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https://www.readbyqxmd.com/read/28230784/the-effects-of-moderate-whole-grain-consumption-on-fasting-glucose-and-lipids-gastrointestinal-symptoms-and-microbiota
#1
Danielle N Cooper, Mary E Kable, Maria L Marco, Angela De Leon, Bret Rust, Julita E Baker, William Horn, Dustin Burnett, Nancy L Keim
This study was designed to determine if providing wheat, corn, and rice as whole (WG) or refined grains (RG) under free-living conditions will change parameters of health over a six-week intervention in healthy, habitual non-WG consumers. Measurements of body composition, fecal microbiota, fasting blood glucose, total cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), and triglycerides were made at baseline and post intervention. Subjects were given adequate servings of either WG or RG products based on their caloric need and asked to keep records of grain consumption, bowel movements, and GI symptoms weekly...
February 21, 2017: Nutrients
https://www.readbyqxmd.com/read/28230522/multinational-outbreak-of-travel-related-salmonella-chester-infections-in-europe-summers-2014-and-2015
#2
Laure Fonteneau, Nathalie Jourdan Da Silva, Laetitia Fabre, Philip Ashton, Mia Torpdahl, Luise Müller, Brahim Bouchrif, Abdellah El Boulani, Eleni Valkanou, Wesley Mattheus, Ingrid Friesema, Silvia Herrera Leon, Carmen Varela Martínez, Joël Mossong, Ettore Severi, Kathie Grant, François-Xavier Weill, Céline M Gossner, Sophie Bertrand, Tim Dallman, Simon Le Hello
Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year...
February 16, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28228131/whole-genome-sequencing-of-one-complex-pedigree-illustrates-challenges-with-genomic-medicine
#3
Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J Lyon
BACKGROUND: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. METHODS: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28223389/analysis-of-serial-isolates-of-mcr-1-positive-escherichia-coli-reveals-a-highly-active-isapl1-transposon
#4
Erik Snesrud, Ana C Ong, Brendan Corey, Yoon I Kwak, Robert Clifford, Todd Gleeson, Shannon Wood, Timothy J Whitman, Emil P Lesho, Mary Hinkle, Patrick Mc Gann
The emergence of the transferable colistin resistance gene mcr-1 is of global concern. The insertion sequence (IS) Apl1 is a key component in the mobilization of this gene, but its role remains poorly understood.Six Escherichia coli were cultured from the same patient over one month in Germany and the USA after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli were collected during follow-up surveillance nine months later...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28219321/genetic-characterization-of-vibrio-cholerae-o1-isolates-from-outbreaks-between-2011-and-2015-in-tanzania
#5
Yazid Kachwamba, A A Mohammed, H Lukupulo, L Urio, M Majigo, F Mosha, M Matonya, R Kishimba, J Mghamba, J Lusekelo, S Nyanga, M Almeida, S Li, D Domman, S Y Massele, O C Stine
BACKGROUND: Cholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed. METHODS: 96 Vibrio cholerae O1 isolates from five regions were characterized, and their genetic relatedness assessed using multi-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). RESULTS: Of the 48 MLVA genotypes observed, 3 were genetically unrelated to any others, while the remaining 45 genotypes separated into three MLVA clonal complexes (CCs) - each comprised of genotypes differing by a single allelic change...
February 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28217442/whole-genome-sequencing-and-analysis-of-campylobacter-coli-yh502-from-retail-chicken-reveals-a-plasmid-borne-type-vi-secretion-system
#6
Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin
Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28212966/estimating-preferences-for-complex-health-technologies-lessons-learned-and-implications-for-personalized-medicine
#7
Deborah A Marshall, Juan Marcos Gonzalez, Karen V MacDonald, F Reed Johnson
We examine key study design challenges of using stated-preference methods to estimate the value of whole-genome sequencing (WGS) as a specific example of genomic testing. Assessing the value of WGS is complex because WGS provides multiple findings, some of which can be incidental in nature and unrelated to the specific health concerns that motivated the test. In addition, WGS results can include actionable findings (variants considered to be clinically useful and can be acted on), findings for which evidence for best clinical action is not available (variants considered clinically valid but do not meet as high of a standard for clinical usefulness), and findings of unknown significance...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212192/genetic-control-of-erythropoiesis
#8
Laxminath Tumburu, Swee Lay Thein
PURPOSE OF REVIEW: The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait. RECENT FINDINGS: Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1)...
February 15, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28211519/palindromic-amplification-of-the-erbb2-oncogene-in-primary-her2-positive-breast-tumors
#9
Michael Marotta, Taku Onodera, Jeffrey Johnson, G Thomas Budd, Takaaki Watanabe, Xiaojiang Cui, Armando E Giuliano, Atsushi Niida, Hisashi Tanaka
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209138/using-whole-genome-sequencing-to-investigate-transmission-in-a-multi-host-system-bovine-tuberculosis-in-new-zealand
#10
Joseph Crispell, Ruth N Zadoks, Simon R Harris, Brent Paterson, Desmond M Collins, Geoffrey W de-Lisle, Paul Livingstone, Mark A Neill, Roman Biek, Samantha J Lycett, Rowland R Kao, Marian Price-Carter
BACKGROUND: Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28202802/multi-laboratory-survey-to-evaluate-salmonella-prevalence-in-diarrheic-and-non-diarrheic-dogs-and-cats-in-the-usa-between-2012-and-2014
#11
Renate Reimschuessel, Michael Grabenstein, Jake Guag, Sarah M Nemser, Kyunghee Song, Junshan Qiu, Kristin A Clothier, Barbara A Byrne, Stanley L Marks, Kyran Cadmus, Kristy Pabilonia, Susan Sanchez, Sreekumari Rajeev, Steve Ensley, Timothy S Frana, Albert E Jergens, Kimberly H Chappell, Siddhartha Thakur, Beverly Byrum, Jing Cui, Yan Zhang, Matthew M Erdman, Shelley C Rankin, Russell Daly, Seema Das, Laura Ruesch, Sara D Lawhon, Shuping Zhang, Timothy Baszler, Dubraska Diaz-Campos, Faye Hartmann, Ogi Okwumabua
Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the USA visiting veterinary clinics. Fecal samples (2965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. Prevalence in dogs (60 of 2422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however 3...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28202795/tuberculosis-outbreak-in-an-educational-institution-in-norway
#12
Gunnstein Norheim, Siri Seterelv, Trude M Arnesen, Anne Torunn Mengshoel, Tone Tønjum, Janne O Rønning, Vegard Eldholm
Within one week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a total of 24 cases in the period 2009-14, among which all of the 22 Mycobacterium tuberculosis isolates available had identical MIRU-VNTR profile (MtbC15-9 code 10287-189), belonging to the Beijing lineage. Whole genome sequencing (WGS) of the M...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28201986/the-origin-of-chow-chows-in-the-light-of-the-east-asian-breeds
#13
Hechuan Yang, Guodong Wang, Meng Wang, Yaping Ma, Tingting Yin, Ruoxi Fan, Hong Wu, Li Zhong, David M Irwin, Weiwei Zhai, Yaping Zhang
BACKGROUND: East Asian dog breeds are one of the most ancient groups of dogs that radiated after the domestication of the dog and represent the most basal lineages of dog evolution. Among these, the Chow Chow is an ancient breed that embodies very distinct morphological and physiological features, such as sturdy build, dense coat, and blue/purple tongue. RESULTS: Using a Restricted site Associated DNA (RAD) sequencing approach, we sequenced the genomes of nine Chow Chows from China...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199135/extreme-trait-whole-genome-sequencing-identifies-ptpro-as-a-novel-candidate-gene-in-emphysema-with-severe-airflow-obstruction
#14
Josiah E Radder, Yingze Zhang, Alyssa D Gregory, Shibing Yu, Neil J Kelly, Joseph K Leader, Naftali Kaminski, Frank C Sciurba, Steven D Shapiro
RATIONALE: Genetic association studies in chronic obstructive pulmonary disease (COPD) have primarily tested for association with common variants, the results of which explain only a portion of disease heritability. As rare variation is also likely to contribute to susceptibility, we employed whole genome sequencing (WGS) of subjects with clinically extreme phenotypes to identify genomic regions enriched for rare variation contributing to COPD susceptibility. OBJECTIVE: Identify regions of rare genetic variation contributing to emphysema with severe airflow obstruction Methods: We identified heavy smokers that were resistant (n=65) or susceptible (n=64) to emphysema with severe airflow obstruction in the Pittsburgh SCCOR cohort...
February 15, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28197720/single-nucleotide-polymorphisms-in-the-whole-genome-sequence-data-of-shiga-toxin-producing-escherichia-coli-o157-h7-h-strains-by-cultivation
#15
Eiji Yokoyama, Shinichiro Hirai, Taichiro Ishige, Satoshi Murakami
Nine Shiga toxin-producing Escherichia coli O157:H7/H- (O157) strains were serially cultured three times on LB agar plates. After each sub-culture, five colonies were picked for DNA isolation and whole genome sequence (WGS) analysis. After exclusion of possible recombination-related SNPs, 11, 9, and 34 single-nucleotide polymorphisms (SNPs) were detected in genes in the backbone, O-island, and mobile elements gene categories. This suggested that those SNPs due to cultivation could influence the threshold value set for molecular epidemiological studies of O157...
February 14, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28194548/investigation-of-intra-herd-spread-of-mycobacterium-caprae-in-cattle-by-generation-and-use-of-a-whole-genome-sequence
#16
S Broeckl, S Krebs, A Varadharajan, R K Straubinger, H Blum, M Buettner
Single nucleotide polymorphisms (SNPs) calculated from whole genome sequencing (WGS) are ideally suited to study evolutionary relationships of pathogens and their epidemiology. Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission within cattle holdings and possible alterations of the genomes of M. caprae during such events. The aim of this study was to study the molecular epidemiology of bovine tuberculosis (bTB) in selected herds based on isolate-specific genome-wide SNPs and to perform a phylogenetic network analysis...
February 13, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28192234/meningococcal-carriage-in-dutch-adolescents-and-young-adults-a-cross-sectional-and-longitudinal-cohort-study
#17
Mariëtte B van Ravenhorst, Merijn W Bijlsma, Marlies A van Houten, Veerle M D Struben, Annaliesa S Anderson, Joseph Eiden, Hao Li, Kathrin U Jansen, Hal Jones, Nicholas Kitchin, Louise Pedneault, Elisabeth A M Sanders, Arie van der Ende
OBJECTIVES: Current information on rates and dynamics of meningococcal carriage is essential for public health policy. This study aimed to determine meningococcal carriage prevalence, its risk factors and duration in the Netherlands, where meningococcal C vaccine coverage is >90%. Several methods to identify serogroups of meningococcal carriage isolates among adolescent and young adults were compared. METHODS: Oropharyngeal swabs from 1715 subjects 13-23 years of age were collected in 2013-2014; 300 were prospectively followed over 8 months...
February 10, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28190455/who-s-who-detecting-and-resolving-sample-anomalies-in-human-dna-sequencing-studies-with-peddy
#18
Brent S Pedersen, Aaron R Quinlan
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190454/somatic-map2k1-mutations-are-associated-with-extracranial-arteriovenous-malformation
#19
Javier A Couto, August Y Huang, Dennis J Konczyk, Jeremy A Goss, Steven J Fishman, John B Mulliken, Matthew L Warman, Arin K Greene
Arteriovenous malformation (AVM) is a fast-flow, congenital vascular anomaly that may arise anywhere in the body. AVMs typically progress, causing destruction of surrounding tissue and, sometimes, cardiac overload. AVMs are difficult to control; they often re-expand after embolization or resection, and pharmacologic therapy is unavailable. We studied extracranial AVMs in order to identify their biological basis. We performed whole-exome sequencing (WES) and whole-genome sequencing (WGS) on AVM tissue from affected individuals...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28186206/unbiased-k-mer-analysis-reveals-changes-in-copy-number-of-highly-repetitive-sequences-during-maize-domestication-and-improvement
#20
Sanzhen Liu, Jun Zheng, Pierre Migeon, Jie Ren, Ying Hu, Cheng He, Hongjun Liu, Junjie Fu, Frank F White, Christopher Toomajian, Guoying Wang
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids...
February 10, 2017: Scientific Reports
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