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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/29327365/millimeter-spatial-resolution-in-vivo-sodium-mri-of-the-human-eye-at-7-t-using-a-dedicated-radiofrequency-transceiver-array
#1
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
https://www.readbyqxmd.com/read/29323667/making-new-genetic-diagnoses-with-old-data-iterative-reanalysis-and-reporting-from-genome-wide-data-in-1-133-families-with-developmental-disorders
#2
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
https://www.readbyqxmd.com/read/29318005/precision-medicine-does-ethnicity-information-complement-genotype-based-prescribing-decisions
#3
REVIEW
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
https://www.readbyqxmd.com/read/29278550/intelligent-use-of-antiepileptic-drugs-is-beneficial-to-patients
#4
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...
December 22, 2017: Current Opinion in Neurology
https://www.readbyqxmd.com/read/29247833/inferring-anatomical-therapeutic-chemical-atc-class-of-drugs-using-shortest-path-and-random-walk-with-restart-algorithms
#5
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
https://www.readbyqxmd.com/read/29240602/unclassified-variants-of-brca1-and-brca2-in-korean-patients-with-ovarian-cancer
#6
Min Chul Choi, Ja-Hyun Jang, Sang Geun Jung, Hyun Park, Won Duk Joo, Seung Hun Song, Chan Lee, Je Ho Lee
OBJECTIVE: The aim of the present study was to investigate unclassified variants (UVs) in BRCA1 and 2 of Korean patients with ovarian cancer. METHODS: We retrospectively analyzed 138 patients diagnosed with ovarian/fallopian tubal/peritoneal cancer between January 2013 and January 2016, whose BRCA genetic test results and clinical characteristics were available for review. Patient peripheral blood lymphocyte specimens were assessed for BRCA mutations and variations by direct sequencing...
December 13, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29215645/cherchez-la-femme-maternal-incidental-findings-can-explain-discordant-prenatal-cell-free-dna-sequencing-results
#7
REVIEW
Diana W Bianchi
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215083/association-detection-between-ordinal-trait-and-rare-variants-based-on-adaptive-combination-of-p-values
#8
Meida Wang, Weijun Ma, Ying Zhou
Next-generation sequencing technology not only presents a new method for the detection of human genomic structural variation, but also provides a large number of genetic data of rare variants for us. Currently, how to detect association between human complex diseases and rare variants using genetical data has attracted extensive attention. In the field of medicine, many people's health and disease conditions are measured by ordinal response variables, namely, the trait value reflects the development stage or severity of a certain condition...
November 7, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29197663/prediction-of-potential-drivers-connecting-different-dysfunctional-levels-in-lung-adenocarcinoma-via-a-protein-protein-interaction-network
#9
Fei Yuan, WenCong Lu
Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. "Cancer driver" theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer...
November 29, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29197659/network-based-method-for-mining-novel-hpv-infection-related-genes-using-random-walk-with-restart-algorithm
#10
Liucun Zhu, Fangchu Su, YaoChen Xu, Quan Zou
The human papillomavirus (HPV), a common virus that infects the reproductive tract, may lead to malignant changes within the infection area in certain cases and is directly associated with such cancers as cervical cancer, anal cancer, and vaginal cancer. Identification of novel HPV infection related genes can lead to a better understanding of the specific signal pathways and cellular processes related to HPV infection, providing information for the development of more efficient therapies. In this study, several novel HPV infection related genes were predicted by a computation method based on the known genes involved in HPV infection from HPVbase...
November 29, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29144791/is-there-a-role-for-programmed-death-ligand-1-testing-and-immunotherapy-in-colorectal-cancer-with-microsatellite-instability-part-i-colorectal-cancer-microsatellite-instability-testing-and-clinical-implications
#11
Esmeralda Celia Marginean, Barbara Melosky
CONTEXT: - Colorectal cancer (CRC) represents the third most-common cancer in developed countries and is a leading cause of cancer deaths worldwide. Two recognized pathways contribute to CRC development: a more-common chromosomal instability pathway and, in 15% of cases, a deficient mismatch repair or microsatellite instability-high (MSI-H) pathway. The MSI-H CRC can be associated with somatic or germline mutations. Microsatellite status has been recognized as a prognostic and predictive biomarker...
November 16, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29127892/estimation-of-the-late-postmortem-interval-using-ftir-spectroscopy-and-chemometrics-in-human-skeletal-remains
#12
Qi Wang, Yinming Zhang, Hancheng Lin, Shuai Zha, Ruoxi Fang, Xin Wei, Shuanliang Fan, Zhenyuan Wang
Due to a lack of reliable and accurate methods, determining the postmortem interval (PMI) of human skeletal remains is one of the most important and challenging tasks in forensic medicine. In this paper, we studied the changes to bone chemistry with increasing PMI in two different experimental conditions using Fourier transform infrared (FTIR) spectroscopy in conjunction with chemometrics methods Paired bone samples collected from 56 human corpses were buried (placed in soil) and unburied (exposed to the air) for intervals between 76 and 552 days...
November 8, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29109033/predicting-and-analyzing-early-wake-up-associated-gene-expressions-by-integrating-gwas-and-eqtl-studies
#13
JiaRui Li, Tao Huang
Circadian rhythms are endogenous 24-hour rhythmic oscillations affecting human behaviors, such as sleep, blood pressure and other biological processes, the disturbance of which lead to circadian rhythm sleep disorders (CRSDs). In this study, based on the data from genome-wide association studies (GWASs) and expression quantitative trait loci (eQTLs), we tried to identify novel gene expression patterns in brain tissues that were associated with early wake-up. First, the maximum-relevance-minimum-redundancy (mRMR) method was adopted to analyze the involved gene expression patterns, yielding a feature list...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29080241/next-generation-sequencing-in-pediatric-hepatology-and-liver-transplantation
#14
REVIEW
Emanuele Nicastro, Lorenzo D'Antiga
Next Generation Sequencing (NGS) has revolutionized the analysis of human genetic variations, offering a highly cost-effective way to diagnose monogenic diseases (MDs). Since nearly half of children with chronic liver disorders have a genetic cause and approximately 20% of pediatric liver transplants are performed in children with MDs, NGS offers the opportunity to significantly improve the diagnostic yield in this field. Among the NGS strategies, the use of targeted gene panels has proven useful to rapidly and reliably confirm a clinical suspicion, whereas the whole exome sequencing (WES) with variants filtering has been adopted to assist the diagnostic work up in unclear clinical scenarios...
October 28, 2017: Liver Transplantation
https://www.readbyqxmd.com/read/29069390/crimetoyhu-a-new-web-tool-to-develop-yeast-based-functional-assays-for-characterizing-cancer-associated-missense-variants
#15
Alberto Mercatanti, Samuele Lodovichi, Tiziana Cervelli, Alvaro Galli
Evaluation of functional impact of cancer-associated missense variants is more difficult to assess as compared to protein-truncating mutations and, consequently, standard guidelines for the interpretation of sequence variants have been recently proposed. A number of algorithms and software products were developed to predict the impact of cancer-associated missense mutations on protein structure and function. Importantly, direct assessment of the variants using high-throughput functional assays using simple genetic systems can help in speeding up the functional evaluation of newly identified cancer associated variants...
October 23, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/29039378/dna-encoding-training-using-3d-gesture-interaction
#16
Stelian Nicola, Flavia-Laura Handrea, Mihaela Crişan-Vida, Lăcrămioara Stoicu-Tivadar
The work described in this paper summarizes the development process and presents the results of a human genetics training application, studying the 20 amino acids formed by the combination of the 3 nucleotides of DNA targeting mainly medical and bioinformatics students. Currently, the domain applications using recognized human gestures of the Leap Motion sensor are used in molecules controlling and learning from Mendeleev table or in visualizing the animated reactions of specific molecules with water. The novelty in the current application consists in using the Leap Motion sensor creating new gestures for the application control and creating a tag based algorithm corresponding to each amino acid, depending on the position in the 3D virtual space of the 4 nucleotides of DNA and their type...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29029584/evidence-for-genetic-risk-contributing-to-long-term-adverse-treatment-effects-in-childhood-cancer-survivors
#17
Maria Monica Gramatges, Smita Bhatia
Survivors of childhood cancer are at increased risk for therapy-related morbidities and mortality. Although the demographic and clinical factors predicting the risk for long-term effects of cancer therapy are well known, the impact of genetic risk for specific late effects is less clearly defined. Here, we review the extant literature and recent research describing genetic modifiers to risk for the more common late effects of childhood cancer therapy. Results of this research support the need for clinical trials that attempt to further refine risk prediction by incorporating genetic testing into existing algorithms that are primarily based on clinical and demographic factors...
October 13, 2017: Annual Review of Medicine
https://www.readbyqxmd.com/read/29021832/pharmacogenomics-in-the-treatment-of-mood-disorders-strategies-and-opportunities-for-personalized-psychiatry
#18
REVIEW
Azmeraw T Amare, Klaus Oliver Schubert, Bernhard T Baune
Personalized medicine (personalized psychiatry in a specific setting) is a new model towards individualized care, in which knowledge from genomics and other omic pillars (microbiome, epigenomes, proteome, and metabolome) will be combined with clinical data to guide efforts to new drug development and targeted prescription of the existing treatment options. In this review, we summarize pharmacogenomic studies in mood disorders that may lay the foundation towards personalized psychiatry. In addition, we have discussed the possible strategies to integrate data from omic pillars as a future path to personalized psychiatry...
September 2017: EPMA Journal
https://www.readbyqxmd.com/read/29020033/genotype-combination-contributes-to-psoriasis-an-exhaustive-algorithm-perspective
#19
Jinfa Dou, Huimin Guo, Fang Cheng, Hequn Huang, Liying Fu, Longnian Li, Chao Yang, Lei Ye, Leilei Wen, Yuyan Cheng, Lili Tang, Caihong Zhu, Zhengwei Zhu, Wenjun Wang, Yujun Sheng, Zaixing Wang, Shengxiu Liu, Xing Fan, Xianbo Zuo, Fusheng Zhou, Liangdan Sun, Xiaodong Zheng, Xuejun Zhang
Researchers have learned that nearly all conditions and diseases have a genetic component. With the benefit of technological advances, many single-nucleotide polymorphisms (SNPs) have been found to be associated with the risk of complex disorders by using genome wide association studies (GWASs). Disease-associated SNPs are sometimes shared by healthy controls and cannot clearly distinguish affected individuals from unaffected ones. The combined effects of multiple independent SNPs contribute to the disease process, but revealing the relationship between genotype and phenotype based on the combinations remains a great challenge...
2017: PloS One
https://www.readbyqxmd.com/read/28968850/epigenetic-regulation-of-gene-expression-in-cancer-techniques-resources-and-analysis
#20
Luciane T Kagohara, Genevieve L Stein-O'Brien, Dylan Kelley, Emily Flam, Heather C Wick, Ludmila V Danilova, Hariharan Easwaran, Alexander V Favorov, Jiang Qian, Daria A Gaykalova, Elana J Fertig
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance...
August 11, 2017: Briefings in Functional Genomics
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