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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/28605458/prioritizing-tests-of-epistasis-through-hierarchical-representation-of-genomic-redundancies
#1
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/28549478/gladiator-a-global-approach-for-elucidating-disease-modules
#2
Yael Silberberg, Martin Kupiec, Roded Sharan
BACKGROUND: Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based approaches for deciphering disease mechanisms. In particular, protein-protein interaction networks were successfully used to illuminate disease modules, i.e., interacting proteins working in concert to drive a disease. The identification of these modules can further our understanding of disease mechanisms...
May 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28495491/a-computational-algorithm-for-personalized-medicine-in-schizophrenia
#3
Beom S Lee, Roger S McIntyre, James E Gentle, Nan Sook Park, David A Chiriboga, Yena Lee, Sabrina Singh, Marie A McPherson
Despite advances in sequencing candidate genes and whole genomes, no method has accurately predicted who will or will not benefit from a specific antipsychotic medication among patients with schizophrenia. We propose a computational algorithm that utilizes a person-centered approach that directly identifies individual patients who will respond to a specific antipsychotic medication. The algorithm was applied to the data obtained from the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) study...
May 8, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28471435/genomic-sequencing-in-cystic-fibrosis-newborn-screening-what-works-best-two-tier-predefined-cftr-mutation-panels-or-second-tier-cftr-panel-followed-by-third-tier-sequencing
#4
Robert J Currier, Stan Sciortino, Ruiling Liu, Tracey Bishop, Rasoul Alikhani Koupaei, Lisa Feuchtbaum
PurposeThe purpose of this study was to model the performance of several known two-tier, predefined mutation panels and three-tier algorithms for cystic fibrosis (CF) screening utilizing the ethnically diverse California population.MethodsThe cystic fibrosis transmembrane conductance regulator (CFTR) mutations identified among the 317 CF cases in California screened between 12 August 2008 and 18 December 2012 were used to compare the expected CF detection rates for several two- and three-tier screening approaches, including the current California approach, which consists of a population-specific 40-mutation panel followed by third-tier sequencing when indicated...
May 4, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28451583/pregnancy-an-underutilized-window-of-opportunity-to-improve-long-term-maternal-and-infant-health-an-appeal-for-continuous-family-care-and-interdisciplinary-communication
#5
REVIEW
Birgit Arabin, Ahmet A Baschat
Physiologic adaptations during pregnancy unmask a woman's predisposition to diseases. Complications are increasingly predicted by first-trimester algorithms, amplify a pre-existing maternal phenotype and accelerate risks for chronic diseases in the offspring up to adulthood (Barker hypothesis). Recent evidence suggests that vice versa, pregnancy diseases also indicate maternal and even grandparent's risks for chronic diseases (reverse Barker hypothesis). Pub-Med and Embase were reviewed for Mesh terms "fetal programming" and "pregnancy complications combined with maternal disease" until January 2017...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28444439/back-to-the-future-part-2-post-mortem-assessment-and-evolutionary-role-of-the-bio-medicolegal-sciences
#6
REVIEW
Santo Davide Ferrara, Giovanni Cecchetto, Rossana Cecchi, Donata Favretto, Silke Grabherr, Takaki Ishikawa, Toshikazu Kondo, Massimo Montisci, Heidi Pfeiffer, Maurizio Rippa Bonati, Dina Shokry, Marielle Vennemann, Thomas Bajanowski
Part 2 of the review "Back to the Future" is dedicated to the evolutionary role of the bio-medicolegal sciences, reporting the historical profiles, the state of the art, and prospects for future development of the main related techniques and methods of the ancillary disciplines that have risen to the role of "autonomous" sciences, namely, Genetics and Genomics, Toxicology, Radiology, and Imaging, involved in historic synergy in the "post-mortem assessment," together with the mother discipline Legal Medicine, by way of its primary fundament, universally denominated as Forensic Pathology...
April 25, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28439010/cyclops-reveals-human-transcriptional-rhythms-in-health-and-disease
#7
Ron C Anafi, Lauren J Francey, John B Hogenesch, Junhyong Kim
Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28431171/heritability-of-heart-rate-response-to-arousals-in-twins
#8
Xiaoling Gao, Ali Azarbarzin, Brendan T Keenan, Michele Ostrowski, Frances M Pack, Bethany Staley, Greg Maislin, Allan I Pack, Magdy Younes, Samuel T Kuna
Objectives: To determine if the large and highly reproducible interindividual differences in arousal intensity and heart rate response to arousal (ΔHR) during non-REM sleep are heritable. Methods: Polysomnograms of 55 monozygotic (14 male and 41 female pairs) and 36 dizygotic (15 male and 21 female pairs) same-sex twin pairs were analyzed. Arousals were scored using the 2012 American Academy of Sleep Medicine criteria. Arousal intensity was scaled (between 0 and 9) using an automatic algorithm based on the change in electroencephalogram time and frequency characteristics...
June 1, 2017: Sleep
https://www.readbyqxmd.com/read/28399500/on-line-monitoring-of-extraction-process-of-flos-lonicerae-japonicae-using-near-infrared-spectroscopy-combined-with-synergy-interval-pls-and-genetic-algorithm
#9
Yue Yang, Lei Wang, Yongjiang Wu, Xuesong Liu, Yuan Bi, Wei Xiao, Yong Chen
There is a growing need for the effective on-line process monitoring during the manufacture of traditional Chinese medicine to ensure quality consistency. In this study, the potential of near infrared (NIR) spectroscopy technique to monitor the extraction process of Flos Lonicerae Japonicae was investigated. A new algorithm of synergy interval PLS with genetic algorithm (Si-GA-PLS) was proposed for modeling. Four different PLS models, namely Full-PLS, Si-PLS, GA-PLS, and Si-GA-PLS, were established, and their performances in predicting two quality parameters (viz...
July 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28357616/prenatal-screening-for-chromosomal-abnormalities-in-ivf-patients-that-opted-for-preimplantation-genetic-screening-diagnosis-pgs-d-a-need-for-revised-algorithms-in-the-era-of-personalized-medicine
#10
Afua Takyi, Joaquin Santolaya-Forgas
Obstetricians offer prenatal screening for most common chromosomal abnormalities to all pregnant women including those that had in vitro fertilization (IVF) and preimplantation genetic screening/diagnosis (PGS/D). We propose that free fetal DNA in maternal circulation together with the second trimester maternal serum alfa feto protein (MSAFP) and ultrasound imaging is the best prenatal screening test for chromosomal abnormalities and congenital anomalies in IVF-PGD/S patients because risk estimations from all other prenatal screening algorithms for chromosomal abnormalities depend heavily on maternal age which is irrelevant in PGS/D patients...
June 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28333918/21-gene-recurrence-score-testing-among-medicare-beneficiaries-with-breast-cancer-in-2010-2013
#11
Julie A Lynch, Brygida Berse, Nicole Coomer, John Kautter
PURPOSE: We evaluated national patient-level utilization of the 21-gene recurrence score (21-gene RS) test among Medicare beneficiaries with breast cancer. We analyzed clinical, demographic, and regional factors that predict testing. METHODS: Using 2010-2013 Medicare claims, we conducted a retrospective study of breast cancer patients. The outcome variable was whether the patient underwent testing. Independent variables expected to predict testing were age, gender, race, Medicaid status, clinical characteristics, and hospital referral region (HRR)...
March 23, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28327571/insights-from-early-experience-of-a-rare-disease-genomic-medicine-multidisciplinary-team-a-qualitative-study
#12
Elizabeth Ormondroyd, Michael P Mackley, Edward Blair, Jude Craft, Julian C Knight, John Taylor, Jenny C Taylor, Andrew Om Wilkie, Hugh Watkins
Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought...
June 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28293716/-diagnostics-in-human-genetics-integration-of-phenotypic-and-genomic-data
#13
Sebastian Köhler, Peter N Robinson
The development of reliable methods for annotation of clinical phenotypes and algorithms to calculate similarity values for clinical phenotype profiles will be a major challenge for genomic personalized medicine, since combined analysis of phenotypic features and genetic variants can increase diagnostic yield, especially with exome or genome sequencing. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for capturing phenotypic abnormalities in human disease in a precise and comprehensive fashion...
March 14, 2017: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
https://www.readbyqxmd.com/read/28257413/uncovering-precision-phenotype-biomarker-associations-in-traumatic-brain-injury-using-topological-data-analysis
#14
Jessica L Nielson, Shelly R Cooper, John K Yue, Marco D Sorani, Tomoo Inoue, Esther L Yuh, Pratik Mukherjee, Tanya C Petrossian, Jesse Paquette, Pek Y Lum, Gunnar E Carlsson, Mary J Vassar, Hester F Lingsma, Wayne A Gordon, Alex B Valadka, David O Okonkwo, Geoffrey T Manley, Adam R Ferguson
BACKGROUND: Traumatic brain injury (TBI) is a complex disorder that is traditionally stratified based on clinical signs and symptoms. Recent imaging and molecular biomarker innovations provide unprecedented opportunities for improved TBI precision medicine, incorporating patho-anatomical and molecular mechanisms. Complete integration of these diverse data for TBI diagnosis and patient stratification remains an unmet challenge. METHODS AND FINDINGS: The Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot multicenter study enrolled 586 acute TBI patients and collected diverse common data elements (TBI-CDEs) across the study population, including imaging, genetics, and clinical outcomes...
2017: PloS One
https://www.readbyqxmd.com/read/28257315/personalized-medicine-and-chronic-obstructive-pulmonary-disease
#15
E F M Wouters, B B R A F Wouters, I M L Augustin, F M E Franssen
PURPOSE OF REVIEW: The current review summarizes ongoing developments in personalized medicine and precision medicine in chronic obstructive pulmonary disease (COPD). Our current approach is far away of personalized management algorithms as current recommendations for COPD are largely based on a reductionist disease description, operationally defined by results of spirometry. RECENT FINDINGS: Besides precision medicine developments, a personalized medicine approach in COPD is described based on a holistic approach of the patient and considering illness as the consequence of dynamic interactions within and between multiple interacting and self-adjusting systems...
May 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28198728/personalized-medicine-in-interstitial-lung-diseases
#16
Paolo Spagnolo, Justin M Oldham, Mark G Jones, Joyce S Lee
PURPOSE OF REVIEW: A number of recent studies have explored the possibility to apply personalized medicine to interstitial lung diseases (ILDs), particularly idiopathic pulmonary fibrosis (IPF), the most common and deadly of the idiopathic interstitial pneumonias. In our review, we summarize and discuss the most recent literature on personalized medicine in IPF as well as hypersensitivity pneumonitis and sarcoidosis, with emphasis on patient subgroups for which a personalized approach to disease prognostication and management may become a reality in the near future...
May 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28198666/design-connecting-gene-expression-with-therapeutics-for-drug-repurposing-and-development
#17
Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
BACKGROUND: The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed to enable effective drugs to enter the clinic. Precision medicine has demonstrated that genetic features of cancer cells can be used for predicting drug response, and emerging evidence suggest that gene-drug connections could be predicted more accurately by exploring the cumulative effects of many genes simultaneously...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197794/therapeutic-options-in-refractory-diabetic-macular-oedema
#18
REVIEW
Sanket U Shah, Raj K Maturi
Diabetic macular oedema (DMO) results from alterations of several biochemical pathways in diabetic eyes. Centre-involving DMO is an important cause of visual loss in diabetes. Anti-vascular endothelial growth factor agents are now the mainstay of centre-involving DMO treatment. Oedema that does not achieve optimal response to these agents occurs in a sizeable proportion of eyes and is called refractory or persistent DMO. Management of refractory DMO is challenging. In this paper, the pathophysiology of DMO, and the definitions used in various studies are summarised...
April 2017: Drugs
https://www.readbyqxmd.com/read/28133611/diagnostic-method-of-diabetes-based-on-support-vector-machine-and-tongue-images
#19
Jianfeng Zhang, Jiatuo Xu, Xiaojuan Hu, Qingguang Chen, Liping Tu, Jingbin Huang, Ji Cui
Objective. The purpose of this research is to develop a diagnostic method of diabetes based on standardized tongue image using support vector machine (SVM). Methods. Tongue images of 296 diabetic subjects and 531 nondiabetic subjects were collected by the TDA-1 digital tongue instrument. Tongue body and tongue coating were separated by the division-merging method and chrominance-threshold method. With extracted color and texture features of the tongue image as input variables, the diagnostic model of diabetes with SVM was trained...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28121178/classification-of-sphingosine-kinase-inhibitors-using-counter-propagation-artificial-neural-networks-a-systematic-route-for-designing-selective-sphk-inhibitors
#20
M S Neiband, A Mani-Varnosfaderani, A Benvidi
Accurate and robust classification models for describing and predicting the activity of 330 chemicals that are sphingosine kinase 1 (SphK1) and/or sphingosine kinase 2 (SphK2) inhibitors were derived. The classification models developed in this work assist in finding selective subspaces in chemical space occupied by particular groups of SphK inhibitors. A combination of a genetic algorithm (GA) and a counter propagation artificial neural network (CPANN) was utilized to select the most efficient subsets of the molecular descriptors...
February 2017: SAR and QSAR in Environmental Research
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