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Genome variation

Daniel B Hawcutt, Ben Francis, Daniel F Carr, Andrea L Jorgensen, Peng Yin, Naomi Wallin, Natalie O'Hara, Eunice J Zhang, Katarzyna M Bloch, Amitava Ganguli, Ben Thompson, Laurence McEvoy, Matthew Peak, Andrew A Crawford, Brian R Walker, Joanne C Blair, Jonathan Couriel, Rosalind L Smyth, Munir Pirmohamed
BACKGROUND: A serious adverse effect of corticosteroid therapy is adrenal suppression. Our aim was to identify genetic variants affecting susceptibility to corticosteroid-induced adrenal suppression. METHODS: We enrolled children with asthma who used inhaled corticosteroids as part of their treatment from 25 sites across the UK (discovery cohort), as part of the Pharmacogenetics of Adrenal Suppression with Inhaled Steroids (PASS) study. We included two validation cohorts, one comprising children with asthma (PASS study) and the other consisting of adults with chronic obstructive pulmonary disorder (COPD) who were recruited from two UK centres for the Pharmacogenomics of Adrenal Suppression in COPD (PASIC) study...
March 15, 2018: Lancet Respiratory Medicine
Trevor J Pemberton, Zachary A Szpiech
Genomic regions of autozygosity (ROAs) represent segments of individual genomes that are homozygous for haplotypes inherited identical-by-descent (IBD) from a common ancestor. ROAs are nonuniformly distributed across the genome, and increased ROA levels are a reported risk factor for numerous complex diseases. Previously, we hypothesized that long ROAs are enriched for deleterious homozygotes as a result of young haplotypes with recent deleterious mutations-relatively untouched by purifying selection-being paired IBD as a consequence of recent parental relatedness, a pattern supported by ROA and whole-exome sequence data on 27 individuals...
March 10, 2018: American Journal of Human Genetics
Zhong-Feng Li, Yong Guo, Lin Ou, Huilong Hong, Jun Wang, Zhang-Xiong Liu, Bingfu Guo, Lijuan Zhang, Lijuan Qiu
GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length...
March 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Asher Haug-Baltzell, Tushar R Bhangale, Diana Chang, Amy Dressen, Brian L Yaspan, Ward Ortmann, Matthew J Brauer, Julie Hunkapiller, Jens Reeder, Kiran Mukhyala, Karen T Cuenco, Jennifer A Tom, Amy Cowgill, Jan Vogel, William F Forrest, Timothy W Behrens, Robert R Graham, Arthur Wuster
In clinical trials, a placebo response refers to improvement in disease symptoms arising from the psychological effect of receiving a treatment rather than the actual treatment under investigation. Previous research has reported genomic variation associated with the likelihood of observing a placebo response, but these studies have been limited in scope and have not been validated. Here, we analyzed whole-genome sequencing data from 784 patients undergoing placebo treatment in Phase III Asthma or Rheumatoid Arthritis trials to assess the impact of previously reported variation on patient outcomes in the placebo arms and to identify novel variants associated with the placebo response...
March 18, 2018: Genes and Immunity
Marco van Zwetselaar, Balthazar Nyombi, Tolbert Sonda, Happiness Kumburu, Nyasatu Chamba, Marieke C J Dekker, Kajiru G Kilonzo, Sarah J Urasa, Blandina T Mmbaga
BACKGROUND: Aeromonas species have been documented to yield false positive results in microbiological tests for Vibrio cholerae. They share many biochemical properties with Vibrio species, with which they were jointly classified in the family Vibrionaceae until genotypic information provided new insights. Aeromonas species are increasingly associated with gastrointestinal infections, albeit with great apparent variation in pathogenicity and virulence both between and within species of the genus...
March 17, 2018: Journal of Medical Case Reports
Ajeet K Sharma, Nabeel Ahmed, Edward P O'Brien
Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5...
February 2018: Physical Review. E
Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Yuval B Simons, Kevin Bullaughey, Richard R Hudson, Guy Sella
Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes-notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space...
March 16, 2018: PLoS Biology
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Chaoting Zhang, Rui Zhang, Zhiqiang Chen, Jing Chen, Jigang Ruan, Zheming Lu, Hongchao Xiong, Wenjun Yang
Objective: This study aimed to comprehensively assess Epstein-Barr virus (EBV)-induced methylation alterations of B cell across whole genome. Methods: We compared DNA methylation patterns of primary B cells and corresponding lymphoblastoid cell lines (LCLs) from eight participants. The genome-wide DNA methylation profiles were compared at over 850,000 genome-wide methylation sites. Results: DNA methylation analysis revealed 87,732 differentially methylated CpG sites, representing approximately 12...
February 2018: Chinese Journal of Cancer Research, Chung-kuo Yen Cheng Yen Chiu
Jeroen Frank, Sebastian Lücker, Rolf H A M Vossen, Mike S M Jetten, Richard J Hall, Huub J M Op den Camp, Seyed Yahya Anvar
Anaerobic ammonium-oxidizing (anammox) bacteria are a group of strictly anaerobic chemolithoautotrophic microorganisms. They are capable of oxidizing ammonium to nitrogen gas using nitrite as a terminal electron acceptor, thereby facilitating the release of fixed nitrogen into the atmosphere. The anammox process is thought to exert a profound impact on the global nitrogen cycle and has been harnessed as an environment-friendly method for nitrogen removal from wastewater. In this study, we present the first closed genome sequence of an anammox bacterium, Kuenenia stuttgartiensis MBR1...
March 15, 2018: Scientific Reports
Jason D Roberts
No abstract text is available yet for this article.
March 2018: Circ Genom Precis Med
Tim Beissinger, Jochen Kruppa, David Cavero, Ngoc-Thuy Ha, Malena Erbe, Henner Simianer
Important traits in agricultural, natural, and human populations are increasingly being shown to be under the control of many genes that individually contribute only a small proportion of genetic variation. However, the majority of modern tools in quantitative and population genetics, including genome wide association studies and selection mapping protocols, are designed to identify individual genes with large effects. We have developed an approach to identify traits that have been under selection and are controlled by large numbers of loci...
March 15, 2018: Genetics
Qing Mao, Robert Chin, Weiwei Xie, Yuqing Deng, Wenwei Zhang, Huixin Xu, Rebecca Yu Zhang, Quan Shi, Erin E Peters, Natali Gulbahce, Zhenyu Li, Fang Chen, Radoje Drmanac, Brock A Peters
BACKGROUND: Amniocentesis is a common procedure, the primary purpose of which is to collect cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single- to multibase defects. Here we demonstrate the feasibility of generating an accurate whole-genome sequence of a fetus from either the cellular or cell-free DNA (cfDNA) of an amniotic sample. METHODS: cfDNA and DNA isolated from the cell pellet of 31 amniocenteses were sequenced to approximately 50× genome coverage by use of the Complete Genomics nanoarray platform...
March 15, 2018: Clinical Chemistry
Nicolien A Van Vliet, Raymond Noordam, Jan B Van Klinken, Rudi G J Westendorp, J H Duncan Bassett, Graham R Williams, Diana Van Heemst
With population aging, prevalence of low bone mineral density (BMD) and associated fracture risk are increased. To determine whether low circulating thyroid stimulating hormone (TSH) levels within the normal range are causally related to BMD, we conducted a two-sample Mendelian randomization (MR) study. Furthermore, we tested whether common genetic variants in the TSH receptor (TSHR) gene and genetic variants influencing expression of TSHR (eQTLs) are associated with BMD. For both analyses, we used summary-level data of genome-wide association studies (GWAS) investigating BMD of the femoral neck (N = 32,735) and the lumbar spine (N = 28,498) in cohorts of European ancestry from the Genetic Factors of Osteoporosis (GEFOS) Consortium...
March 15, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Maurizio Manca, Veridiana Pessoa, Ana Illera Lopez, Patrick T Harrison, Fabio Miyajima, Helen Sharp, Andrew Pickles, Jonathan Hill, Chris Murgatroyd, Vivien J Bubb, John P Quinn
The monoamine oxidase A (MAOA) uVNTR (upstream variable number tandem repeat) is one of the most often cited examples of a gene by environment interaction (GxE) in relation to behavioral traits. However, MAOA possesses a second VNTR, 500 bp upstream of the uVNTR, which is termed d- or distal VNTR. Furthermore, genomic analysis indicates that there are a minimum of two transcriptional start sites (TSSs) for MAOA, one of which encompasses the uVNTR within the 5' untranslated region of one of the isoforms. Through expression analysis in semi-haploid HAP1 cell lines genetically engineered in order to knockout (KO) either the uVNTR, dVNTR, or both VNTRs, we assessed the effect of the two MAOA VNTRs, either alone or in combination, on gene expression directed from the different TSSs...
March 14, 2018: Journal of Molecular Neuroscience: MN
Ignacio Trucillo Silva, Hari Kishan R Abbaraju, Lynne P Fallis, Hongjun Liu, Michael Lee, Kanwarpal S Dhugga
Intracellular factors differentially affected enzyme activities of N assimilation in the roots of maize testcrosses where alanine aminotransferase and glutamate synthase were the main enzymes regulating the levels of glutamate. N is a key macronutrient for plant growth and development. Breeding maize with improved efficiency in N use could help reduce environmental contamination as well as increase profitability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures...
March 14, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Roberta Pastorino, Anna Puggina, Robert Carreras-Torres, Pagona Lagiou, Ivana Holcátová, Lorenzo Richiardi, Kristina Kjaerheim, Antonio Agudo, Xavier Castellsagué, Tatiana V Macfarlane, Luigi Barzan, Cristina Canova, Nalin S Thakker, David I Conway, Ariana Znaor, Claire M Healy, Wolfgang Ahrens, David Zaridze, Neonilia Szeszenia-Dabrowska, Jolanta Lissowska, Eleonora Fabianova, Ioan Nicolae Mates, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Paul Brennan, Valérie Gaborieau, James D McKay, Stefania Boccia
With the aim to dissect the effect of adult height on head and neck cancer (HNC), we use the Mendelian randomization (MR) approach to test the association between genetic instruments for height and the risk of HNC. 599 single nucleotide polymorphisms (SNPs) were identified as genetic instruments for height, accounting for 16% of the phenotypic variation. Genetic data concerning HNC cases and controls were obtained from a genome-wide association study. Summary statistics for genetic association were used in complementary MR approaches: the weighted genetic risk score (GRS) and the inverse-variance weighted (IVW)...
March 14, 2018: Scientific Reports
Joanna A Pulit-Penaloza, Joyce Jones, Xiangjie Sun, Yunho Jang, Sharmi Thor, Jessica A Belser, Natosha Zanders, Hannah M Creager, Callie Ridenour, Li Wang, Thomas J Stark, Rebecca Garten, Li-Mei Chen, John Barnes, Terrence M Tumpey, David E Wentworth, Taronna R Maines, C Todd Davis
Influenza A(H1) viruses circulating in swine represent an emerging virus threat as zoonotic infections occur sporadically following exposure to swine. A fatal infection caused by an H1N1 variant (H1N1v) virus was detected in a patient with reported exposure to swine and who presented with pneumonia, respiratory failure, and cardiac arrest. To understand the genetic and phenotypic characteristics of the virus, genome sequence analysis, antigenic characterization, and ferret pathogenesis and transmissibility experiments were performed...
March 14, 2018: Journal of Virology
François Vasseur, Moises Exposito-Alonso, Oscar J Ayala-Garay, George Wang, Brian J Enquist, Denis Vile, Cyrille Violle, Detlef Weigel
Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species...
March 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
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