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genome-wide association

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https://www.readbyqxmd.com/read/29232693/host-factors-that-promote-retrotransposon-integration-are-similar-in-distantly-related-eukaryotes
#1
Sudhir Kumar Rai, Maya Sangesland, Michael Lee, Caroline Esnault, Yujin Cui, Atreyi Ghatak Chatterjee, Henry L Levin
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration...
December 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29232479/metabolomic-pathways-to-osteoporosis-in-middle-aged-women-a-genome-metabolome-wide-mendelian-randomization-study
#2
Alireza Moayyeri, Ching-Lung Cheung, Kathryn Cb Tan, John A Morris, Agustin Cerani, Robert P Mohney, J Brent Richard, Christopher Hammond, Tim D Spector, Cristina Menni
The metabolic state of the body can be a major determinant of bone health. We used a Mendelian Randomization approach to identify metabolites causally associated with bone mass to better understand the biological mechanisms of osteoporosis. We tested bone phenotypes (femoral neck, total hip, and lumbar spine BMD) for association with 280 fasting blood metabolites in 6055 women from TwinsUK cohort with genome-wide genotyping scans. Causal associations between metabolites and bone phenotypes were further assessed in a bidirectional Mendelian Randomization study using genetic markers/scores as instrumental variables...
December 12, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29230882/molecular-profiling-and-genome-wide-analysis-based-on-somatic-copy-number-alterations-in-advanced-colorectal-cancers
#3
Tamotsu Sugai, Yayoi Takahashi, Makoto Eizuka, Ryo Sugimoto, Yasuko Fujita, Wataru Habano, Kouki Otsuka, Akira Sasaki, Eiichiro Yamamoto, Takayuki Matsumoto, Hiromu Suzuki
To characterize somatic alterations in colorectal cancer (CRC), we conducted a genome-scale analysis of 106 CRC specimens. We assessed comprehensive somatic copy number alterations (SCNAs) in these CRC specimens. In addition, we examined microsatellite instability (MSI; low and high), genetic mutations (KRAS, BRAF, TP53, and PIK3CA), and DNA methylation status (classified into low, intermediate, and high type). We stratified molecular alterations in the CRCs using a hierarchical cluster analysis. The examined CRCs could be categorized into 3 subgroups using hierarchical cluster analysis...
December 12, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29230835/genetic-contributions-to-precocity-traits-in-racing-thoroughbreds
#4
G Farries, P A McGettigan, K F Gough, B A McGivney, D E MacHugh, L M Katz, E W Hill
Adaptation to early training and racing (i.e. precocity), which is highly variable in racing Thoroughbreds, has implications for the selection and training of horses. We hypothesised that precocity in Thoroughbred racehorses is heritable. Age at first sprint training session (work day), age at first race and age at best race were used as phenotypes to quantify precocity. Using high-density SNP array data, additive SNP heritability (hSNP2) was estimated to be 0.17, 0.14 and 0.17 for the three traits respectively...
December 12, 2017: Animal Genetics
https://www.readbyqxmd.com/read/29230810/trauma-exposure-interacts-with-the-genetic-risk-of-bipolar-disorder-in-alcohol-misuse-of-us-soldiers
#5
R Polimanti, J Kaufman, H Zhao, H R Kranzler, R J Ursano, R C Kessler, M B Stein, J Gelernter
OBJECTIVE: To investigate whether trauma exposure moderates the genetic correlation between substance use disorders and psychiatric disorders, we tested whether trauma exposure modifies the association of genetic risks for mental disorders with alcohol misuse and nicotine dependence (ND) symptoms. METHODS: High-resolution polygenic risk scores (PRSs) were calculated for 10 732 US Army soldiers (8346 trauma-exposed and 2386 trauma-unexposed) based on genome-wide association studies of bipolar disorder (BD), major depressive disorder, and schizophrenia...
December 11, 2017: Acta Psychiatrica Scandinavica
https://www.readbyqxmd.com/read/29230585/identification-of-novel-genes-significantly-affecting-growth-in-catfish-through-gwas-analysis
#6
Ning Li, Tao Zhou, Xin Geng, Yulin Jin, Xiaozhu Wang, Shikai Liu, Xiaoyan Xu, Dongya Gao, Qi Li, Zhanjiang Liu
Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis...
December 12, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29230380/the-axolotl-limb-regeneration-model-as-a-discovery-tool-for-engineering-the-stem-cell-niche
#7
Negar Seyedhassantehrani, Takayoshi Otsuka, Shambhavi Singh, David M Gardiner
Purpose of review: Recent advances in genomics and gene editing have expanded the range of model organisms to include those with interesting biological capabilities such as regeneration. Among these are the classic models of regeneration biology, the salamander. Although stimulating endogenous regeneration in humans likely is many years away, with advances in stem cell biology and biomedical engineering (e.g. bio-inspired materials), it is evident that there is great potential to enhance regenerative outcomes by approaching the problem from an engineering perspective...
September 2017: Current Stem Cell Reports
https://www.readbyqxmd.com/read/29230205/bacterial-genetic-architecture-of-ecological-interactions-in-co-culture-by-gwas-taking-escherichia-coli-and-staphylococcus-aureus-as-an-example
#8
Xiaoqing He, Yi Jin, Meixia Ye, Nan Chen, Jing Zhu, Jingqi Wang, Libo Jiang, Rongling Wu
How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29230059/genome-wide-association-study-of-delay-discounting-in-23-217-adult-research-participants-of-european-ancestry
#9
Sandra Sanchez-Roige, Pierre Fontanillas, Sarah L Elson, Anita Pandit, Ellen M Schmidt, Johanna R Foerster, Gonçalo R Abecasis, Joshua C Gray, Harriet de Wit, Lea K Davis, James MacKillop, Abraham A Palmer
Delay discounting (DD), the tendency to discount the value of delayed versus current rewards, is elevated in a constellation of diseases and behavioral conditions. We performed a genome-wide association study of DD using 23,127 research participants of European ancestry. The most significantly associated single-nucleotide polymorphism was rs6528024 (P = 2.40 × 10-8), which is located in an intron of the gene GPM6B. We also showed that 12% of the variance in DD was accounted for by genotype and that the genetic signature of DD overlapped with attention-deficit/hyperactivity disorder, schizophrenia, major depression, smoking, personality, cognition and body weight...
December 11, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/29230020/snp-co-association-and-network-analyses-identify-e2f3-kdm5a-and-bach2-as-key-regulators-of-the-bovine-milk-fatty-acid-profile
#10
Sara Pegolo, Christos Dadousis, Núria Mach, Yuliaxis Ramayo-Caldas, Marcello Mele, Giuseppe Conte, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The fatty acid (FA) profile has a considerable impact on the nutritional and technological quality of milk and dairy products. The molecular mechanism underlying the regulation of fat metabolism in bovine mammary gland have been not completely elucidated. We conducted genome-wide association studies (GWAS) across 65 milk FAs and fat percentage in 1,152 Brown Swiss cows. In total, we identified 175 significant single nucleotide polymorphism (SNPs) spanning all chromosomes. Pathway analyses revealed that 12:0 was associated with the greatest number of overrepresented categories/pathways (e...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229917/whole-genome-sequencing-and-snv-genotyping-of-nebbiolo-vitis-vinifera-l-clones
#11
Giorgio Gambino, Alessandra Dal Molin, Paolo Boccacci, Andrea Minio, Walter Chitarra, Carla Giuseppina Avanzato, Paola Tononi, Irene Perrone, Stefano Raimondi, Anna Schneider, Mario Pezzotti, Franco Mannini, Ivana Gribaudo, Massimo Delledonne
'Nebbiolo' (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three 'Nebbiolo' clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of 'Nebbiolo' and its intra-varietal variability useful for clonal identification were reported...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229836/single-cell-analysis-resolves-the-cell-state-transition-and-signaling-dynamics-associated-with-melanoma-drug-induced-resistance
#12
Yapeng Su, Wei Wei, Lidia Robert, Min Xue, Jennifer Tsoi, Angel Garcia-Diaz, Blanca Homet Moreno, Jungwoo Kim, Rachel H Ng, Jihoon W Lee, Richard C Koya, Begonya Comin-Anduix, Thomas G Graeber, Antoni Ribas, James R Heath
Continuous BRAF inhibition of BRAF mutant melanomas triggers a series of cell state changes that lead to therapy resistance and escape from immune control before establishing acquired resistance genetically. We used genome-wide transcriptomics and single-cell phenotyping to explore the response kinetics to BRAF inhibition for a panel of patient-derived BRAFV600 -mutant melanoma cell lines. A subset of plastic cell lines, which followed a trajectory covering multiple known cell state transitions, provided models for more detailed biophysical investigations...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229769/cytoplasmic-polyadenylation-mediated-translational-control-of-maternal-mrnas-directs-maternal-to-zygotic-transition
#13
Cecilia Lanny Winata, Maciej Łapiński, Leszek Pryszcz, Candida Vaz, Muhammad Hisyam Bin Ismail, Srikanth Nama, Hajira Shreen Hajan, Serene Gek Ping Lee, Vladimir Korzh, Prabha Sampath, Vivek Tanavde, Sinnakaruppan Mathavan
In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs...
December 11, 2017: Development
https://www.readbyqxmd.com/read/29229607/race-disparities-in-the-contribution-of-mirna-isoforms-and-trna-derived-fragments-to-triple-negative-breast-cancer
#14
Aristeidis G Telonis, Isidore Rigoutsos
Triple-Negative Breast Cancer (TNBC) is a breast cancer subtype characterized by marked differences between White and Black/African-American women. We performed a systems-level analysis on datasets from The Cancer Genome Atlas (TCGA) to elucidate how the expression patterns of messenger RNAs (mRNAs) are shaped by regulatory non-coding RNAs (ncRNAs). Specifically, we studied isomiRs, i.e. isoforms of microRNAs (miRNAs), and tRNA-derived fragments (tRFs). In normal breast tissue, we observed a marked cohesiveness in both the ncRNA and mRNA layers and the associations between them...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29229094/no-genetic-association-detected-with-mepolizumab-efficacy-in-severe-asthma
#15
Lynn Condreay, Mathias Chiano, Hector Ortega, Natalie Buchan, Elizabeth Harris, Eugene R Bleecker, Philip J Thompson, Marc Humbert, Peter Gibson, Steven Yancey, Soumitra Ghosh
BACKGROUND AND OBJECTIVES: Treatment with mepolizumab, a humanized monoclonal antibody to interleukin-5, reduces the rate of asthma exacerbations and the requirement for systemic glucocorticoids while maintaining asthma control. Treatment decisions are guided by predictors of response, including blood eosinophil thresholds in patients with frequent exacerbations despite intensive anti-inflammatory and controller treatment. Identification of additional predictors of response could aid treatment decisions...
November 2017: Respiratory Medicine
https://www.readbyqxmd.com/read/29228715/bayesian-and-frequentist-analysis-of-an-austrian-genome-wide-association-study-of-colorectal-cancer-and-advanced-adenomas
#16
Philipp Hofer, Michael Hagmann, Stefanie Brezina, Erich Dolejsi, Karl Mach, Gernot Leeb, Andreas Baierl, Stephan Buch, Hedwig Sutterlüty-Fall, Judith Karner-Hanusch, Michael M Bergmann, Thomas Bachleitner-Hofmann, Anton Stift, Armin Gerger, Katharina Rötzer, Josef Karner, Stefan Stättner, Melanie Waldenberger, Thomas Meitinger, Konstantin Strauch, Jakob Linseisen, Christian Gieger, Florian Frommlet, Andrea Gsur
Most genome-wide association studies (GWAS) were analyzed using single marker tests in combination with stringent correction procedures for multiple testing. Thus, a substantial proportion of associated single nucleotide polymorphisms (SNPs) remained undetected and may account for missing heritability in complex traits. Model selection procedures present a powerful alternative to identify associated SNPs in high-dimensional settings. In this GWAS including 1060 colorectal cancer cases, 689 cases of advanced colorectal adenomas and 4367 controls we pursued a dual approach to investigate genome-wide associations with disease risk applying both, single marker analysis and model selection based on the modified Bayesian information criterion, mBIC2, implemented in the software package MOSGWA...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228687/interactions-between-rasa2-cadm1-hif1an-gene-polymorphisms-and-body-fatness-with-breast-cancer-a-population-based-case-control-study-in-china
#17
Zheng Zhu, Zhimei Teng, Fränzel J B van Duijnhoven, Meihua Dong, Yun Qian, Hao Yu, Jie Yang, Renqiang Han, Jian Su, Wencong Du, Xingyu Huang, Jinyi Zhou, Xiaojin Yu, Ellen Kampman, Ming Wu
Genome-wide association studies (GWAS) have indicated that gene polymorphisms in alleles of RAS p21 protein activator 2 (RASA2), cell adhesion molecule 1 (CADM1) and hypoxia inducible factor 1 alpha subunit inhibitor (HIF1AN) are associated with the risk of obesity. In this study, we explored the interactions between candidate SNPs of RASA2 (rs16851483), CADM1 (rs12286929) and HIF1AN (rs17094222) and body fatness for breast cancer risk. Unconditional logistic regression models were applied to measure the associations of related factors with breast cancer by odds ratios (ORs) and 95% confidence intervals (CIs)...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228658/dna-methylation-landscape-of-hepatoblastomas-reveals-arrest-at-early-stages-of-liver-differentiation-and-cancer-related-alterations
#18
Mariana Maschietto, Tatiane Cristina Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araujo, Talita Ferreira Marques Aguiar, Cecilia Maria Lima da Costa, Isabela Werneck da Cunha, Luciana Dos Reis Vasques, Monica Cypriano, Helena Brentani, Silvia Regina Caminada de Toledo, Peter Lees Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana C V Krepischi
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228370/a-nf-%C3%AE%C2%BAb-signature-predicts-low-grade-glioma-prognosis-a-precision-medicine-approach-based-on-patient-derived-stem-cells
#19
Tamara Ius, Yari Ciani, Maria Elisabetta Ruaro, Miriam Isola, Marisa Sorrentino, Michela Bulfoni, Veronica Candotti, Cecilia Correcig, Evgenia Bourkoula, Ivana Manini, Enrico Pegolo, Damiano Mangoni, Stefania Marzinotto, Slobodanka Radovic, Barbara Toffoletto, Federica Caponnetto, Andrea Zanello, Laura Mariuzzi, Carla Di Loreto, Antonio Paolo Beltrami, Silvano Piazza, Miran Skrap, Daniela Cesselli
Background: While recent genome wide association studies have suggested novel low-grade glioma (LGG) stratification models based on a molecular classification, we explored the potential clinical utility of patient-derived cells. Specifically, we assayed glioma-associated stem cells (GASC) that are patient-derived stem cells representative of the glioma microenvironment. Methods: By next generation sequencing, we analyzed the transcriptional profile of GASC derived from patients that underwent anaplastic transformation either within 48 months (GASC-BAD) or ≥7 years (GASC-GOOD) after surgery...
December 7, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29228366/genotype-influences-day-to-day-variability-in-sleep-in-drosophila-melanogaster
#20
Katherine J Wu, Shailesh Kumar, Yazmin L Serrano Negron, Susan T Harbison
Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One possibility is that these daily fluctuations in sleep are caused by the underlying genotype of the individual. However, differences attributable to genetic causes are difficult to distinguish from environmental factors in outbred populations such as humans. We therefore employed Drosophila as a model of intra-individual variability in sleep using previously collected sleep and activity data from the Drosophila Genetic Reference Panel, a collection of wild-derived inbred lines...
December 8, 2017: Sleep
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