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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/28727716/the-relationship-between-body-mass-index-and-fluoroscopy-time-during-intraarticular-hip-injection-a-multicenter-cohort-study
#2
Zachary L McCormick, Meghan Bhave, David T Lee, Paul Scholten, Samuel K Chu, Ashwin N Babu, Mary Caldwell, Craig Ziegler, Humaira Ashraf, Ryan Clark, Claire Gross, Jeffrey Cara, Kristen McCormick, Brendon Ross, Joel Press, David R Walega, Daniel Cushman
BACKGROUND: Higher body mass index (BMI) is associated with difficulty in obtaining imaging studies. While there is a small body of literature regarding the relationship between fluoroscopy time and BMI during injections for pain management, this has not been studied for intraarticular (IA) hip injections. Further, in academic training centers, trainee involvement may affect this relationship. OBJECTIVE: To determine the relationship between BMI and fluoroscopy time during IA hip injections, both with and without involvement of a trainee...
July 2017: Pain Physician
https://www.readbyqxmd.com/read/28725962/optimal-positioning-of-the-nipple-areola-complex-in-men-using-the-mohrenheim-estimated-tangential-tracking-line-mett-line-an-intuitive-approach
#3
Tobias R Mett, Nicco Krezdorn, Rosalia Luketina, Maria K Boyce, Helga Henseler, Ramin Ipaktchi, Peter M Vogt
INTRODUCTION: The reconstruction of the body shape after post-bariatric surgery or high-grade gynecomastia involves, besides skin tightening, the repositioning of anatomical, apparent landmarks. The surgeon usually defines these during the preoperative planning. In particular, the positions of the nipple-areola complexes (NAC) should contribute to the gender-appropriate appearance. While in the female breast numerous methods have been developed to determine the optimal position of the NACs, there are only a few, metric and often impractical algorithms for positioning the nipples and areoles in the male...
July 19, 2017: Aesthetic Plastic Surgery
https://www.readbyqxmd.com/read/28699564/detecting-clinically-relevant-new-information-in-clinical-notes-across-specialties-and-settings
#4
Rui Zhang, Serguei V S Pakhomov, Elliot G Arsoniadis, Janet T Lee, Yan Wang, Genevieve B Melton
BACKGROUND: Automated methods for identifying clinically relevant new versus redundant information in electronic health record (EHR) clinical notes is useful for clinicians and researchers involved in patient care and clinical research, respectively. We evaluated methods to automatically identify clinically relevant new information in clinical notes, and compared the quantity of redundant information across specialties and clinical settings. METHODS: Statistical language models augmented with semantic similarity measures were evaluated as a means to detect and quantify clinically relevant new and redundant information over longitudinal clinical notes for a given patient...
July 5, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28697713/an-update-of-the-italian-stroke-organization-stroke-prevention-awareness-diffusion-group-guidelines-on-carotid-endarterectomy-and-stenting-a-personalized-medicine-approach
#5
Gaetano Lanza, Carlo Setacci, Stefano Ricci, Patrizio Castelli, Alberto Cremonesi, Jessica Lanza, Claudio Novali, Carlo Pratesi, Paola Santalucia, Francesco Speziale, Augusto Zaninelli, Gian Franco Gensini
Although proof-based medicine has generated much valid evidence for the drawing up of guidelines and recommendations for best clinical practice in symptomatic and asymptomatic carotid stenosis, whether and when it is better to employ endarterectomy or stenting as the intervention of choice still remain matters of debate. Moreover, guidelines have been targeted up to now to the 'representative' patient, as resulting from the statistical analyses of the studies conducted on the safety and efficacy of both interventions as well as on medical therapy alone...
July 2017: International Journal of Stroke: Official Journal of the International Stroke Society
https://www.readbyqxmd.com/read/28686320/the-emerging-science-of-precision-medicine-and-pharmacogenomics-for-parkinson-s-disease
#6
Haydeh Payami
Current therapies for Parkinson's disease are problematic because they are symptomatic and have adverse effects. New drugs have failed in clinical trials because of inadequate efficacy. At the core of the problem is trying to make one drug work for all Parkinson's disease patients, when we know this premise is wrong because (1) Parkinson's disease is not a single disease, and (2) no two individuals have the same biological makeup. Precision medicine is the goal to strive for, but we are only at the beginning stages of building the infrastructure for one of the most complex projects in the history of science, and it will be a long time before Parkinson's disease reaps the benefits...
July 7, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28665803/methylation-differences-reveal-heterogeneity-in-preterm-pathophysiology-results-from-bipartite-network-analyses
#7
Suresh K Bhavnani, Bryant Dang, Varun Kilaru, Maria Caro, Shyam Visweswaran, George Saade, Alicia K Smith, Ramkumar Menon
BACKGROUND: Recent studies have shown that epigenetic differences can increase the risk of spontaneous preterm birth (PTB). However, little is known about heterogeneity underlying such epigenetic differences, which could lead to hypotheses for biological pathways in specific patient subgroups, and corresponding targeted interventions critical for precision medicine. Using bipartite network analysis of fetal DNA methylation data we demonstrate a novel method for classification of PTB. METHODS: The data consisted of DNA methylation across the genome (HumanMethylation450 BeadChip) in cord blood from 50 African-American subjects consisting of 22 cases of early spontaneous PTB (24-34 weeks of gestation) and 28 controls (>39 weeks of gestation)...
June 30, 2017: Journal of Perinatal Medicine
https://www.readbyqxmd.com/read/28650955/netnorm-capturing-cancer-relevant-information-in-somatic-exome-mutation-data-with-gene-networks-for-cancer-stratification-and-prognosis
#8
Marine Le Morvan, Andrei Zinovyev, Jean-Philippe Vert
Genome-wide somatic mutation profiles of tumours can now be assessed efficiently and promise to move precision medicine forward. Statistical analysis of mutation profiles is however challenging due to the low frequency of most mutations, the varying mutation rates across tumours, and the presence of a majority of passenger events that hide the contribution of driver events. Here we propose a method, NetNorM, to represent whole-exome somatic mutation data in a form that enhances cancer-relevant information using a gene network as background knowledge...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28649647/moonshots-and-metastatic-disease-the-need-for-a-multi-faceted-approach-when-studying-atypical-responses
#9
REVIEW
Kristine De La Torre, Elly Cohen, Anne Loeser, Marc Hurlbert
Clinical research generally focuses on results involving a statistical mean with little attention in trial design to patients who respond considerably better or worse than average. Exploring the reasons underlying an "atypical response" will increase understanding of the mechanisms involved in cancer progression and treatment resistance, accelerate biomarker identification, and improve precision medicine by allowing clinicians to prospectively select optimal treatments. Based on our review, we suggest two ways to move this field forward...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649437/integrating-personalized-gene-expression-profiles-into-predictive-disease-associated-gene-pools
#10
Jörg Menche, Emre Guney, Amitabh Sharma, Patrick J Branigan, Matthew J Loza, Frédéric Baribaud, Radu Dobrin, Albert-László Barabási
Gene expression data are routinely used to identify genes that on average exhibit different expression levels between a case and a control group. Yet, very few of such differentially expressed genes are detectably perturbed in individual patients. Here, we develop a framework to construct personalized perturbation profiles for individual subjects, identifying the set of genes that are significantly perturbed in each individual. This allows us to characterize the heterogeneity of the molecular manifestations of complex diseases by quantifying the expression-level similarities and differences among patients with the same phenotype...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28648253/statistical-validation-of-1-h-nmr-protocol-vs-standard-biochemical-assay-in-quality-control-of-rbc-packed-units
#11
Thelma A Pertinhez, Emanuela Casali, Laura Zambianchi, Alberto Spisni, Roberto Baricchi
BACKGROUND: Time dependent quantification of endogenous metabolites in biological samples (blood, urine, biological tissues extracts) in normal and pathological conditions as well as following therapeutic protocols is well established. In the clinical practice, such a dynamic flux of information allows the physician to identify and appreciate alterations associated to biochemical pathways of specific organs. In the years, many biochemical assays have been developed to detect, selectively, this vast array of molecules...
June 15, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28636403/applying-precision-medicine-to-trial-design-using-physiology-extracorporeal-co2-removal-for-ards
#12
Ewan C Goligher, Marcelo B P Amato, Arthur S Slutsky
In clinical trials of therapies for ARDS, the average treatment effect in the study population may be attenuated because individual patient responses vary widely. This inflates sample size requirements and increases the cost and difficulty of conducting successful clinical trials. One solution is to enrich the study population with patients most likely to benefit based on predicted patient response to treatment (predictive enrichment). In this perspective, we apply the precision medicine paradigm to the emerging use of extracorporeal CO2 removal (ECCO2R) for ultra-protective ventilation in ARDS...
June 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28633724/change-in-end-expiratory-lung-volume-during-sleep-in-patients-at-risk-for-obstructive-sleep-apnea
#13
Patrick Koo, Eric J Gartman, Jigme M Sethi, Eyad Kawar, F Dennis McCool
STUDY OBJECTIVES: As lung volume decreases radial traction on the upper airway is reduced, making it more collapsible. The purpose of this study was to measure change in end-expiratory lung volume (EELV) following sleep onset and to evaluate the relationship between change in EELV and sleep-disordered breathing. METHODS: Twenty subjects underwent overnight polysomnography, of whom 14 (70%) had obstructive sleep apnea (OSA). Change in EELV was measured throughout the night using magnetometry...
June 16, 2017: Journal of Clinical Sleep Medicine: JCSM: Official Publication of the American Academy of Sleep Medicine
https://www.readbyqxmd.com/read/28617226/contextualization-of-drug-mediator-relations-using-evidence-networks
#14
Hai Joey Tran, Gil Speyer, Jeff Kiefer, Seungchan Kim
BACKGROUND: Genomic analysis of drug response can provide unique insights into therapies that can be used to match the "right drug to the right patient." However, the process of discovering such therapeutic insights using genomic data is not straightforward and represents an area of active investigation. EDDY (Evaluation of Differential DependencY), a statistical test to detect differential statistical dependencies, is one method that leverages genomic data to identify differential genetic dependencies...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28605458/prioritizing-tests-of-epistasis-through-hierarchical-representation-of-genomic-redundancies
#15
Tyler Cowman, Mehmet Koyutürk
Epistasis is defined as a statistical interaction between two or more genomic loci in terms of their association with a phenotype of interest. Epistatic loci that are identified using data from Genome-Wide Association Studies (GWAS) provide insights into the interplay among multiple genetic factors, with applications including assessment of susceptibility to complex diseases, decision making in precision medicine, and gaining insights into disease mechanisms. Since the number of genomic loci assayed by GWAS is extremely large (usually in the order of millions), identification of epistatic loci is a statistically difficult and computationally intensive problem...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28598966/joint-modeling-of-genetically-correlated-diseases-and-functional-annotations-increases-accuracy-of-polygenic-risk-prediction
#16
Yiming Hu, Qiongshi Lu, Wei Liu, Yuhua Zhang, Mo Li, Hongyu Zhao
Accurate prediction of disease risk based on genetic factors is an important goal in human genetics research and precision medicine. Advanced prediction models will lead to more effective disease prevention and treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome-wide association studies (GWAS) in the past decade, accuracy of genetic risk prediction 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...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28596117/disrupted-white-matter-structural-networks-in-healthy-older-adult-apoe-%C3%AE%C2%B54-carriers-an-international-multicenter-dti-study
#17
Enrica Cavedo, Simone Lista, Katrine Rojkova, Patrizia A Chiesa, Marion Houot, Katharina Brueggen, Janusch Blautzik, Arun L W Bokde, Bruno Dubois, Frederik Barkhof, Petra J W Pouwels, Stefan Teipel, Harald Hampel
The ε4 allelic variant of the Apolipoprotein E gene (APOE ε4) is the best-established genetic risk factor for late-onset Alzheimer's disease (AD). White matter (WM) microstructural damages measured with Diffusion Tensor Imaging (DTI) represent an early sign of fiber tract disconnection in AD. We examined the impact of APOE ε4 on WM microstructure in elderly individuals from the multicenter European DTI Study on Dementia. Voxelwise statistical analysis of fractional anisotropy (FA), mean diffusivity, radial and axial diffusivity (MD, radD and axD respectively) was carried out using Tract-Based Spatial Statistics...
June 6, 2017: Neuroscience
https://www.readbyqxmd.com/read/28595259/molecular-profiling-of-signet-ring-cell-colorectal-cancer-provides-a-strong-rationale-for-genomic-targeted-and-immune-checkpoint-inhibitor-therapies
#18
Muhammad A Alvi, Maurice B Loughrey, Philip Dunne, Stephen McQuaid, Richard Turkington, Marc-Aurel Fuchs, Claire McGready, Victoria Bingham, Brendan Pang, Wendy Moore, Perry Maxwell, Mark Lawler, Jacqueline A James, Graeme I Murray, Richard H Wilson, Manuel Salto-Tellez
BACKGROUND: Signet ring cell colorectal cancer (SRCCa) has a bleak prognosis. Employing molecular pathology techniques we investigated the potential of precision medicine in this disease. METHODS: Using test (n=26) and validation (n=18) cohorts, analysis of mutations, DNA methylation and transcriptome was carried out. Microsatellite instability (MSI) status was established and immunohistochemistry (IHC) was used to test for adaptive immunity (CD3) and the immune checkpoint PDL1...
July 11, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28594818/leveraging-functional-annotations-in-genetic-risk-prediction-for-human-complex-diseases
#19
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/28559747/structure-leveraged-methods-in-breast-cancer-risk-prediction
#20
Jun Fan, Yirong Wu, Ming Yuan, David Page, Jie Liu, Irene M Ong, Peggy Peissig, Elizabeth Burnside
Predicting breast cancer risk has long been a goal of medical research in the pursuit of precision medicine. The goal of this study is to develop novel penalized methods to improve breast cancer risk prediction by leveraging structure information in electronic health records. We conducted a retrospective case-control study, garnering 49 mammography descriptors and 77 high-frequency/low-penetrance single-nucleotide polymorphisms (SNPs) from an existing personalized medicine data repository. Structured mammography reports and breast imaging features have long been part of a standard electronic health record (EHR), and genetic markers likely will be in the near future...
December 2016: Journal of Machine Learning Research: JMLR
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