underlie addiction liability using these approaches. This situation became especially clear in genome-wide association studies (GWAS) of addiction. Moreover, the results of GWAS brought into clarity many of the shortcomings of those early genetic approaches. GWAS studies stripped away those preconceived notions, examining genes that would not previously have been considered in the study of addiction, consequently creating a shift in our understanding...
2018: Neural Plasticity
https://www.readbyqxmd.com/read/29674722/implications-of-publicly-available-genomic-data-resources-in-searching-for-therapeutic-targets-of-obesity-and-type-2-diabetes
#13
REVIEW
Sungwon Jung
Obesity and type 2 diabetes (T2D) are two major conditions that are related to metabolic disorders and affect a large population. Although there have been significant efforts to identify their therapeutic targets, few benefits have come from comprehensive molecular profiling. This limited availability of comprehensive molecular profiling of obesity and T2D may be due to multiple challenges, as these conditions involve multiple organs and collecting tissue samples from subjects is more difficult in obesity and T2D than in other diseases, where surgical treatments are popular choices...
April 20, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29674364/health-and-prevention-enhancement-h-peace-a-retrospective-population-based-cohort-study-conducted-at-the-seoul-national-university-hospital-gangnam-center-korea
#14
Changhyun Lee, Eun Kyung Choe, Ji Min Choi, Yunji Hwang, Young Lee, Boram Park, Su Jin Chung, Min-Sun Kwak, Jong-Eun Lee, Joo Sung Kim, Sue Kyung Park, Sang-Heon Cho
PURPOSE: The Health and Prevention Enhancement (H-PEACE) study was designed to investigate the association of diagnostic imaging results, biomarkers and the predisease stage of non-communicable diseases (NCDs), such as malignancies and metabolic diseases, in an average-risk population in Korea. PARTICIPANTS: This study enrolled a large-scale retrospective cohort at the Healthcare System Gangnam Center, Seoul National University Hospital, from October 2003 to December 2014...
April 19, 2018: BMJ Open
https://www.readbyqxmd.com/read/29674289/novel-association-between-cdkal1-and-cholesterol-efflux-capacity-replication-after-gwas-based-discovery
#15
Eun Jeong Cheon, Do Hyeon Cha, Sung Kweon Cho, Hye-Min Noh, Sungha Park, Seok-Min Kang, Heon Yung Gee, Sang-Hak Lee
BACKGROUND AND AIMS: Although the importance of the functional properties of high-density lipoprotein (HDL) has been increasingly emphasized, studies on the genetic factors associated with HDL function are highly limited. The aim of this study was to identify genetic variants associated with an individual's cholesterol efflux capacity (CEC) using a genome-wide association study approach. METHODS: This study included a discovery group of 607 subjects with coronary artery disease and an independent replication group of 158 subjects...
April 12, 2018: Atherosclerosis
https://www.readbyqxmd.com/read/29673983/population-genetics-informed-meta-analysis-in-seven-genes-associated-with-risk-to-dengue-fever-disease
#16
Marisa Oliveira, Diana P Saraiva, Bruno Cavadas, Verónica Fernandes, Nicole Pedro, Isabelle Casademont, Fanny Koeth, Farida Alshamali, Nourdin Harich, Lotfi Cherni, Beatriz Sierra, Maria G Guzman, Anavaj Sakuntabhai, Luisa Pereira
Population genetics theory predicted that rare frequent markers would be the main contributors for heritability of complex diseases, but meta-analyses of genome-wide association studies are revealing otherwise common markers, present in all population groups, as the identified candidate genes. In this work, we applied a population-genetics informed meta-analysis to 10 markers located in seven genes said to be associated with dengue fever disease. Seven markers (in PLCE1, CD32, CD209, OAS1 and OAS3 genes) have high-frequency and the other three (in MICB and TNFA genes) have intermediate frequency...
April 16, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29673965/a-review-on-neuroimaging-studies-of-genetic-and-environmental-influences-on-early-brain-development
#17
REVIEW
Wei Gao, Karen Grewen, Rebecca C Knickmeyer, Anqi Qiu, Andrew Salzwedel, Weili Lin, John H Gilmore
The past decades witnessed a surge of interest in neuroimaging study of normal and abnormal early brain development. Structural and functional studies of normal early brain development revealed massive structural maturation as well as sequential, coordinated, and hierarchical emergence of functional networks during the infancy period, providing a great foundation for the investigation of abnormal early brain development mechanisms. Indeed, studies of altered brain development associated with either genetic or environmental risks emerged and thrived...
April 16, 2018: NeuroImage
https://www.readbyqxmd.com/read/29673576/the-role-of-genetic-variation-of-human-metabolism-for-bmi-mental-traits-and-mental-disorders
#18
Johannes Hebebrand, Triinu Peters, Dick Schijven, Moritz Hebebrand, Corinna Grasemann, Thomas W Winkler, Iris M Heid, Jochen Antel, Manuel Föcker, Lisa Tegeler, Lena Brauner, Roger A H Adan, Jurjen J Luykx, Christoph U Correll, Inke R König, Anke Hinney, Lars Libuda
OBJECTIVE: The aim was to assess whether loci associated with metabolic traits also have a significant role in BMI and mental traits/disorders METHODS: We first assessed the number of single nucleotide polymorphisms (SNPs) with genome-wide significance for human metabolism (NHGRI-EBI Catalog). These 516 SNPs (216 independent loci) were looked-up in genome-wide association studies for association with body mass index (BMI) and the mental traits/disorders educational attainment, neuroticism, schizophrenia, well-being, anxiety, depressive symptoms, major depressive disorder, autism-spectrum disorder, attention-deficit/hyperactivity disorder, Alzheimer's disease, bipolar disorder, aggressive behavior, and internalizing problems...
April 3, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29673549/tau-and-neuroinflammation-what-impact-for-alzheimer-s-disease-and-tauopathies
#19
REVIEW
Cyril Laurent, Luc Buée, David Blum
Alzheimer's Disease (AD) is a chronic neurodegenerative disorder and the most common type of dementia (60-80% of cases). In 2016, nearly 44 million people were affected by AD or related dementia. AD is characterized by progressive neuronal damages leading to subtle and latter obvious decline in cognitive functions including symptoms such as memory loss or confusion, which ultimately require full-time medical care. Its neuropathology is defined by the extracellular accumulation of amyloid-β (Aβ) peptide into amyloid plaques, and intraneuronal neurofibrillary tangles (NFT) consisting of aggregated hyper- and abnormal phosphorylation of tau protein...
February 2018: Biomedical Journal
https://www.readbyqxmd.com/read/29673480/thalamic-reticular-dysfunction-as-a-circuit-endophenotype-in-neurodevelopmental-disorders
#20
REVIEW
Alexandra Krol, Ralf D Wimmer, Michael M Halassa, Guoping Feng
Diagnoses of behavioral disorders such as autism spectrum disorder and schizophrenia are based on symptomatic descriptions that have been difficult to connect to mechanism. Although psychiatric genetics provide insight into the genetic underpinning of such disorders, with a majority of cases explained by polygenic factors, it remains difficult to design rational treatments. In this review, we highlight the value of understanding neural circuit function both as an intermediate level of explanatory description that links gene to behavior and as a pathway for developing rational diagnostics and therapeutics for behavioral disorders...
April 18, 2018: Neuron
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