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Precision medicine risk prediction

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https://www.readbyqxmd.com/read/28757202/leveraging-multi-ethnic-evidence-for-risk-assessment-of-quantitative-traits-in-minority-populations
#1
Marc A Coram, Huaying Fang, Sophie I Candille, Themistocles L Assimes, Hua Tang
An essential component of precision medicine is the ability to predict an individual's risk of disease based on genetic and non-genetic factors. For complex traits and diseases, assessing the risk due to genetic factors is challenging because it requires knowledge of both the identity of variants that influence the trait and their corresponding allelic effects. Although the set of risk variants and their allelic effects may vary between populations, a large proportion of these variants were identified based on studies in populations of European descent...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28744848/systems-and-precision-medicine-approaches-to-diabetes-heterogeneity-a-big-data-perspective
#2
Enrico Capobianco
Big Data, and in particular Electronic Health Records, provide the medical community with a great opportunity to analyze multiple pathological conditions at an unprecedented depth for many complex diseases, including diabetes. How can we infer on diabetes from large heterogeneous datasets? A possible solution is provided by invoking next-generation computational methods and data analytics tools within systems medicine approaches. By deciphering the multi-faceted complexity of biological systems, the potential of emerging diagnostic tools and therapeutic functions can be ultimately revealed...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28740468/evolution-of-precision-medicine-and-surgical-strategies-for-bicuspid-aortic-valve-associated-aortopathy
#3
Ali Fatehi Hassanabad, Alex J Barker, David Guzzardi, Michael Markl, Chris Malaisrie, Patrick M McCarthy, Paul W M Fedak
Bicuspid aortic valve (BAV) is a common congenital cardiac malformation affecting 1-2% of people. BAV results from fusion of two adjacent aortic valve cusps, and is associated with dilatation of the aorta, known as bicuspid valve associated aortopathy. Bicuspid valve aortopathy is progressive and associated with catastrophic clinical events, such as aortic dissection and rupture. Therefore, frequent monitoring and early intervention with prophylactic surgical resection of the proximal aorta is often recommended...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28686075/pharmacogenetics-and-the-treatment-of-functional-gastrointestinal-disorders
#4
Houssam Halawi, Michael Camilleri
The diagnosis and management of functional gastrointestinal disorders (FGIDs) remain very challenging. In the era of precision medicine, it is important to individualize the treatment of these conditions by providing targeted and effective therapies while minimizing the risk of medication side effects. By using genetic information that predicts and affects the responses to specific medications, it is anticipated that the science of pharmacogenetics in FGIDs will advance the practice of precision medicine. The pathophysiology of FGIDs is complex, involving the interaction between predisposing genetic and environmental factors...
July 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28665803/methylation-differences-reveal-heterogeneity-in-preterm-pathophysiology-results-from-bipartite-network-analyses
#5
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/28654205/driving-toward-precision-medicine-for-acute-leukemias-are-we-there-yet
#6
Clement Chung, Hilary Ma
Despite recent progress in the understanding of the molecular basis of acute leukemias, treatment options for these diseases have not shown significant changes over the last few decades. In this review, we present a nonexhaustive key summary of the current cytogenetic and molecular changes associated with acute leukemias in disease prognostication and potential targeted therapies. An emerging paradigm is that many genetic or molecular alterations target similar signal transduction, transcriptional, and epigenetic pathways...
June 27, 2017: Pharmacotherapy
https://www.readbyqxmd.com/read/28636403/applying-precision-medicine-to-trial-design-using-physiology-extracorporeal-co2-removal-for-ards
#7
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/28634997/working-toward-precision-medicine-predicting-phenotypes-from-exomes-in-the-critical-assessment-of-genome-interpretation-cagi-challenges
#8
Roxana Daneshjou, Yanran Wang, Yana Bromberg, Samuele Bovo, Pier L Martelli, Giulia Babbi, Pietro Di Lena, Rita Casadio, Matthew Edwards, David Gifford, David T Jones, Laksshman Sundaram, Rajendra Bhat, Xiaolin Li, Lipika R Pal, Kunal Kundu, Yizhou Yin, John Moult, Yuxiang Jiang, Vikas Pejaver, Kymberleigh A Pagel, Biao Li, Sean D Mooney, Predrag Radivojac, Sohela Shah, Marco Carraro, Alessandra Gasparini, Emanuela Leonardi, Manuel Giollo, Carlo Ferrari, Silvio C E Tosatto, Eran Bachar, Johnathan R Azaria, Yanay Ofran, Ron Unger, Abhishek Niroula, Mauno Vihinen, Billy Chang, Maggie H Wang, Andre Franke, Britt-Sabina Petersen, Mehdi Pirooznia, Peter Zandi, Richard McCombie, James B Potash, Russ B Altman, Teri E Klein, Roger A Hoskins, Susanna Repo, Steven E Brenner, Alexander A Morgan
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge...
June 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28624849/the-accuracy-of-68-ga-psma-pet-ct-in-primary-lymph-node-staging-in-high-risk-prostate-cancer
#9
Can Öbek, Tünkut Doğanca, Emre Demirci, Meltem Ocak, Ali Rıza Kural, Asıf Yıldırım, Uğur Yücetaş, Çetin Demirdağ, Sarper M Erdoğan, Levent Kabasakal
PURPOSE: To assess the diagnostic accuracy of (68)Ga-PSMA PET in predicting lymph node (LN) metastases in primary N staging in high-risk and very high-risk nonmetastatic prostate cancer in comparison with morphological imaging. METHODS: This was a multicentre trial of the Society of Urologic Oncology in Turkey in conjunction with the Nuclear Medicine Department of Cerrahpasa School of Medicine, Istanbul University. Patients were accrued from eight centres. Patients with high-risk and very high-risk disease scheduled to undergo surgical treatment with extended LN dissection between July 2014 and October 2015 were included...
June 18, 2017: European Journal of Nuclear Medicine and Molecular Imaging
https://www.readbyqxmd.com/read/28598966/joint-modeling-of-genetically-correlated-diseases-and-functional-annotations-increases-accuracy-of-polygenic-risk-prediction
#10
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/28594818/leveraging-functional-annotations-in-genetic-risk-prediction-for-human-complex-diseases
#11
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/28573413/-molecular-biomarkers-and-prognostic-factors-for-prostate-cancer
#12
A Kretschmer, Y Tolkach, J Ellinger, G Kristiansen
In the era of personalized medicine and precision oncology, innovative genetic biomarkers are of emerging interest to close the diagnostic and prognostic gap that is left by current clinicopathologic risk classifiers. The current review article summarizes evidence regarding prognostic and predictive genetic biomarkers that are currently in widespread clinical use at initial diagnosis as well as following definitive treatment of prostate cancer. We give a brief summary about basic principles of biomarker research studies and present current data for the Progensa PC3 test, TMPRSS2:ERG gene fusion, ConfirmMDx, Prolaris gene panel, OncotypeDX Genomic Prostate score, and Decipher classifier...
July 2017: Der Urologe. Ausg. A
https://www.readbyqxmd.com/read/28570546/electrophysiological-analysis-of-human-pluripotent-stem-cell-derived-cardiomyocytes-hpsc-cms-using-multi-electrode-arrays-meas
#13
Luca Sala, Dorien Ward-van Oostwaard, Leon G J Tertoolen, Christine L Mummery, Milena Bellin
Cardiomyocytes can now be derived with high efficiency from both human embryonic and human induced-Pluripotent Stem Cells (hPSC). hPSC-derived cardiomyocytes (hPSC-CMs) are increasingly recognized as having great value for modeling cardiovascular diseases in humans, especially arrhythmia syndromes. They have also demonstrated relevance as in vitro systems for predicting drug responses, which makes them potentially useful for drug-screening and discovery, safety pharmacology and perhaps eventually for personalized medicine...
May 12, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28562095/the-advancement-of-multidimensional-qsar-for-novel-drug-discovery-where-are-we-headed
#14
REVIEW
Tao Wang, Xin-Song Yuan, Mian-Bin Wu, Jian-Ping Lin, Li-Rong Yang
The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application...
August 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28561668/established-and-novel-prognostic-biomarkers-in-multiple-myeloma
#15
Mark Bustoros, Tarek H Mouhieddine, Alexandre Detappe, Irene M Ghobrial
Multiple myeloma (MM) is an incurable plasma cell malignancy characterized by notable interpatient heterogeneity. There have been important advances in therapy and overall survival, but some patients with high-risk features still have poor survival rates. Therefore, accurate identification of this subset of patients has been integral to improvement of patient outcome. During the last few years, cytogenetics, gene expression profiling, MRI and PET/CT, as well as serum free light chain assays have been used as accurate biomarkers to better characterize the diverse course and outcome of the disease...
2017: American Society of Clinical Oncology Educational Book
https://www.readbyqxmd.com/read/28560038/mutational-status-predicts-the-risk-of-thromboembolic-events-in-lung-adenocarcinoma
#16
Elsa Davidsson, Nicola Murgia, Cristian Ortiz-Villalón, Emil Wiklundh, Magnus Sköld, Karl Gustav Kölbeck, Giovanni Ferrara
BACKGROUND: Precision medicine promises to improve prognosis of patients affected by untreatable diseases. Patients with lung cancer (especially lung adenocarcinoma) bear an increased risk of VTE. Mutations in the EGFR and rearrangement in the ALK genes identify specific subgroups of patients. Aim of this study was to investigate the role of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutational status on the risk of venous thromboembolism (VTE) in lung adenocarcinoma...
2017: Multidisciplinary Respiratory Medicine
https://www.readbyqxmd.com/read/28559747/structure-leveraged-methods-in-breast-cancer-risk-prediction
#17
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
https://www.readbyqxmd.com/read/28524737/utilizing-next-generation-sequencing-in-the-management-of-multiple-myeloma
#18
Marta Lionetti, Antonino Neri
Multiple myeloma (MM) is a bone marrow plasma cell malignancy characterized by wide clinical presentation and heterogeneous genetic background. Despite the recent advances in patient outcome, new markers are needed for improving risk prediction and choice of a more appropriate therapy. In this perspective, the genetic makeup of MM cells is being better characterized by means of next-generation sequencing (NGS) technologies. Areas covered: The authors discuss how the application of NGS has improved our knowledge of MM biology by discovering its mutational landscape, identifying the operating mutational processes, and revealing the clonal composition of tumors and the dynamics of its evolution; and how this can have important clinical implications in terms of prognostication, therapeutic choices, and response assessment...
July 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28523274/identification-of-braf-positive-cases-based-on-whole-slide-image-analysis
#19
Vlad Popovici, Aleš Křenek, Eva Budinská
A key requirement for precision medicine is the accurate identification of patients that would respond to a specific treatment or those that represent a high-risk group, and a plethora of molecular biomarkers have been proposed for this purpose during the last decade. Their application in clinical settings, however, is not always straightforward due to relatively high costs of some tests, limited availability of the biological material and time, and procedural constraints. Hence, there is an increasing interest in constructing tissue-based surrogate biomarkers that could be applied with minimal overhead directly to histopathology images and which could be used for guiding the selection of eventual further molecular tests...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28499030/moderator-s-view-predictive-models-a-prelude-to-precision-nephrology
#20
Carmine Zoccali
Appropriate diagnosis is fundamental in medicine because it sets the basis for the prediction of disease outcome at the single patient level (prognosis) and decisions regarding the most appropriate therapy. However, given the large series of social, clinical and biological factors that determine the likelihood of an individual's future outcome, prognosis only partly depends on diagnosis and aetiology and treatment is not decided solely on the basis of the underlying diagnosis. This issue is crucial in multifactorial diseases like atherosclerosis, where the use of statins has now shifted from 'treating hypercholesterolaemia' to 'treating the risk of adverse cardiovascular events'...
May 1, 2017: Nephrology, Dialysis, Transplantation
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