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https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#1
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29790902/combining-probabilistic-alignments-with-read-pair-information-improves-accuracy-of-split-alignments
#2
Anish M S Shrestha, Naruki Yoshikawa, Kiyoshi Asai
Motivation: Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is challenging when aligning a short read to a large and repetitive reference, as it tends to produce many spurious local alignments leading to ambiguities in identifying the correct split-alignment. This problem is further exacerbated by the fact that rearrangements tend to occur in repeat-rich regions...
May 18, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29789686/the-personal-and-clinical-utility-of-polygenic-risk-scores
#3
REVIEW
Ali Torkamani, Nathan E Wineinger, Eric J Topol
Initial expectations for genome-wide association studies were high, as such studies promised to rapidly transform personalized medicine with individualized disease risk predictions, prevention strategies and treatments. Early findings, however, revealed a more complex genetic architecture than was anticipated for most common diseases - complexity that seemed to limit the immediate utility of these findings. As a result, the practice of utilizing the DNA of an individual to predict disease has been judged to provide little to no useful information...
May 22, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29788239/circulating-selenium-and-prostate-cancer-risk-a-mendelian-randomization-analysis
#4
James Yarmolinsky, Carolina Bonilla, Philip C Haycock, Ryan J Q Langdon, Luca A Lotta, Claudia Langenberg, Caroline L Relton, Sarah J Lewis, David M Evans, George Davey Smith, Richard M Martin
In the Selenium and Vitamin E Cancer Prevention Trial (SELECT), selenium supplementation (causing a median 114 μg/L increase in circulating selenium) did not lower overall prostate cancer risk, but increased risk of high-grade prostate cancer and type 2 diabetes. Mendelian randomization analysis uses genetic variants to proxy modifiable risk factors and can strengthen causal inference in observational studies. We constructed a genetic instrument comprising 11 single nucleotide polymorphisms robustly (P < 5 × 10-8) associated with circulating selenium in genome-wide association studies...
May 17, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29788113/differences-in-performance-among-test-statistics-for-assessing-phylogenomic-model-adequacy
#5
David A Duchêne, Sebastian Duchêne, Simon Y W Ho
Statistical phylogenetic analyses of genomic data depend on models of nucleotide or amino acid substitution. The adequacy of these substitution models can be assessed using a number of test statistics, allowing the model to be rejected when it is found to provide a poor description of the evolutionary process. A potentially valuable use of model-adequacy test statistics is to identify when data sets are likely to produce unreliable phylogenetic estimates, but their differences in performance are rarely explored...
May 18, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29788099/biomarkers-for-homologous-recombination-deficiency-in-cancer
#6
Michal M Hoppe, Raghav Sundar, David S P Tan, Anand D Jeyasekharan
Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice...
May 18, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29788045/molecular-epidemiology-of-candida-auris-in-colombia-reveals-a-highly-related-country-wide-colonization-with-regional-patterns-in-amphotericin-b-resistance
#7
Patricia Escandón, Nancy A Chow, Diego H Caceres, Lalitha Gade, Elizabeth L Berkow, Paige Armstrong, Sandra Rivera, Elizabeth Misas, Carolina Duarte, Heather Moulton-Meissner, Rory M Welsh, Claudia Parra, Luz Angela Pescador, Nohora Villalobos, Soraya Salcedo, Indira Berrio, Carmen Varón, Andrés Espinosa-Bode, Shawn R Lockhart, Brendan R Jackson, Anastasia P Litvintseva, Mauricio Beltran, Tom M Chiller
Background: Candida auris is a multidrug-resistant yeast associated with hospital outbreaks worldwide. During 2015-2016, multiple outbreaks were reported in Colombia. We aimed to understand the extent of contamination in healthcare settings and to characterize the molecular epidemiology of C. auris in Colombia. Methods: We sampled patients, patient contacts, healthcare workers, and the environment in four hospitals with recent C. auris outbreaks. Using standardized protocols, people were swabbed at different body sites...
May 16, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29785944/-overview-of-the-genetic-control-of-horse-coat-color-patterns
#8
Ruo Yang Zhao, Yi Ping Zhao, Bei Li, Gerelchimeg Bou, Xin Zhuang Zhang, Togtokh Mongke, Tugeqin Bao, Shurenchimeg Gereliin, Tsimbai Gereltuuin, Chao Li, Dong Yi Bai, Mang Lai Dugarjaviin
Mammalian coat color is one of the first phenotypic changes resulting from positive selection by humans, and it serves important roles in genetic and evolutionary processes. Among them, horses show a broad variety of coat color patterns, based on which it is difficult to distinguish the real phenotypes, resulting in confused records in horse breed registration. Thus, research in the genetic mechanisms on the development of coat color patterns is significant in horse reproduction and breeding. With the recent establishment of genomics and sequencing technologies, there are significant advances in research in the genetics of horse coat colors, which demonstrate that special coat colors could be associated with certain diseases...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29784605/code-seq-an-augmented-whole-exome-sequencing-enables-the-accurate-detection-of-cnvs-and-mutations-in-mendelian-obesity-and-intellectual-disability
#9
Louise Montagne, Mehdi Derhourhi, Amélie Piton, Bénédicte Toussaint, Emmanuelle Durand, Emmanuel Vaillant, Dorothée Thuillier, Stefan Gaget, Franck De Graeve, Iandry Rabearivelo, Amélie Lansiaux, Bruno Lenne, Sylvie Sukno, Rachel Desailloud, Miriam Cnop, Ramona Nicolescu, Lior Cohen, Jean-François Zagury, Mélanie Amouyal, Jacques Weill, Jean Muller, Olivier Sand, Bruno Delobel, Philippe Froguel, Amélie Bonnefond
OBJECTIVE: The molecular diagnosis of extreme forms of obesity, in which accurate detection of both copy number variations (CNVs) and point mutations, is crucial for an optimal care of the patients and genetic counseling for their families. Whole-exome sequencing (WES) has benefited considerably this molecular diagnosis, but its poor ability to detect CNVs remains a major limitation. We aimed to develop a method (CoDE-seq) enabling the accurate detection of both CNVs and point mutations in one step...
May 16, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29783026/a-prolonged-and-large-outbreak-of-invasive-group-a-streptococcal-disease-within-a-nursing-home-repeated-intra-facility-transmission-of-a-single-strain
#10
S A Nanduri, B J Metcalf, M A Arwady, C Edens, M A Lavin, J Morgan, W Clegg, A Beron, J P Albertson, R Link-Gelles, A Ogundimu, J Gold, D Jackson, S Chochua, N Stone, C Van Beneden, K Fleming-Dutra, B Beall
OBJECTIVES: Multiple invasive group A streptococcal (GAS) infections were reported to public health by a skilled nursing facility (Facility A) in Illinois between May 2014 and August 2016. Cases continued despite interventions including antibiotic prophylaxis for all residents and staff. Two other geographically close facilities reported contemporaneous outbreaks of GAS. We investigated potential reasons for ongoing transmission. METHODS: We obtained epidemiologic data from chart review of cases and review of facility and public health records from previous investigations into the outbreak...
May 18, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29782924/emerging-biomarkers-for-immune-checkpoint-inhibition-in-lung-cancer
#11
REVIEW
George Cyriac, Leena Gandhi
Immune checkpoint inhibition with anti-PD-1 therapy has been notably successful in non-small cell lung cancer (NSCLC) and changed standard practice in multiple settings. However, despite some durable benefits seen, the majority of unselected patients with NSCLC fail to respond to checkpoint inhibitors. Patient selection is crucial and will become even more important in the development of combination therapies with immune checkpoint inhibitors. PD-L1 expression by immunohistochemistry (IHC) has emerged as the most commonly used clinical biomarker of response and overall tumor mutational burden (TMB) is being explored as a clinical biomarker...
May 18, 2018: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29782485/evaluation-and-application-of-summary-statistic-imputation-to-discover-new-height-associated-loci
#12
Sina Rüeger, Aaron McDaid, Zoltán Kutalik
As most of the heritability of complex traits is attributed to common and low frequency genetic variants, imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits. Association summary statistics from genome-wide meta-analyses are available for hundreds of traits. Updating these to ever-increasing reference panels is very cumbersome as it requires reimputation of the genetic data, rerunning the association scan, and meta-analysing the results...
May 21, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29780833/the-growing-genetic-and-functional-diversity-of-extended-spectrum-beta-lactamases
#13
REVIEW
Sadeeq Ur Rahman, Tariq Ali, Ijaz Ali, Nazir Ahmad Khan, Bo Han, Jian Gao
The β -lactams-a large class of diverse compounds-due to their excellent safety profile and broad antimicrobial spectrum are considered to be the most widely used therapeutic class of antibacterials prescribed in human and veterinary clinical practices. This, unfortunately, has also given rise to a continuous increased resistance globally in health care settings as well as in the community due to their permanent selective force driving diversification of the resistance mechanism. Resistance against β -lactams is increasing rapidly as novel β -lactamases, enzymes that degrade β -lactams, are being discovered each day such as recent emergence of extended spectrum β -lactamases (ESBL) that have the ability to inactivate most of the cephalosporins...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29780001/automated-typing-of-red-blood-cell-and-platelet-antigens-a-whole-genome-sequencing-study
#14
William J Lane, Connie M Westhoff, Nicholas S Gleadall, Maria Aguad, Robin Smeland-Wagman, Sunitha Vege, Daimon P Simmons, Helen H Mah, Matthew S Lebo, Klaudia Walter, Nicole Soranzo, Emanuele Di Angelantonio, John Danesh, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Richard M Kaufman, Heidi L Rehm, Leslie E Silberstein, Robert C Green
BACKGROUND: There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone...
May 17, 2018: Lancet Haematology
https://www.readbyqxmd.com/read/29779780/on-sunspots-click-science-and-molecular-iconography
#15
Igor Mokrousov
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29779130/the-present-and-the-future-of-genetic-testing-in-familial-hypercholesterolemia-opportunities-and-caveats
#16
REVIEW
Amanda J Hooper, John R Burnett, Damon A Bell, Gerald F Watts
PURPOSE OF REVIEW: We summarize recent advances in the understanding of genetic testing in familial hypercholesterolemia (FH), the use of expanded FH next-generation sequencing panels, and directions for future research. RECENT FINDINGS: The uptake of massively parallel sequencing in research and diagnostic laboratories has enabled expanded testing for FH and its phenocopies, with the added advantage that copy number variants can be detected. However, increasing the number of genes tested increases the number of variants detected, which may or may not be pathogenic...
May 19, 2018: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/29778193/single-nucleotide-variants-in-innate-immune-genes-associated-with-salmonella-shedding-and-colonization-in-swine-on-commercial-farms
#17
Margaret H Ainslie-Garcia, Abdolvahab Farzan, Mohsen Jafarikia, Brandon N Lillie
Foodborne human salmonellosis is an important food safety concern worldwide. Food-producing animals are one of the major sources of human salmonellosis, and thus control of Salmonella at the farm level could reduce Salmonella spread in the food supply system. Genetic selection of pigs with resistance to Salmonella infection may be one way to control Salmonella on swine farms. The objective of this study was to investigate the association between genetic variants in the porcine innate immune system with on-farm Salmonella shedding and Salmonella colonization tested at slaughter...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29773584/mechanisms-in-endocrinology-cell-cycle-regulation-in-adrenocortical-carcinoma
#18
Sofia Pereira, Mariana P Monteiro, Isabelle Bourdeau, Andre Lacroix, Duarte Pignatelli
Adrenocortical carcinomas are rather rare endocrine tumors that often have a poor prognosis. The reduced survival rate associated with these tumors is due to their aggressive biological behavior, combined with the scarcity of effective treatment options that are currently available. The recent identification of the genomic alterations present in ACC have provided further molecular mechanisms to develop consistent strategies for the diagnosis, prevention of progression and treatment of advanced ACCs. Taken together, molecular and genomic advances could be leading the way to develop personalized medicine in ACCs similarly to similar developments in lung or breast cancers...
May 17, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29772020/so-many-genes-so-little-time-a-practical-approach-to-divergence-time-estimation-in-the-genomic-era
#19
Stephen A Smith, Joseph W Brown, Joseph F Walker
Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern...
2018: PloS One
https://www.readbyqxmd.com/read/29769697/establishment-of-a-nasopharyngeal-carcinoma-cell-line-capable-of-undergoing-lytic-epstein-barr-virus-reactivation
#20
Yim Ling Yip, Weitao Lin, Wen Deng, Lin Jia, Kwok Wai Lo, Pierre Busson, Benjamin Vérillaud, Xuefeng Liu, Chi Man Tsang, Maria Li Lung, Sai Wah Tsao
Epstein-Barr virus (EBV) infects more than 90% of the adult human population. Undifferentiated nasopharyngeal carcinoma (NPC) is common in Southeast Asia, with a particularly high incidence among southern Chinese. The EBV genome can be detected in practically all cancer cells in undifferentiated NPC. The role of EBV in pathogenesis of undifferentiated NPC remains elusive. NPC cell lines are known to be difficult to establish in culture. The EBV+ve NPC cell lines, even if established in culture, rapidly lost their EBV episomes upon prolonged propagation...
May 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
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