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Genetic algorithms in medicine

Renata C Gallagher, Laura Pollard, Anna I Scott, Suzette Huguenin, Stephen Goodman, Qin Sun
Disclaimer: These ACMG Standards are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards is voluntary and does not necessarily assure a successful medical outcome. These Standards should not be considered inclusive of all proper procedures and tests, or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Alexander Malafeev, Ximena Omlin, Aleksandra Wierzbicka, Adam Wichniak, Wojciech Jernajczyk, Robert Riener, Peter Achermann
Quantitative electroencephalogram analysis (e.g. spectral analysis) has become an important tool in sleep research and sleep medicine. However, reliable results are only obtained if artefacts are removed or excluded. Artefact detection is often performed manually during sleep stage scoring, which is time consuming and prevents application to large datasets. We aimed to test the performance of mostly simple algorithms of artefact detection in polysomnographic recordings, derive optimal parameters and test their generalization capacity...
March 8, 2018: Journal of Sleep Research
Luc J J Derijks, Dennis R Wong, Daniel W Hommes, Adriaan A van Bodegraven
According to recent clinical consensus, pharmacotherapy of inflammatory bowel disease (IBD) is, or should be, personalized medicine. IBD treatment is complex, with highly different treatment classes and relatively few data on treatment strategy. Although thorough evidence-based international IBD guidelines currently exist, appropriate drug and dose choice remains challenging as many disease (disease type, location of disease, disease activity and course, extraintestinal manifestations, complications) and patient characteristics [(pharmaco-)genetic predisposition, response to previous medications, side-effect profile, necessary onset of response, convenience, concurrent therapy, adherence to (maintenance) therapy] are involved...
March 6, 2018: Clinical Pharmacokinetics
Fangying Xie, Juliana C N Chan, Ronald C W Ma
Diabetes has become a major burden of healthcare expenditure. Diabetes management following a uniform treatment algorithm is often associated with progressive treatment failure and development of diabetic complications. Recent advances in our understanding in the genomic architecture of diabetes and its complications have provided the framework for development of precision medicine to personalize diabetes prevention and management. In this review, we summarized recent advances in the understanding of the genetic basis of diabetes and its complications...
March 2, 2018: Journal of Diabetes Investigation
Monia Jebri, José Tarrazó, José Bon, Hélène Desmorieux, Mehrez Romdhane
The current study deals with an innovation in the hot air convective drying process consisting of the application of two consecutive drying steps. Temperatures ranging between 60 and 80 ℃ for times between 200 and 600 s were applied for the first stage, and from 40 to 80 ℃ for the second stage. Salvia officinalis, an aromatic, medicinal Mediterranean plant with remarkable antioxidant properties, was selected for this study. A management of the process regarding the antioxidant capacity of S. officinalis extracts and energy consumption was carried out: (i) artificial neural networks were applied to model the evolution of the antioxidant capacity and moisture content of the product in the drying process; (ii) a genetic algorithm and a multiobjective genetic algorithm were selected to optimize the drying process, considering the antioxidant capacity and/or the energy consumption in the objective function...
January 1, 2018: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
Karin Huijsdens-van Amsterdam, Roy Straver, Merel C van Maarle, Alida C Knegt, Diane Van Opstal, Frank Sleutels, Dominique Smeets, Erik A Sistermans
PurposeUsing genome-wide noninvasive prenatal screening (NIPS), we detected a 20-megabase specific deletion starting at 10q25 in eight pregnancies. The deletion could not be confirmed by invasive testing. Since all 10(q25→︀qter) deletions started close to the FRA10B fragile site in 10q25, we investigated whether the pregnant women were indeed carriers of FRA10B.MethodsWe performed NIPS analysis for all autosomes using single-read sequencing. Analysis was done with the WISECONDOR algorithm. Culture of blood lymphocytes with bromodeoxyuridine was used to detect FRA10B expansions...
March 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Jingjing Xu, Yanbin Tan, Minming Zhang
Tumor precision medicine is an emerging approach for tumor diagnosis, treatment and prevention, which takes account of individual variability of environment, lifestyle and genetic information. Tumor precision medicine is built up on the medical imaging innovations developed during the past decades, including the new hardware, new imaging agents, standardized protocols, image analysis and multimodal imaging fusion technology. Also the development of automated and reproducible analysis algorithm has extracted large amount of information from image-based features...
May 25, 2017: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
Robert Chase Cockrell, Gary An
Sepsis, a manifestation of the body's inflammatory response to injury and infection, has a mortality rate of between 28%-50% and affects approximately 1 million patients annually in the United States. Currently, there are no therapies targeting the cellular/molecular processes driving sepsis that have demonstrated the ability to control this disease process in the clinical setting. We propose that this is in great part due to the considerable heterogeneity of the clinical trajectories that constitute clinical "sepsis," and that determining how this system can be controlled back into a state of health requires the application of concepts drawn from the field of dynamical systems...
February 2018: PLoS Computational Biology
Igor F Tsigelny
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations...
February 9, 2018: Briefings in Bioinformatics
Alessandro Serretti
Precision medicine is a concept which is recently gaining momentum in all branches of medicine. In particular in psychiatry it is greatly needed given the huge societal costs of psychiatric disorders and given the long time needed to observe benefit from treatments and the response variability. The future will be based on biological determinants, however until such an interesting but still futuristic aim will be reached, at present we may only rely on clinical features to guide our individualized prescription which is currently still frequently based on personal opinion and subjective previous experiences...
February 28, 2018: Clinical Psychopharmacology and Neuroscience: the Official Scientific Journal of the Korean College of Neuropsychopharmacology
Christopher A Cassa, Daniel M Jordan, Ivan Adzhubei, Shamil Sunyaev
PurposeOver 150,000 variants have been reported to cause Mendelian disease in the medical literature. It is still difficult to leverage this knowledge base in clinical practice, as many reports lack strong statistical evidence or may include false associations. Clinical laboratories assess whether these variants (along with newly observed variants that are adjacent to these published ones) underlie clinical disorders.MethodsWe investigated whether citation data-including journal impact factor and the number of cited variants (NCV) in each gene with published disease associations-can be used to improve variant assessment...
February 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Ashley Brenton, Chee Lee, Katrina Lewis, Maneesh Sharma, Svetlana Kantorovich, Gregory A Smith, Brian Meshkin
Purpose: The purpose of this study was to determine the clinical utility of an algorithm-based decision tool designed to assess risk associated with opioid use. Specifically, we sought to assess how physicians were using the profile in patient care and how its use affected patient outcomes. Patients and methods: A prospective, longitudinal study was conducted to assess the utility of precision medicine testing in 5,397 patients across 100 clinics in the USA. Using a patent-protected, validated algorithm combining specific genetic risk factors with phenotypic traits, patients were categorized into low-, moderate-, and high-risk patients for opioid abuse...
2018: Journal of Pain Research
Charles Addo-Quaye, Mitch Tuinstra, Nicola Carraro, Clifford Weil, Brian P Dilkes
The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS) treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive induced variants in next-generation sequencing data permits higher throughput variant detection with greater accuracy...
January 29, 2018: G3: Genes—Genomes—Genetics
Yasmin Busch, Andreas Menke
Major depressive disorder is a common, serious and in some cases, life-threatening condition and affects approximately 350 million people globally. Although there is effective treatment available for it, more than 50% of the patients fail to respond to the first antidepressant they receive. The selection of a distinct treatment is still exclusively based on clinical judgment without incorporating lab-derived objective measures. However, there is growing evidence of biomarkers that it helps to improve diagnostic processes and treatment algorithms...
January 27, 2018: Journal of Neural Transmission
Anna Marie Williams, Yong Liu, Kevin R Regner, Fabrice Jotterand, Pengyuan Liu, Mingyu Liang
Big data is a major driver in the development of precision medicine. Efficient analysis methods are needed to transform big data into clinically-actionable knowledge. To accomplish this, many researchers are turning towards machine learning (ML), an approach of artificial intelligence (AI) that utilizes modern algorithms to give computers the ability to learn. Much of the effort to advance ML for precision medicine has been focused on the development and implementation of algorithms and the generation of ever larger quantities of genomic sequence data and electronic health records...
January 26, 2018: Physiological Genomics
Daniel Wenz, Andre Kuehne, Till Huelnhagen, Armin M Nagel, Helmar Waiczies, Oliver Weinberger, Celal Oezerdem, Oliver Stachs, Soenke Langner, Erdmann Seeliger, Bert Flemming, Russell Hodge, Thoralf Niendorf
PURPOSE: The aim of this study was to achieve millimeter spatial resolution sodium in vivo MRI of the human eye at 7 T using a dedicated six-channel transceiver array. We present a detailed description of the radiofrequency coil design, along with electromagnetic field and specific absorption ratio simulations, data validation, and in vivo application. METHODS: Electromagnetic field and specific absorption ratio simulations were performed. Transmit field uniformity was optimized by using a multi-objective genetic algorithm...
January 12, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord, Alejandro Sifrim, Rosemary Kelsell, Michael J Parker, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
PurposeGiven the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.MethodsWe tested this hypothesis in the United Kingdom-wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Rashmi R Shah, Andrea Gaedigk
Inter-ethnic differences in drug response are all too well known. These are underpinned by a number of factors, including pharmacogenetic differences across various ethnic populations. Precision medicine relies on genotype-based prescribing decisions with the aim of maximizing efficacy and mitigating the risks. When there is no access to genotyping tests, ethnicity is frequently regarded as a proxy of the patient's probable genotype on the basis of overall population-based frequency of genetic variations in the ethnic group the patient belongs to, with some variations being ethnicity-specific...
January 2018: Therapeutic Advances in Drug Safety
Jocelyn Y Cheng, Jacqueline A French
PURPOSE OF REVIEW: To describe the most important issues a clinician must consider whenever selecting and administering antiepileptic drugs (AEDs). There is no available algorithm that identifies how to individualize selection of AEDs. Proper selection and administration can make an enormous difference in both effectiveness and tolerability. RECENT FINDINGS: Many principles of AED selection remain unchanged. Selection of AEDs must be based on understanding of epilepsy syndrome and seizure type, comorbidities, risk of adverse events, as well as on patient characteristics such as age and sex...
April 2018: Current Opinion in Neurology
Lei Chen, Tao Liu, Xian Zhao
The anatomical therapeutic chemical (ATC) classification system is a widely accepted drug classification scheme. This system comprises five levels and includes several classes in each level. Drugs are classified into classes according to their therapeutic effects and characteristics. The first level includes 14 main classes. In this study, we proposed two network-based models to infer novel potential chemicals deemed to belong in the first level of ATC classification. To build these models, two large chemical networks were constructed using the chemical-chemical interaction information retrieved from the Search Tool for Interactions of Chemicals (STITCH)...
December 13, 2017: Biochimica et Biophysica Acta
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