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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/27897013/harnessing-big-data-for-precision-medicine-infrastructures-and-applications
#1
Kun-Hsing Yu, Steven N Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen C J Parker, Michael Snyder
Precision medicine is a health management approach that accounts for individual differences in genetic backgrounds and environmental exposures. With the recent advancements in high-throughput omics profiling technologies, collections of large study cohorts, and the developments of data mining algorithms, big data in biomedicine is expected to provide novel insights into health and disease states, which can be translated into personalized disease prevention and treatment plans. However, petabytes of biomedical data generated by multiple measurement modalities poses a significant challenge for data analysis, integration, storage, and result interpretation...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896995/muse-a-multi-locus-sampling-based-epistasis-algorithm-for-quantitative-genetic-trait-prediction
#2
Dan He, Laxmi Parida
Quantitative genetic trait prediction based on high-density genotyping arrays plays an important role for plant and animal breeding, as well as genetic epidemiology such as complex diseases. The prediction can be very helpful to develop breeding strategies and is crucial to translate the findings in genetics to precision medicine. Epistasis, the phenomena where the SNPs interact with each other, has been studied extensively in Genome Wide Association Studies (GWAS) but received relatively less attention for quantitative genetic trait prediction...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27860446/a-genetic-algorithm-based-framework-for-wavelength-selection-on-sample-categorization
#3
Michel J Anzanello, Gabrielli Yamashita, Marcelo Marcelo, Flavio F Fogliatto, Rafael S Ortiz, Kristiane Mariotti, Marco F Ferrão
In forensic and pharmaceutical scenarios, the application of chemometrics and optimization techniques have unveiled common and peculiar features of seized medicine and drug samples, helping investigative forces towards tracking illegal operations. This paper proposes a novel framework aimed at identifying relevant subsets of attenuated total reflectance Fourier transform infrared (ATR-FTIR) wavelengths for classifying samples into two classes, e.g. authentic or forged categories in case of medicines, or salt or base form in cocaine analysis...
November 18, 2016: Drug Testing and Analysis
https://www.readbyqxmd.com/read/27798253/oxytocin-receptor-gene-variations-predict-neural-and-behavioral-response-to-oxytocin-in-autism
#4
Takamitsu Watanabe, Takeshi Otowa, Osamu Abe, Hitoshi Kuwabara, Yuta Aoki, Tatsunobu Natsubori, Hidemasa Takao, Chihiro Kakiuchi, Kenji Kondo, Masashi Ikeda, Nakao Iwata, Kiyoto Kasai, Tsukasa Sasaki, Hidenori Yamasue
Oxytocin appears beneficial for autism spectrum disorder (ASD), and more than 20 single-nucleotide polymorphisms (SNPs) in oxytocin receptor (OXTR) are relevant to ASD. However, neither biological functions of OXTR SNPs in ASD nor critical OXTR SNPs that determine oxytocin's effects on ASD remain unknown. Here, using a machine-learning algorithm that was designed to evaluate collective effects of multiple SNPs and automatically identify most informative SNPs, we examined relationships between 27 representative OXTR SNPs and six types of behavioral/neural response to oxytocin in ASD individuals...
October 19, 2016: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/27792843/integrative-genetic-risk-prediction-using-non-parametric-empirical-bayes-classification
#5
Sihai Dave Zhao
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are trained. One way to increase the effective sample size is to integrate information from previously existing studies. However, it can be difficult to find existing data that examine the target disease of interest, especially if that disease is rare or poorly studied. Furthermore, individual-level genotype data from these auxiliary studies are typically difficult to obtain...
October 28, 2016: Biometrics
https://www.readbyqxmd.com/read/27730209/combinatorial-microfluidic-droplet-engineering-for-biomimetic-material-synthesis
#6
Lukmaan A Bawazer, Ciara S McNally, Christopher J Empson, William J Marchant, Tim P Comyn, Xize Niu, Soongwon Cho, Michael J McPherson, Bernard P Binks, Andrew deMello, Fiona C Meldrum
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated...
October 2016: Science Advances
https://www.readbyqxmd.com/read/27718149/the-topology-prediction-of-membrane-proteins-a-web-based-tutorial
#7
Cagin Kandemir-Cavas, Levent Cavas, Hakan Alyuruk
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics...
October 7, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27649726/optimization-of-the-production-of-extracellular-polysaccharide-from-the-shiitake-medicinal-mushroom-lentinus-edodes-agaricomycetes-using-mutation-and-a-genetic-algorithm-coupled-artificial-neural-network-ga-ann
#8
Adeyemi Ojutalayo Adeeyo, Agbaje Lateef, Evariste Bosco Gueguim-Kana
Exopolysaccharide (EPS) production by a strain of Lentinus edodes was studied via the effects of treatments with ultraviolet (UV) irradiation and acridine orange. Furthermore, optimization of EPS production was studied using a genetic algorithm coupled with an artificial neural network in submerged fermentation. Exposure to irradiation and acridine orange resulted in improved EPS production (2.783 and 5.548 g/L, respectively) when compared with the wild strain (1.044 g/L), whereas optimization led to improved productivity (23...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27595102/a-computational-method-for-optimizing-experimental-environments-for-phellinus-igniarius-via-genetic-algorithm-and-bp-neural-network
#9
Zhongwei Li, Beibei Sun, Yuezhen Xin, Xun Wang, Hu Zhu
Flavones, the secondary metabolites of Phellinus igniarius fungus, have the properties of antioxidation and anticancer. Because of the great medicinal value, there are large demands on flavones for medical use and research. Flavones abstracted from natural Phellinus can not meet the medical and research need, since Phellinus in the natural environment is very rare and is hard to be cultivated artificially. The production of flavones is mainly related to the fermentation culture of Phellinus, which made the optimization of culture conditions an important problem...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27586041/xmrf-an-r-package-to-fit-markov-networks-to-high-throughput-genetics-data
#10
Ying-Wooi Wan, Genevera I Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson, Zhandong Liu
BACKGROUND: Technological advances in medicine have led to a rapid proliferation of high-throughput "omics" data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understanding complicated interactions between genes, mutations and aberrations, and epi-genetic markers. RESULTS: We developed an R software package, XMRF, that can be used to fit Markov Networks to various types of high-throughput genomics data. Encoding the models and estimation techniques of the recently proposed exponential family Markov Random Fields (Yang et al...
2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27509654/-frequency-and-medical-social-aspects-premature-birth
#11
REVIEW
M Sandeva, E Uchikova
Premature birth (PB) remains an unresolved problem, despite progress in prenatal medicine and the introduction of new methods and techniques of prolonged respiratory resuscitation in recent decades. Premature birth is the cause of 70% of neonatal mortality and 50% of long-term neurological complications in newborns, many of whom debilitating. Notwithstanding the significant progress prenatal care in the last twenty years in developed countries is a trend towards a gradual and continuous increase in premature births...
2016: Akusherstvo i Ginekologii︠a︡
https://www.readbyqxmd.com/read/27456280/multilocus-sequence-typing-of-candida-tropicalis-shows-clonal-cluster-enrichment-in-azole-resistant-isolates-from-patients-in-shanghai-china
#12
Ying Wang, Ce Shi, Jin-Yan Liu, Wen-Jing Li, Yue Zhao, Ming-Jie Xiang
To explore the putative correlation between the multilocus sequence types (MLST) and antifungal susceptibility of clinical Candida tropicalis isolates in Mainland China. Eighty-two clinical C. tropicalis isolates were collected from sixty-nine patients at Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, from July 2012 to February 2015, and antifungal susceptibility tests were performed. Genetic profiles of those 82 isolates (30 azole-resistant and 52 azole-susceptible) were characterised by multilocus sequence typing...
October 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27417569/systematic-review-genetic-biomarkers-associated-with-anti-tnf-treatment-response-in-inflammatory-bowel-diseases
#13
REVIEW
S Bek, J V Nielsen, A B Bojesen, A Franke, S Bank, U Vogel, V Andersen
BACKGROUND: Personalised medicine, including biomarkers for treatment selection, may provide new algorithms for more effective treatment of patients. Genetic variation may impact drug response and genetic markers could help selecting the best treatment strategy for the individual patient. AIM: To identify polymorphisms and candidate genes from the literature that are associated with anti-tumour necrosis factor (TNF) treatment response in patients with inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis...
September 2016: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/27399692/chemical-structure-biological-activity-models-for-pharmacophores-3d-interactions
#14
REVIEW
Mihai V Putz, Corina Duda-Seiman, Daniel Duda-Seiman, Ana-Maria Putz, Iulia Alexandrescu, Maria Mernea, Speranta Avram
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions...
2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27363492/diagnostic-and-predictive-biomarkers-for-lymphoma-diagnosis-and-treatment-in-the-era-of-precision-medicine
#15
REVIEW
Ruifang Sun, L Jeffrey Medeiros, Ken H Young
Lymphomas are a group of hematological malignancies derived from lymphocytes. Lymphomas are clinically and biologically heterogeneous and have overlapping diagnostic features. With the advance of new technologies and the application of efficient and feasible detection platforms, an unprecedented number of novel biomarkers have been discovered or are under investigation at the genetic, epigenetic, and protein level as well as the tumor microenvironment. These biomarkers have enabled new clinical and pathological insights into the mechanisms underlying lymphomagenesis and also have facilitated improvements in the diagnostic workup, sub-classification, outcome stratification, and personalized therapy for lymphoma patients...
October 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27343475/bayesian-state-space-models-for-dynamic-genetic-network-construction-across-multiple-tissues
#16
Yulan Liang, Arpad Kelemen
Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models...
August 1, 2016: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/27245544/application-of-advanced-molecular-technology-in-the-diagnosis-and-management-of-genetic-disorders-in-south-africa
#17
M Kotze
BACKGROUND: Genetic testing has evolved from a niche speciality for diagnosis of rare disorders and carrier screening to subtyping of complex medical conditions for targeted treatment. Genes causing monogenic disorders are well characterised, but risk management of multifactorial and polygenic disorders guided from the genetic background remains a challenge. Objective. This study describes the use of a pathology-supported genetic testing (PSGT) strategy designed to facilitate the move from single- to multi-gene testing and next-generation sequencing (NGS)...
June 2016: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
https://www.readbyqxmd.com/read/27209738/-study-on-application-of-nir-spectral-information-screening-in-identification-of-maca-origin
#18
Yuan-zhong Wang, Yan-li Zhao, Ji Zhang, Hang Jin
Medicinal and edible plant Maca is rich in various nutrients and owns great medicinal value. Based on near infrared diffuse reflectance spectra, 139 Maca samples collected from Peru and Yunnan were used to identify their geographical origins. Multiplication signal correction (MSC) coupled with second derivative (SD) and Norris derivative filter (ND) was employed in spectral pretreatment. Spectrum range (7,500-4,061 cm⁻¹) was chosen by spectrum standard deviation. Combined with principal component analysis-mahalanobis distance (PCA-MD), the appropriate number of principal components was selected as 5...
February 2016: Guang Pu Xue Yu Guang Pu Fen Xi, Guang Pu
https://www.readbyqxmd.com/read/27171545/breast-cancer-risk-prediction-using-a-polygenic-risk-score-in-the-familial-setting-a-prospective-study-from-the-breast-cancer-family-registry-and-kconfab
#19
Hongyan Li, Bingjian Feng, Alexander Miron, Xiaoqing Chen, Jonathan Beesley, Emmanuella Bimeh, Daniel Barrowdale, Esther M John, Mary B Daly, Irene L Andrulis, Saundra S Buys, Peter Kraft, Heather Thorne, Georgia Chenevix-Trench, Melissa C Southey, Antonis C Antoniou, Paul A James, Mary Beth Terry, Kelly-Anne Phillips, John L Hopper, Gillian Mitchell, David E Goldgar
PURPOSE: This study examined the utility of sets of single-nucleotide polymorphisms (SNPs) in familial but non-BRCA-associated breast cancer (BC). METHODS: We derived a polygenic risk score (PRS) based on 24 known BC risk SNPs for 4,365 women from the Breast Cancer Family Registry and Kathleen Cuningham Consortium Foundation for Research into Familial Breast Cancer familial BC cohorts. We compared scores for women based on cancer status at baseline; 2,599 women unaffected at enrollment were followed-up for an average of 7...
May 12, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27168765/identification-of-genetic-interaction-networks-via-an-evolutionary-algorithm-evolved-bayesian-network
#20
Ruowang Li, Scott M Dudek, Dokyoon Kim, Molly A Hall, Yuki Bradford, Peggy L Peissig, Murray H Brilliant, James G Linneman, Catherine A McCarty, Le Bao, Marylyn D Ritchie
BACKGROUND: The future of medicine is moving towards the phase of precision medicine, with the goal to prevent and treat diseases by taking inter-individual variability into account. A large part of the variability lies in our genetic makeup. With the fast paced improvement of high-throughput methods for genome sequencing, a tremendous amount of genetics data have already been generated. The next hurdle for precision medicine is to have sufficient computational tools for analyzing large sets of data...
2016: BioData Mining
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