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https://www.readbyqxmd.com/read/28323875/the-clinical-features-outcomes-and-genetic-characteristics-of-hypertrophic-cardiomyopathy-patients-with-severe-right-ventricular-hypertrophy
#1
Xiying Guo, Chaomei Fan, Lei Tian, Yanling Liu, Hongyue Wang, Shihua Zhao, Fujian Duan, Xiuling Zhang, Xing Zhao, Fengqi Wang, Hongguang Zhu, Aiqing Lin, Xia Wu, Yishi Li
INTRODUCTION: Severe right ventricular hypertrophy (SRVH) is a rare phenotype in hypertrophic cardiomyopathy (HCM) for which limited information is available. This study was undertaken to investigate the clinical, prognostic and genetic characteristics of HCM patients with SRVH. METHODS: HCM with SRVH was defined as HCM with a maximum right ventricular wall thickness ≥10 mm. Whole-genome sequencing (WGS) was performed in HCM patients with SRVH. Multivariate Cox proportional hazards regression models were used to identify risk factors for cardiac death and events in HCM with SRVH...
2017: PloS One
https://www.readbyqxmd.com/read/28318110/on-the-association-analysis-of-genome-sequencing-data-a-spatial-clustering-approach-for-partitioning-the-entire-genome-into-nonoverlapping-windows
#2
Heide Loehlein Fier, Dmitry Prokopenko, Julian Hecker, Michael H Cho, Edwin K Silverman, Scott T Weiss, Rudolph E Tanzi, Christoph Lange
For the association analysis of whole-genome sequencing (WGS) studies, we propose an efficient and fast spatial-clustering algorithm. Compared to existing analysis approaches for WGS data, that define the tested regions either by sliding or consecutive windows of fixed sizes along variants, a meaningful grouping of nearby variants into consecutive regions has the advantage that, compared to sliding window approaches, the number of tested regions is likely to be smaller. In comparison to consecutive, fixed-window approaches, our approach is likely to group nearby variants together...
March 20, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28317136/noninvasive-prenatal-screening-at-low-fetal-fraction-comparing-whole-genome-sequencing-and-single-nucleotide-polymorphism-methods
#3
Carlo G Artieri, Carrie Haverty, Eric A Evans, James D Goldberg, Imran S Haque, Yuval Yaron, Dale Muzzey
OBJECTIVE: Performance of noninvasive prenatal screening (NIPS) methodologies when applied to low fetal fraction samples is not well established. The single-nucleotide polymorphism (SNP) method fails samples below a predetermined fetal fraction threshold, whereas some laboratories employing the whole-genome sequencing (WGS) method report aneuploidy calls for all samples. Here, the performance of the two methods was compared to determine which approach actually detects more fetal aneuploidies...
March 20, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28316112/molecular-ecology-studies-of-species-radiations-current-research-gaps-opportunities-and-challenges
#4
Marylaure de la Harpe, Margot Paris, Dirk N Karger, Jonathan Rolland, Michael Kessler, Nicolas Salamin, Christian Lexer
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28315434/identifying-the-clonal-relationship-model-of-multifocal-papillary-thyroid-carcinoma-by-whole-genome-sequencing
#5
Mao Xia, Hengyu Li, Qian Ma, Dong Yu, Jing Li, Yi Zhang, Yuan Sheng, Yingjun Guo
PURPOSE: To evaluate the application of whole genome sequencing (WGS) in determining the inter-foci clonal relationship of multifocal papillary thyroid carcinoma (mPTC). METHODS: After reviewing PTC patient profiles, 8 cancer foci and germline control samples from 3 mPTC patients were analyzed by WGS. Single nucleotide variations (SNVs), copy number variation (CNV), structural variation and mutational signature were examined. RESULTS: The multifocality rate of PTC was 35...
March 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28303425/common-data-elements-for-clinical-research-in-mitochondrial-disease-a-national-institute-for-neurological-disorders-and-stroke-project
#6
Amel Karaa, Shamima Rahman, Anne Lombès, Patrick Yu-Wai-Man, Muniza K Sheikh, Sherita Alai-Hansen, Bruce H Cohen, David Dimmock, Lisa Emrick, Marni J Falk, Shana McCormack, David Mirsky, Tony Moore, Sumit Parikh, John Shoffner, Tanja Taivassalo, Mark Tarnopolsky, Ingrid Tein, Joanne C Odenkirchen, Amy Goldstein
OBJECTIVES: The common data elements (CDE) project was developed by the National Institute of Neurological Disorders and Stroke (NINDS) to provide clinical researchers with tools to improve data quality and allow for harmonization of data collected in different research studies. CDEs have been created for several neurological diseases; the aim of this project was to develop CDEs specifically curated for mitochondrial disease (Mito) to enhance clinical research. METHODS: Nine working groups (WGs), composed of international mitochondrial disease experts, provided recommendations for Mito clinical research...
March 16, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28298902/global-distribution-and-evolutionary-history-of-enterovirus-d68-with-emphasis-on-the-2014-outbreak-in-ontario-canada
#7
Alireza Eshaghi, Venkata R Duvvuri, Sandra Isabel, Philip Banh, Aimin Li, Adriana Peci, Samir N Patel, Jonathan B Gubbay
Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines, and the Netherlands. The most recent and largest outbreak of EV-D68 associated with severe respiratory illness took place in North America between August 2014 and January 2015. Between September 1 and October 31 2014, EV-D68 infection was laboratory confirmed among 153/907 (16...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#8
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28287625/a-novel-strategy-for-clustering-major-depression-individuals-using-whole-genome-sequencing-variant-data
#9
Chenglong Yu, Bernhard T Baune, Julio Licinio, Ma-Li Wong
Major depressive disorder (MDD) is highly prevalent, resulting in an exceedingly high disease burden. The identification of generic risk factors could lead to advance prevention and therapeutics. Current approaches examine genotyping data to identify specific variations between cases and controls. Compared to genotyping, whole-genome sequencing (WGS) allows for the detection of private mutations. In this proof-of-concept study, we establish a conceptually novel computational approach that clusters subjects based on the entirety of their WGS...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28284188/the-peach-v2-0-release-high-resolution-linkage-mapping-and-deep-resequencing-improve-chromosome-scale-assembly-and-contiguity
#10
Ignazio Verde, Jerry Jenkins, Luca Dondini, Sabrina Micali, Giulia Pagliarani, Elisa Vendramin, Roberta Paris, Valeria Aramini, Laura Gazza, Laura Rossini, Daniele Bassi, Michela Troggio, Shengqiang Shu, Jane Grimwood, Stefano Tartarini, Maria Teresa Dettori, Jeremy Schmutz
BACKGROUND: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99...
March 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28281083/whole-genome-sequencing-implications-for-infection-prevention-and-outbreak-investigations
#11
REVIEW
Kyle J Popovich, Evan S Snitkin
PURPOSE OF REVIEW: Whole genome sequencing (WGS) is a laboratory method that has emerged as a promising tool for epidemiologic investigations. RECENT FINDINGS: Genomic epidemiology approaches have been utilized in outbreak settings, community settings, within acute care hospitals, and across healthcare facilities to better understand transmission and spread of potential pathogens. These studies have highlighted how essential robust epidemiologic data is in these analyses as well as how results can be translated into clinical practice and infection control and prevention...
April 2017: Current Infectious Disease Reports
https://www.readbyqxmd.com/read/28275074/same-day-diagnostic-and-surveillance-data-for-tuberculosis-via-whole-genome-sequencing-of-direct-respiratory-samples
#12
Antonina A Votintseva, Phelim Bradley, Louise Pankhurst, Carlos Del Ojo Elias, Matthew Loose, Kayzad Nilgiriwala, Anirvan Chatterjee, E Grace Smith, Nicolas Sanderson, Timothy M Walker, Marcus R Morgan, David H Wyllie, A Sarah Walker, Tim E A Peto, Derrick W Crook, Zamin Iqbal
Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near point of care.We demonstrate a low-cost DNA extraction method for TB WGS direct from patient samples. We initially evaluated the method using the Illumina MiSeq sequencer (40 smear-positive respiratory samples, obtained after routine clinical testing, and 27 matched liquid cultures)...
March 8, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28262012/active-site-and-electronic-structure-elucidation-of-pt-nanoparticles-supported-on-phase-pure-molybdenum-carbide-nanotubes
#13
Shuai Tan, Lucun Wang, Shibely Saha, Rebecca R Fushimi, Dongmei Li
We recently showed that phase-pure molybdenum carbide nanotubes can be durable supports for platinum (Pt) nanoparticles in hydrogen evolution reaction (HER). In this paper we further characterize surface properties of the same Pt/β-Mo2C catalyst platform using carbon monoxide (CO)-Pt and CO-Mo2C bond strength of different Pt particle sizes in the <3 nm range. Results from diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and temporal analysis of products (TAP) revealed the existence of different active sites as Pt particle size increases...
March 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28258043/whole-genome-single-nucleotide-variant-distribution-on-genomic-regions-and-its-relationship-to-major-depression
#14
Chenglong Yu, Bernhard T Baune, Julio Licinio, Ma-Li Wong
Recent advances in DNA technologies have provided unprecedented opportunities for biological and medical research. In contrast to current popular genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows for the detection of all private mutations within an individual. Major depressive disorder (MDD) is a chronic condition with enormous medical, social and economic impacts. Genetic analysis, by identifying risk variants and thereby increasing our understanding of how MDD arises, could lead to improved prevention and the development of new and more effective treatments...
February 20, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28257899/short-read-whole-genome-sequencing-for-determination-of-antimicrobial-resistance-mechanisms-and-capsular-serotypes-of-current-invasive-streptococcus-agalactiae-recovered-in-the-united-states
#15
Benjamin J Metcalf, Sopio Chochua, Robert E Gertz, Paulina A Hawkins, Jessica Ricaldi, Zhongya Li, Hollis Walker, Theresa Tran, Joy Rivers, Saundra Mathis, Delois Jackson, Anita Glennen, Ruth Lynfield, Lesley McGee, Bernard Beall
OBJECTIVES: Our objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS). METHODS: For 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions to broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing β-lactams.. Conventional serotyping was compared to WGS-based assignments for 302 isolates...
February 28, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28257443/analysis-of-large-versus-small-dogs-reveals-three-genes-on-the-canine-x-chromosome-associated-with-body-weight-muscling-and-back-fat-thickness
#16
Jocelyn Plassais, Maud Rimbault, Falina J Williams, Brian W Davis, Jeffrey J Schoenebeck, Elaine A Ostrander
Domestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during the formation and maintenance of modern breeds. While previous studies focused on the identification of alleles that contribute to small skeletal size, little is known about the underlying genetics controlling large size. We first performed a genome-wide association study (GWAS) using the Illumina Canine HD 170,000 single nucleotide polymorphism (SNP) array which compared 165 large-breed dogs from 19 breeds (defined as having a Standard Breed Weight (SBW) >41 kg [90 lb]) to 690 dogs from 69 small breeds (SBW ≤41 kg)...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28249998/whole-genome-sequencing-in-the-epidemiology-of-campylobacter-jejuni-infections
#17
Ann-Katrin Llarena, Eduardo Taboada, Mirko Rossi
This review provides the current state of knowledge on the application of whole-genome sequencing (WGS) in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen and how WGS has the potential to improve surveillance and outbreak detection. We have identified hurdles towards the full implementation of WGS in public health settings. However, despite these challenges, we believe that ample evidence is available to support the benefit of integrating WGS in the routine monitoring of C...
March 1, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28249607/molecular-typing-of-mycobacterium-tuberculosis-complex-isolated-from-pulmonary-tuberculosis-patients-in-central-ethiopia
#18
Zufan Bedewi, Adane Worku, Yalemtsehay Mekonnen, Getnet Yimer, Girmay Medhin, Gezahegne Mamo, Rembert Pieper, Gobena Ameni
BACKGROUND: Identification of the types of strains of Mycobacterium tuberculosis (M. tuberculosis) complex causing tuberculosis (TB) could contribute to TB control program of specific geographic region as well as it could add knowledge onto the existing literature on TB worldwide. The objective of the present study was to identify the species and strains of M. tuberculosis complex causing pulmonary tuberculosis in central Ethiopia. METHODS: A health institution- based cross-sectional study was conducted on 338 smear positive TB cases visiting three hospitals between October 2012 and September 2013...
March 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28249021/single-locus-genotyping-to-track-leishmania-donovani-in-the-indian-subcontinent-application-in-nepal
#19
Keshav Rai, Narayan Raj Bhattarai, Manu Vanaerschot, Hideo Imamura, Gebreyohans Gebru, Basudha Khanal, Suman Rijal, Marleen Boelaert, Chiranjib Pal, Prahlad Karki, Jean-Claude Dujardin, Gert Van der Auwera
BACKGROUND: We designed a straightforward method for discriminating circulating Leishmania populations in the Indian subcontinent (ISC). Research on transmission dynamics of visceral leishmaniasis (VL, or Kala-azar) was recently identified as one of the key research priorities for elimination of the disease in the ISC. VL in Bangladesh, India, and Nepal is caused by genetically homogeneous populations of Leishmania donovani parasites, transmitted by female sandflies. Classical methods to study diversity of these protozoa in other regions of the world, such as microsatellite typing, have proven of little use in the area, as they are not able to discriminate most genotypes...
March 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28230784/the-effects-of-moderate-whole-grain-consumption-on-fasting-glucose-and-lipids-gastrointestinal-symptoms-and-microbiota
#20
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
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