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Comparative genomics

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https://www.readbyqxmd.com/read/28431395/correlation-of-genomic-alterations-assessed-by-next-generation-sequencing-ngs-of-tumor-tissue-dna-and-circulating-tumor-dna-ctdna-in-metastatic-renal-cell-carcinoma-mrcc-potential-clinical-implications
#1
Andrew W Hahn, David M Gill, Benjamin Maughan, Archana Agarwal, Lubina Arjyal, Sumati Gupta, Jessica Streeter, Erin Bailey, Sumanta K Pal, Neeraj Agarwal
INTRODUCTION: Tumor tissue and circulating tumor DNA (ctDNA) next-generation sequencing (NGS) testing are frequently performed to detect genomic alterations (GAs) to help guide treatment in metastatic renal cell carcinoma (mRCC), especially after progression on standard systemic therapy. Our objective was to assess if GAs detected by ctDNA NGS are different from those detected by tumor tissue NGS, specifically in patients with mRCC, and if these platforms are interchangeable or complimentary...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#2
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Background: Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430989/gene-fractionation-and-function-in-the-ancient-subgenomes-of-maize
#3
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts...
April 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#4
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430825/discovery-and-fine-mapping-of-adiposity-loci-using-high-density-imputation-of-genome-wide-association-studies-in-individuals-of-african-ancestry-african-ancestry-anthropometry-genetics-consortium
#5
Maggie C Y Ng, Mariaelisa Graff, Yingchang Lu, Anne E Justice, Poorva Mudgal, Ching-Ti Liu, Kristin Young, Lisa R Yanek, Mary F Feitosa, Mary K Wojczynski, Kristin Rand, Jennifer A Brody, Brian E Cade, Latchezar Dimitrov, Qing Duan, Xiuqing Guo, Leslie A Lange, Michael A Nalls, Hayrettin Okut, Salman M Tajuddin, Bamidele O Tayo, Sailaja Vedantam, Jonathan P Bradfield, Guanjie Chen, Wei-Min Chen, Alessandra Chesi, Marguerite R Irvin, Badri Padhukasahasram, Jennifer A Smith, Wei Zheng, Matthew A Allison, Christine B Ambrosone, Elisa V Bandera, Traci M Bartz, Sonja I Berndt, Leslie Bernstein, William J Blot, Erwin P Bottinger, John Carpten, Stephen J Chanock, Yii-Der Ida Chen, David V Conti, Richard S Cooper, Myriam Fornage, Barry I Freedman, Melissa Garcia, Phyllis J Goodman, Yu-Han H Hsu, Jennifer Hu, Chad D Huff, Sue A Ingles, Esther M John, Rick Kittles, Eric Klein, Jin Li, Barbara McKnight, Uma Nayak, Barbara Nemesure, Adesola Ogunniyi, Andrew Olshan, Michael F Press, Rebecca Rohde, Benjamin A Rybicki, Babatunde Salako, Maureen Sanderson, Yaming Shao, David S Siscovick, Janet L Stanford, Victoria L Stevens, Alex Stram, Sara S Strom, Dhananjay Vaidya, John S Witte, Jie Yao, Xiaofeng Zhu, Regina G Ziegler, Alan B Zonderman, Adebowale Adeyemo, Stefan Ambs, Mary Cushman, Jessica D Faul, Hakon Hakonarson, Albert M Levin, Katherine L Nathanson, Erin B Ware, David R Weir, Wei Zhao, Degui Zhi, Donna K Arnett, Struan F A Grant, Sharon L R Kardia, Olufunmilayo I Oloapde, D C Rao, Charles N Rotimi, Michele M Sale, L Keoki Williams, Babette S Zemel, Diane M Becker, Ingrid B Borecki, Michele K Evans, Tamara B Harris, Joel N Hirschhorn, Yun Li, Sanjay R Patel, Bruce M Psaty, Jerome I Rotter, James G Wilson, Donald W Bowden, L Adrienne Cupples, Christopher A Haiman, Ruth J F Loos, Kari E North
Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes...
April 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#6
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28430581/association-between-en1-rs4144782-and-susceptibility-of-knee-osteoarthritis-a-case-control-study
#7
Li Haohuan, Zhang Xiaolong, Cao Yiping, Hu Song, Peng Fei, Zhou Jianlin, Li Jianping
Osteoarthritis (OA) is a complex disease that affects the whole joint, resulting from the combined influence of biomechanical factors and genetic factors. The heritable component for primary OA accounts for about 60% of variation in population liability to the disease. So far, genome-wide association studies (GWAS) and candidate gene studies have established many OA-related loci. However, these findings account for only a rather small fraction of the genetic component. To further reveal the genetic architecture of OA, we conducted this case-control study to explore the association of locus EN1 rs4144782 and knee OA susceptibility in a Chinese population...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430373/a-five-mirna-expression-signature-predicts-survival-in-hepatocellular-carcinoma
#8
Gang Liu, Hui Wang, Jin-Dong Fu, Jing-Ying Liu, Ai-Guo Yan, Yan-Yan Guan
The aim of this study was to identify a microRNA (miRNA) expression signature for predicting HCC (hepatocellular carcinoma) survival. A total of 322 HCC patients in The Cancer Genome Atlas (TCGA) database were randomly divided into training and testing set. miRNAs, associated with survival time in the training set, were identified by using univariate Cox regression analysis. The risk score was formulated based on the expression levels of these miRNAs. Then the miRNA signature was validated in testing set through Kaplan-Meier analysis and log-rank test...
April 21, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28430356/crispr-cas9-an-rna-guided-highly-precise-synthetic-tool-for-plant-genome-editing
#9
REVIEW
Yeliz Demirci, Baohong Zhang, Turgay Unver
CRISPR/Cas 9 is a newly developed and naturally occurred genome editing tool, which is originally used by bacteria for immune defence. In the past years, it has been quickly employed and modified to precisely edit genome sequences in both plants and animals. Compared with the well-developed zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR/Cas 9 has lots of advantages, including easier to design and implement, higher targeting efficiency, and less expensive. Thus, it is becoming one of the most powerful tools for knockout of an individual gene as well as insertion of one gene and/or control of gene transcription...
April 21, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28430102/variable-virulence-phenotype-of-xenorhabdus-bovienii-%C3%AE-proteobacteria-enterobacteriaceae-in-the-absence-of-their-vector-hosts
#10
John G McMullen, Rebecca McQuade, Jean-Claude Ogier, Sylvie Pagès, Sophie Gaudriault, S Patricia Stock
Xenorhabdus bovienii bacteria have a dual lifestyle: they are mutualistic symbionts to many species of Steinernema nematodes and are pathogens to a wide array of insects. Previous studies have shown that virulence of X.bovienii-Steinernema spp. pairs decreases when the nematodes associate with non-cognate bacterial strains. However, the virulence of the X. bovienii strains alone has not been fully investigated. In this study, we characterized the virulence of nine X. bovienii strains in Galleria mellonella and Spodoptera littoralis and performed a comparative genomic analysis to correlate observed phenotypes with strain genotypes...
April 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28429747/imaging-genetics-approach-to-parkinson-s-disease-and-its-correlation-with-clinical-score
#11
Mansu Kim, Jonghoon Kim, Seung-Hak Lee, Hyunjin Park
Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with both underlying genetic factors and neuroimaging findings. Existing neuroimaging studies related to the genome in PD have mostly focused on certain candidate genes. The aim of our study was to construct a linear regression model using both genetic and neuroimaging features to better predict clinical scores compared to conventional approaches. We obtained neuroimaging and DNA genotyping data from a research database. Connectivity analysis was applied to identify neuroimaging features that could differentiate between healthy control (HC) and PD groups...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429731/the-evolutionary-life-cycle-of-the-polysaccharide-biosynthetic-gene-cluster-based-on-the-sphingomonadaceae
#12
Mengmeng Wu, Haidong Huang, Guoqiang Li, Yi Ren, Zhong Shi, Xiaoyan Li, Xiaohui Dai, Ge Gao, Mengnan Ren, Ting Ma
Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429680/the-inhibitory-effects-of-hydamtiq-a-novel-parp-inhibitor-on-growth-in-human-tumor-cell-lines-with-defective-dna-damage-response-pathways
#13
Enrico Mini, Ida Landini, Laura Lucarini, Andrea Lapucci, Cristina Napoli, Gabriele Perrone, Renato Tassi, Emanuela Masini, Flavio Moroni, Stefania Nobili
The poly(ADP-ribose) polymerase (PARP) enzymes play key roles in the regulation of cellular processes (e.g. DNA damagerepair, genomic stability). It has been shown that PARP inhibitors (PARPIs) are selectively cytotoxic against cells with dysfunctions in genes involved in DNA repair mechanisms (synthetic lethality). Drug induced PARP inhibition potentiates the activity of anticancer drugs such as 5-fluorouracil in enhancing DNA damage, whose repair involves PARP1 activity.The aim of this study was to evaluate the growth inhibitory effects of a novel PARPI, HYDAMTIQ, on human tumor cell lines characterized by different features with regard to DNA damage response pathways (BRCA mutational status, microsatellite status and ATM expression level) and degree of sensitivity/resistance to 5-fluorouracil...
April 20, 2017: Oncology Research
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#14
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429132/development-of-a-real-time-recombinase-polymerase-amplification-assay-for-rapid-and-sensitive-detection-of-porcine-circovirus-2
#15
Jianchang Wang, Jinfeng Wang, Libing Liu, Wanzhe Yuan
Porcine diseases associated with porcine circovirus 2 (PCV-2) infection have resulted in significant economic losses worldwide. A real-time recombinase polymerase amplification (RPA) assay was developed to detect PCV-2 using primers and an exo probe specific for the ORF2 gene. The reaction process can be completed in 20 min at 38 °C. The assay only detects PCV-2, as there was no cross-reaction with other pathogens important in pigs. Using the PCV-2 genomic DNA as template, the analytical sensitivity of the real-time RPA was 103 copies...
April 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28429058/effects-of-genome-duplication-on-phenotypes-and-industrial-applications-of-saccharomyces-cerevisiae-strains
#16
Ke Zhang, Ya-Hong Fang, Ke-Hui Gao, Yang Sui, Dao-Qiong Zheng, Xue-Chang Wu
Polyploidy is common in Saccharomyces cerevisiae strains, but the physiological and phenotypic effects of ploidy changes have not been fully clarified. Here, isogenic diploid, triploid, and tetraploid S. cerevisiae strains were constructed from a haploid strain, CEN.PK2-1C. Stress tolerance and ethanol fermentation performance of the four euploid strains were compared. Each euploid strain had strengths and weaknesses in tolerance to certain stressors, and no single strain was tolerant of all stressors. The diploid had higher ethanol production than the other strains in normal fermentation medium, while the triploid strain showed the fastest fermentation rate in the presence of inhibitors found in lignocellulosic hydrolysate...
April 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28429027/a-metabolomic-study-on-high-risk-stroke-patients-determines-low-levels-of-serum-lysine-metabolites-a-retrospective-cohort-study
#17
Yeseung Lee, Adnan Khan, Seri Hong, Sun Ha Jee, Youngja H Park
Identifying changes in serum metabolites during cerebral ischemia is an important approach for early diagnosis of thrombotic stroke. Herein, we highlight novel biomarkers for early diagnosis of patients at high risk of thrombotic stroke using high resolution metabolomics (HRM). In this retrospective cohort study, serum samples obtained from patients at risk of thrombotic stroke (n  =  62) and non-risk individuals (n  =  348) were tested using HRM, coupled with LC-MS/MS, to discriminate between metabolic profiles of control and stroke risk patients...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428989/generation-and-characterization-of-the-blood-transcriptome-of-macaca-thibetana-and-comparative-analysis-with-m-mulatta
#18
Peng Li, Lianming Du, Wujiao Li, Zhenxin Fan, Daiwen Zeng, Hui Chen, Liang Zhou, Yong Yi, Na Yang, Kefeng Dou, Bisong Yue, Jing Li
Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428843/rad-sequencing-reveals-genomewide-divergence-between-independent-invasions-of-the-european-green-crab-carcinus-maenas-in-the-northwest-atlantic
#19
Nicholas W Jeffery, Claudio DiBacco, Mallory Van Wyngaarden, Lorraine C Hamilton, Ryan R E Stanley, Renée Bernier, Jennifer FitzGerald, K Matheson, C H McKenzie, Praveen Nadukkalam Ravindran, Robert Beiko, Ian R Bradbury
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428834/genome-sequencing-and-analysis-of-ralstonia-solanacearum-phylotype-i-strains-fjat-91-fjat-452-and-fjat-462-isolated-from-tomato-eggplant-and-chili-pepper-in-china
#20
Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu, Alberto P Macho
Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide range of host plants. Here we report the draft genome sequences of the strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili pepper, respectively, in China. In addition to the genome annotation, we performed a search for type-III secreted effectors in these strains, providing a detailed annotation of their presence and distinctive features compared to the effector repertoire of the reference phylotype I strain (GMI1000)...
2017: Standards in Genomic Sciences
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