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https://www.readbyqxmd.com/read/28532386/extremely-low-coverage-whole-genome-sequencing-in-south-asians-captures-population-genomics-information
#1
Navin Rustagi, Anbo Zhou, W Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A Gibbs, Lynn B Jorde, Fuli Yu, Jinchuan Xing
BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28530786/morphine-for-chronic-neuropathic-pain-in-adults
#2
REVIEW
Tess E Cooper, Junqiao Chen, Philip J Wiffen, Sheena Derry, Daniel B Carr, Dominic Aldington, Peter Cole, R Andrew Moore
BACKGROUND: Neuropathic pain, which is caused by a lesion or disease affecting the somatosensory system, may be central or peripheral in origin. Neuropathic pain often includes symptoms such as burning or shooting sensations, abnormal sensitivity to normally painless stimuli, or an increased sensitivity to normally painful stimuli. Neuropathic pain is a common symptom in many diseases of the nervous system. Opioid drugs, including morphine, are commonly used to treat neuropathic pain...
May 22, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28530675/reevaluation-of-snp-heritability-in-complex-human-traits
#3
Doug Speed, Na Cai, Michael R Johnson, Sergey Nejentsev, David J Balding
SNP heritability, the proportion of phenotypic variance explained by SNPs, has been reported for many hundreds of traits. Its estimation requires strong prior assumptions about the distribution of heritability across the genome, but current assumptions have not been thoroughly tested. By analyzing imputed data for a large number of human traits, we empirically derive a model that more accurately describes how heritability varies with minor allele frequency (MAF), linkage disequilibrium (LD) and genotype certainty...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28529606/comparison-of-prognostic-nomograms-based-on-different-nodal-staging-systems-in-patients-with-resected-gastric-cancer
#4
Zi-Xian Wang, Miao-Zhen Qiu, Yu-Ming Jiang, Zhi-Wei Zhou, Guo-Xin Li, Rui-Hua Xu
Purpose: Previous studies addressing the optimal nodal staging system in patients with resected gastric cancer have shown inconsistent results, and the optimal system for development of prognostic nomograms remains unclear. In this study, we compared prognostic nomograms based on the metastatic lymph node (MLN) count, lymph node ratio (LNR), and log odds of metastatic lymph nodes (LODDS) to predict the 5-year overall survival in patients with resected gastric cancer. Methods: We analysed 15,320 patients with resected gastric cancer in the Surveillance, Epidemiology, and End Results (SEER) database between 1988 and 2010...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28529188/grade-guidelines-17-assessing-the-risk-of-bias-associated-with-missing-participant-outcome-data-in-a-body-of-evidence
#5
Gordon H Guyatt, Shanil Ebrahim, Pablo Alonso-Coello, Bradley C Johnston, Alexander G Mathioudakis, Matthias Briel, Reem A Mustafa, Xin Sun, Stephen D Walter, Diane Heels-Ansdell, Ignacio Neumann, Lara A Kahale, Alfonso Iorio, Joerg Meerpohl, Holger J Schünemann, Elie A Akl
OBJECTIVE: To provide GRADE guidance for assessing risk of bias across an entire body of evidence consequent on missing data for systematic reviews of both binary and continuous outcomes. STUDY DESIGN: Systematic survey of published methodological research, iterative discussions, testing in systematic reviews, and feedback from the GRADE Working Group. RESULTS: Approaches begin with a primary meta-analysis using a complete case analysis followed by sensitivity meta-analyses imputing, in each study, data for those with missing data, and then pooling across studies...
May 18, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28527809/accuracy-of-genomic-predictions-in-gyr-bos-indicus-dairy-cattle
#6
S A Boison, A T H Utsunomiya, D J A Santos, H H R Neves, R Carvalheiro, G Mészáros, Y T Utsunomiya, A S do Carmo, R S Verneque, M A Machado, J C C Panetto, J F Garcia, J Sölkner, M V G B da Silva
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28527750/estimating-serum-concentrations-of-dioxin-like-compounds-in-the-u-s-population-effective-2005-2006-and-2007-2008-a-multiple-imputation-and-trending-approach-incorporating-nhanes-pooled-sample-data
#7
Anne Bichteler, Daniele S Wikoff, Francis Loko, Mark A Harris
Dioxin-like compounds (DLCs) are monitored in the U.S. population using data collected with the National Health and Nutrition Examination Survey (NHANES). Until recently, participants' serum samples have been analyzed individually, and summary statistics defining reference ranges by age, gender, and race/ethnicity have served as the background by which other biomonitoring data can be evaluated. In the most recent NHANES DLC data, 2005-2006 and 2007-2008, participants' sera have been physically pooled prior to laboratory analysis, introducing major challenges to their utility as a reference population: variability among individuals and relations with covariates are lost, and individual design effects cannot be applied...
May 18, 2017: Environment International
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#8
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28525968/survivalgwas_sv-software-for-the-analysis-of-genome-wide-association-studies-of-imputed-genotypes-with-time-to-event-outcomes
#9
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Analysis of genome-wide association studies (GWAS) with "time to event" outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, disease remission or the occurrence of an adverse drug reaction. However, methodology and software that can efficiently handle the scale and complexity of genetic data from GWAS with time to event outcomes has not been extensively developed. RESULTS: SurvivalGWAS_SV is an easy to use software implemented using C# and run on Linux, Mac OS X & Windows operating systems...
May 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28523795/efficacy-of-an-oral-health-literacy-intervention-among-indigenous-australian-adults
#10
Xiangqun Ju, David Brennan, Eleanor Parker, Helen Mills, Kostas Kapellas, Lisa Jamieson
OBJECTIVE: To determine the effect of an oral health literacy intervention on oral health literacy-related outcomes among rural-dwelling Indigenous Australian adults. METHODS: A total of 400 Indigenous adults (203 intervention and 197 control participants) were recruited into a randomized controlled trial; a functional, context-specific oral health literacy interventions were developed and implemented by Indigenous staff. The intervention comprised five sessions, each lasting 1...
May 19, 2017: Community Dentistry and Oral Epidemiology
https://www.readbyqxmd.com/read/28522745/randomised-controlled-trial-of-stand-alone-tailored-emails-for-smoking-cessation
#11
J Lee Westmaas, Jeuneviette Bontemps-Jones, Peter S Hendricks, Jihye Kim, Lorien C Abroms
INTRODUCTION: Digital technology has created opportunities for delivering smoking cessation assistance at the population level. However, the efficacy of sending multiple, automated, tailored emails providing motivation, support and information for quitting is unknown. METHODS: Smokers planning to quit (n=1070) were randomly assigned to (1) 27 tailored cessation emails (deluxe email group (DEG)), (2) 3 to 4 tailored emails with links to downloadable booklets (basic email group (BEG)) or (3) a single non-tailored email (single email group (SEG))...
May 18, 2017: Tobacco Control
https://www.readbyqxmd.com/read/28522181/safety-and-efficacy-of-edaravone-in-well-defined-patients-with-amyotrophic-lateral-sclerosis-a-randomised-double-blind-placebo-controlled-trial
#12
(no author information available yet)
BACKGROUND: In a previous phase 3 study in patients with amyotrophic lateral sclerosis (ALS), edaravone did not show a significant difference in the Revised ALS Functional Rating Scale (ALSFRS-R) score compared with placebo. Post-hoc analysis of these data revealed that patients in an early stage with definite or probable diagnosis of ALS, defined by the revised El Escorial criteria, who met a select set of inclusion criteria showed a greater magnitude of effect than did the full study population...
May 15, 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28521758/genome-wide-association-study-for-feed-efficiency-and-growth-traits-in-u-s-beef-cattle
#13
Christopher M Seabury, David L Oldeschulte, Mahdi Saatchi, Jonathan E Beever, Jared E Decker, Yvette A Halley, Eric K Bhattarai, Maral Molaei, Harvey C Freetly, Stephanie L Hansen, Helen Yampara-Iquise, Kristen A Johnson, Monty S Kerley, JaeWoo Kim, Daniel D Loy, Elisa Marques, Holly L Neibergs, Robert D Schnabel, Daniel W Shike, Matthew L Spangler, Robert L Weaber, Dorian J Garrick, Jeremy F Taylor
BACKGROUND: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521728/a-method-for-the-allocation-of-sequencing-resources-in-genotyped-livestock-populations
#14
Serap Gonen, Roger Ros-Freixedes, Mara Battagin, Gregor Gorjanc, John M Hickey
BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level...
May 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28521362/association-of-common-genetic-variants-with-contralateral-breast-cancer-risk-in-the-wecare-study
#15
Mark E Robson, Anne S Reiner, Jennifer D Brooks, Patrick J Concannon, Esther M John, Lene Mellemkjaer, Leslie Bernstein, Kathleen E Malone, Julia A Knight, Charles F Lynch, Meghan Woods, Xiaolin Liang, Robert W Haile, David J Duggan, Roy E Shore, Susan A Smith, Duncan C Thomas, Daniel O Stram, Jonine L Bernstein
Background: Women with unilateral breast cancer (UBC) are at risk of developing a subsequent contralateral breast cancer (CBC). Common variants are associated with breast cancer risk. Whether these influence CBC risk is unknown. Methods: Participants were breast cancer cases from the population-based Women's Environmental Cancer and Radiation Epidemiology (WECARE) Study. Sixty-seven established breast cancer risk loci were genotyped directly or by imputation in 1459 case subjects with CBC and 2126 UBC control subjects...
October 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28520984/genome-wide-association-study-of-heavy-smoking-and-daily-nondaily-smoking-in-the-hispanic-community-health-study-study-of-latinos-hchs-sol
#16
Nancy L Saccone, Leslie S Emery, Tamar Sofer, Stephanie M Gogarten, Diane M Becker, Erwin P Bottinger, Li-Shiun Chen, Robert C Culverhouse, Weimin Duan, Dana B Hancock, H Dean Hosgood, Eric O Johnson, Ruth J F Loos, Tin Louie, George Papanicolaou, Krista M Perreira, Erik J Rodriquez, Claudia Schurmann, Adrienne M Stilp, Adam A Szpiro, Gregory A Talavera, Kent D Taylor, James F Thrasher, Lisa R Yanek, Cathy C Laurie, Eliseo J Pérez-Stable, Laura J Bierut, Robert C Kaplan
Introduction: Genetic variants associated with nicotine dependence have previously been identified, primarily in European-ancestry populations. No genome-wide association studies (GWAS) have been reported for smoking behaviors in Hispanics/Latinos in the U.S. and Latin America, who are of mixed ancestry with European, African, and American Indigenous components. Methods: We examined genetic associations with smoking behaviors in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) [N=12,741 with smoking data, 5,119 ever smokers], using ~2...
May 17, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/28520805/identification-of-key-contributors-in-complex-population-structures
#17
Markus Neuditschko, Herman W Raadsma, Mehar S Khatkar, Elisabeth Jonas, Eike J Steinig, Christine Flury, Heidi Signer-Hasler, Mirjam Frischknecht, Ruedi von Niederhäusern, Tosso Leeb, Stefan Rieder
Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures...
2017: PloS One
https://www.readbyqxmd.com/read/28516318/effect-of-apixaban-on-all-cause-death-in-patients-with-atrial-fibrillation-a-meta-analysis-based-on-imputed-placebo-effect
#18
Patrícia O Guimarães, Renato D Lopes, Daniel M Wojdyla, Azmil H Abdul-Rahim, Stuart J Connolly, Greg C Flaker, Junyuan Wang, Michael Hanna, Christopher B Granger, Lars Wallentin, Kennedy R Lees, John H Alexander, John J V McMurray
PURPOSE: Vitamin K antagonists (VKAs) are the standard of care for stroke prevention in patients with atrial fibrillation (AF); therefore, there is not equipoise when comparing newer oral anticoagulants with placebo in this setting. METHODS: To explore the effect of apixaban on mortality in patients with AF, we performed a meta-analysis of apixaban versus placebo using a putative placebo analysis based on randomized controlled clinical trials that compared warfarin, aspirin, and no antithrombotic control...
May 18, 2017: Cardiovascular Drugs and Therapy
https://www.readbyqxmd.com/read/28512778/cagi4-crohn-s-exome-challenge-marker-snp-versus-exome-variant-models-for-assigning-risk-of-crohn-disease
#19
Lipika R Pal, Kunal Kundu, Yizhou Yin, John Moult
Understanding the basis of complex trait disease is a fundamental problem in human genetics. The CAGI Crohn's Exome challenges are providing insight into the adequacy of current disease models by requiring participants to identify which of a set of individuals has been diagnosed with the disease, given exome data. For the CAGI4 round, we developed a method that used the genotypes from exome sequencing data only to impute the status of Genome Wide Association Studies (GWAS) marker single nucleotide polymorphisms (SNPs)...
May 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28512766/mental-health-outcomes-of-developmental-coordination-disorder-in-late-adolescence
#20
Ian Harrowell, Linda Hollén, Raghu Lingam, Alan Emond
AIM: To assess the relationship between developmental coordination disorder (DCD) and mental health outcomes in late adolescence. METHOD: Data were analyzed from the Avon Longitudinal Study of Parents and Children. Moderate-to-severe DCD was defined at 7 to 8 years according to the DSM-IV-TR criteria. Mental health was assessed at 16 to 18 years using self-reported questionnaires: Strengths and Difficulties Questionnaire, Short Moods and Feelings Questionnaire, and the Warwick-Edinburgh Mental Well-being Scale...
May 16, 2017: Developmental Medicine and Child Neurology
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