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Precision medicine Bayesian Statistics

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https://www.readbyqxmd.com/read/28729710/learning-a-health-knowledge-graph-from-electronic-medical-records
#1
Maya Rotmensch, Yoni Halpern, Abdulhakim Tlimat, Steven Horng, David Sontag
Demand for clinical decision support systems in medicine and self-diagnostic symptom checkers has substantially increased in recent years. Existing platforms rely on knowledge bases manually compiled through a labor-intensive process or automatically derived using simple pairwise statistics. This study explored an automated process to learn high quality knowledge bases linking diseases and symptoms directly from electronic medical records. Medical concepts were extracted from 273,174 de-identified patient records and maximum likelihood estimation of three probabilistic models was used to automatically construct knowledge graphs: logistic regression, naive Bayes classifier and a Bayesian network using noisy OR gates...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28594818/leveraging-functional-annotations-in-genetic-risk-prediction-for-human-complex-diseases
#2
Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu, Hongyu Zhao
Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541380/a-fully-bayesian-latent-variable-model-for-integrative-clustering-analysis-of-multi-type-omics-data
#3
Qianxing Mo, Ronglai Shen, Cui Guo, Marina Vannucci, Keith S Chan, Susan G Hilsenbeck
Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data...
May 24, 2017: Biostatistics
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#4
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/27807752/bayesian-computation-methods-for-inferring-regulatory-network-models-using-biomedical-data
#5
REVIEW
Tianhai Tian
The rapid advancement of high-throughput technologies provides huge amounts of information for gene expression and protein activity in the genome-wide scale. The availability of genomics, transcriptomics, proteomics, and metabolomics dataset gives an unprecedented opportunity to study detailed molecular regulations that is very important to precision medicine. However, it is still a significant challenge to design effective and efficient method to infer the network structure and dynamic property of regulatory networks...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/26932678/assessing-variation-in-life-history-tactics-within-a-population-using-mixture-regression-models-a-practical-guide-for-evolutionary-ecologists
#6
Sandra Hamel, Nigel G Yoccoz, Jean-Michel Gaillard
Mixed models are now well-established methods in ecology and evolution because they allow accounting for and quantifying within- and between-individual variation. However, the required normal distribution of the random effects can often be violated by the presence of clusters among subjects, which leads to multi-modal distributions. In such cases, using what is known as mixture regression models might offer a more appropriate approach. These models are widely used in psychology, sociology, and medicine to describe the diversity of trajectories occurring within a population over time (e...
May 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/26029012/extracting-knowledge-from-chemical-imaging-data-using-computational-algorithms-for-digital-cancer-diagnosis
#7
REVIEW
Saumya Tiwari, Rohit Bhargava
Fourier transform infrared (FTIR) spectroscopic imaging is an emerging microscopy modality for clinical histopathologic diagnoses as well as for biomedical research. Spectral data recorded in this modality are indicative of the underlying, spatially resolved biochemical composition but need computerized algorithms to digitally recognize and transform this information to a diagnostic tool to identify cancer or other physiologic conditions. Statistical pattern recognition forms the backbone of these recognition protocols and can be used for highly accurate results...
June 2015: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/25276624/multiple-treatment-and-indirect-treatment-comparisons-an-overview-of-network-meta-analysis
#8
Nidhi Bhatnagar, P V M Lakshmi, Kathiresan Jeyashree
Randomized control trials and its meta-analysis has occupied the pinnacle in levels of evidence available for research. However, there were several limitations of these trials. Network meta-analysis (NMA) is a recent tool for evidence-based medicine that draws strength from direct and indirect evidence generated from randomized control trials. It facilitates comparisons across multiple treatment options, direct comparisons of which have not been attempted till date due to multitude of reasons. These indirect treatment comparisons of randomized controlled trials are based on similarity and consistency assumptions that follow Bayesian or frequentist statistics...
October 2014: Perspectives in Clinical Research
https://www.readbyqxmd.com/read/25051387/-magnitude-based-inference-a-statistical-review
#9
Alan H Welsh, Emma J Knight
PURPOSE: We consider "magnitude-based inference" and its interpretation by examining in detail its use in the problem of comparing two means. METHODS: We extract from the spreadsheets, which are provided to users of the analysis (http://www.sportsci.org/), a precise description of how "magnitude-based inference" is implemented. We compare the implemented version of the method with general descriptions of it and interpret the method in familiar statistical terms...
April 2015: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/24824338/methods-for-specifying-the-target-difference-in-a-randomised-controlled-trial-the-difference-elicitation-in-trials-delta-systematic-review
#10
REVIEW
Jenni Hislop, Temitope E Adewuyi, Luke D Vale, Kirsten Harrild, Cynthia Fraser, Tara Gurung, Douglas G Altman, Andrew H Briggs, Peter Fayers, Craig R Ramsay, John D Norrie, Ian M Harvey, Brian Buckley, Jonathan A Cook
BACKGROUND: Randomised controlled trials (RCTs) are widely accepted as the preferred study design for evaluating healthcare interventions. When the sample size is determined, a (target) difference is typically specified that the RCT is designed to detect. This provides reassurance that the study will be informative, i.e., should such a difference exist, it is likely to be detected with the required statistical precision. The aim of this review was to identify potential methods for specifying the target difference in an RCT sample size calculation...
May 2014: PLoS Medicine
https://www.readbyqxmd.com/read/24475099/feature-engineering-and-a-proposed-decision-support-system-for-systematic-reviewers-of-medical-evidence
#11
Tanja Bekhuis, Eugene Tseytlin, Kevin J Mitchell, Dina Demner-Fushman
OBJECTIVES: Evidence-based medicine depends on the timely synthesis of research findings. An important source of synthesized evidence resides in systematic reviews. However, a bottleneck in review production involves dual screening of citations with titles and abstracts to find eligible studies. For this research, we tested the effect of various kinds of textual information (features) on performance of a machine learning classifier. Based on our findings, we propose an automated system to reduce screeing burden, as well as offer quality assurance...
2014: PloS One
https://www.readbyqxmd.com/read/23849149/single-patient-n-of-1-trials-a-pragmatic-clinical-decision-methodology-for-patient-centered-comparative-effectiveness-research
#12
REVIEW
Naihua Duan, Richard L Kravitz, Christopher H Schmid
OBJECTIVE: To raise awareness among clinicians and epidemiologists that single-patient (n-of-1) trials are potentially useful for informing personalized treatment decisions for patients with chronic conditions. STUDY DESIGN AND SETTING: We reviewed the clinical and statistical literature on methods and applications of single-patient trials and then critically evaluated the needs for further methodological developments. RESULTS: Existing literature reports application of 2,154 single-patient trials in 108 studies for diverse clinical conditions; various recent commentaries advocate for wider application of such trials in clinical decision making...
August 2013: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/22129650/-populational-pharmacokinetics-of-doxorubicin-applied-to-personalised-its-dosing-in-cancer-patients
#13
V Escudero-Ortiz, A Ramón-López, M A J Duart, J J Pérez-Ruixo, B Valenzuela
OBJECTIVE: To develop and internally validate a population pharmacokinetic model for doxorubicin and to evaluate its predictive performance for dose individualization in cancer patients. METHODS: Doxorubicin plasma concentrations were determined in thirty-three cancer patients treated with intravenous doxorubicin. A three-compartment pharmacokinetic model was implemented in the NONMEN VI programme to determine the doxorubicin pharmacokinetic parameters. The identifiability of the parameters was assessed by parametric bootstrap and model validation was performed using nonparametric bootstrap, visual predictive check, and numerical predictive check...
July 2012: Farmacia Hospitalaria
https://www.readbyqxmd.com/read/21254282/cancer-risk-with-tumor-necrosis-factor-alpha-tnf-inhibitors-meta-analysis-of-randomized-controlled-trials-of-adalimumab-etanercept-and-infliximab-using-patient-level-data
#14
Johan Askling, Kyle Fahrbach, Beth Nordstrom, Susan Ross, Christopher H Schmid, Deborah Symmons
PURPOSE: Uncertain short- and long-term cancer risks with anti-TNF therapies is a concern, and led to a recent black box warning. This meta-analysis, requested by the European Medicines Agency, aimed at better assessing short-term risks by using meta-analytic techniques based on individual patient data from all corporate-sponsored randomized controlled trials (RCTs) of adalimumab, etanercept, and infliximab. METHODS: All 74 RCTs of TNF inhibitors of at least 4 weeks duration were provided to independent investigators, including case narratives for events occurring between trial start until 30 days after planned end of treatment and indicating a possible cancer...
February 2011: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/20863658/individual-n-of-1-trials-can-be-combined-to-give-population-comparative-treatment-effect-estimates-methodologic-considerations
#15
COMPARATIVE STUDY
Deborah R Zucker, Robin Ruthazer, Christopher H Schmid
OBJECTIVE: To compare different statistical models for combining N-of-1 trials to estimate a population treatment effect. STUDY DESIGN AND SETTING: Data from a published series of N-of-1 trials comparing amitriptyline (AMT) therapy and combination treatment (AMT+fluoxetine [FL]) were analyzed to compare summary and individual participant data meta-analysis; repeated-measure models; Bayesian hierarchical models; and single-period, single-pair, and averaged outcome crossover models...
December 2010: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/19620636/invited-review-use-of-meta-analysis-in-animal-health-and-reproduction-methods-and-applications
#16
REVIEW
I J Lean, A R Rabiee, T F Duffield, I R Dohoo
The objectives of this paper are to provide an introduction to meta-analysis and systematic review and to discuss the rationale for this type of research and other general considerations. We highlight methods used to produce a rigorous meta-analysis and discuss some aspects of interpretation of meta-analysis drawing on examples from the animal and veterinary science literature. Meta-analysis is a rapidly expanding area of research that has been relatively underutilized in animal and veterinary science. It is a quantitative, formal, epidemiological study design used to systematically assess previous research studies to derive conclusions about that body of research...
August 2009: Journal of Dairy Science
https://www.readbyqxmd.com/read/19473413/clinical-trials-and-haemophilia-does-the-bayesian-approach-make-the-ideal-and-desirable-good-friends
#17
REVIEW
A Iorio, M Marcucci
When the disease is rare and/or the outcome is uncommon the trial design does not warrant precise and unbiased estimates due to a lack of power or the expected length of recruitment and observation periods. Is there any reliable method to control for bias and consequently achieve an advantage from estimates generated by different study designs? An interesting statistical approach suitable to solve this problem has been theorized by Thomas Bayes. A Bayesian analysis is aimed at answering the question 'How this trial will modify our belief about that treatment effect?' In summary, the Bayesian approach can be defined as the explicit and quantitative use of any kind of external evidence in the design, analysis, and interpretation of an experimental trial...
July 2009: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/18382682/measurable-prediction-for-the-single-patient-and-the-results-of-large-double-blind-controlled-randomized-trials
#18
Cathy M Helgason, Thomas H Jobe
BACKGROUND: It has been shown that the clinical state of one patient can be represented by known measured variables of interest, each of which then form the element of a fuzzy set as point in the unit hypercube. We hypothesized that precise comparison of a single patient with the average patient of a large double blind controlled randomized study is possible using fuzzy theory. METHODS/PRINCIPLE FINDINGS: The sets as points unit hypercube geometry allows fuzzy subsethood to define in measures of fuzzy cardinality different conditions, similarity and comparison between fuzzy sets...
2008: PloS One
https://www.readbyqxmd.com/read/18280095/suprarenal-endograft-fixation-and-medium-term-renal-function-systematic-review-and-meta-analysis
#19
REVIEW
Stewart R Walsh, Jonathan R Boyle, Andrew G Lynch, Umar Sadat, Jeffrey P Carpenter, Tjun Y Tang, Michael E Gaunt
BACKGROUND: Suprarenal fixation is widely used in endovascular aneurysm repair. Numerous small, underpowered studies have concluded that it does not increase the risk of renal impairment compared with infrarenal fixation. A recent meta-analysis demonstrated that renal infarction is more common with suprarenal fixation, but the effect on renal function remains unclear. METHODS: Electronic abstract databases, article reference lists, and conference proceedings were searched for series reporting renal function data after suprarenal fixation...
June 2008: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/12424124/finding-relevant-references-to-genes-and-proteins-in-medline-using-a-bayesian-approach
#20
Julie E Leonard, Jeffrey B Colombe, Joshua L Levy
MOTIVATION: Mining the biomedical literature for references to genes and proteins always involves a tradeoff between high precision with false negatives, and high recall with false positives. Having a reliable method for assessing the relevance of literature mining results is crucial to finding ways to balance precision and recall, and for subsequently building automated systems to analyze these results. We hypothesize that abstracts and titles that discuss the same gene or protein use similar words...
November 2002: Bioinformatics
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