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Precision medicine statistics

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https://www.readbyqxmd.com/read/28167869/bearings-in-hip-arthroplasty-joint-registries-vs-precision-medicine-review-article
#1
REVIEW
Mark J Pearson, Liam M Grover, Janet M Lord, Simon W Jones, Edward T Davis
BACKGROUND: Precision medicine has been adopted in a range of clinical settings where omics data have led to greater characterisation of disease and stratification of patients into subcategories of phenotypes and pathologies. However, in orthopaedics, precision medicine lags behind other disciplines such as cancer. Joint registries have now amassed a huge body of data pertaining to implant performance which can be broken down into performance statistics for different material types in different cohorts of patients...
February 2017: HSS Journal: the Musculoskeletal Journal of Hospital for Special Surgery
https://www.readbyqxmd.com/read/28130429/modeling-diseases-in-multiple-mouse-strains-for-precision-medicine-studies
#2
Andres D Klein
The genetic basis of the phenotypic variability observed in patients can be studied in mice by generating disease models through genetic or chemical interventions in many genetic backgrounds where the clinical phenotypes can be assessed and used for Genome-Wide Association Studies (GWAS). This is particularly relevant for rare disorders, where patients sharing identical mutations can present with a wide variety of symptoms, but there are not enough number of patients to ensure statistical power of GWAS. Inbred strains are homozygous for each loci and their Single Nucleotide Polymorphisms (SNPs) catalogues are known and freely available, facilitating the bioinformatics and reducing the costs of the study since it is not required to genotype every mouse...
January 27, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28129750/disarticle-a-web-server-for-svm-based-discrimination-of-articles-on-traditional-medicine
#3
Sang-Kyun Kim, SeJin Nam, SangHyun Kim
BACKGROUND: Much research has been done in Northeast Asia to show the efficacy of traditional medicine. While MEDLINE contains many biomedical articles including those on traditional medicine, it does not categorize those articles by specific research area. The aim of this study was to provide a method that searches for articles only on traditional medicine in Northeast Asia, including traditional Chinese medicine, from among the articles in MEDLINE. RESULTS: This research established an SVM-based classifier model to identify articles on traditional medicine...
January 28, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28112324/inference-of-cancer-mechanisms-through-computational-systems-analysis
#4
Zhen Qi, Eberhard O Voit
Large amounts of metabolomics data have been accumulated to study metabolic alterations in cancer that allow cancer cells to synthesize molecular materials necessary for cell growth and proliferation. Although metabolic reprogramming in cancer was discovered almost a century ago, the underlying biochemical mechanisms are still unclear. We show that metabolomics data can be used to infer likely biochemical mechanisms associated with cancer. The proposed inference method is data-driven and quite generic; its efficacy is demonstrated by the analysis of changes in purine metabolism of human renal cell carcinoma...
January 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28092685/precision-oncology-for-acute-myeloid-leukemia-using-a-knowledge-bank-approach
#5
Moritz Gerstung, Elli Papaemmanuil, Inigo Martincorena, Lars Bullinger, Verena I Gaidzik, Peter Paschka, Michael Heuser, Felicitas Thol, Niccolo Bolli, Peter Ganly, Arnold Ganser, Ultan McDermott, Konstanze Döhner, Richard F Schlenk, Hartmut Döhner, Peter J Campbell
Underpinning the vision of precision medicine is the concept that causative mutations in a patient's cancer drive its biology and, by extension, its clinical features and treatment response. However, considerable between-patient heterogeneity in driver mutations complicates evidence-based personalization of cancer care. Here, by reanalyzing data from 1,540 patients with acute myeloid leukemia (AML), we explore how large knowledge banks of matched genomic-clinical data can support clinical decision-making. Inclusive, multistage statistical models accurately predicted likelihoods of remission, relapse and mortality, which were validated using data from independent patients in The Cancer Genome Atlas...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#6
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28040479/chest-imaging-in-cystic-fibrosis-studies-what-counts-and-can-be-counted
#7
REVIEW
Rhonda Szczesniak, Lidija Turkovic, Eleni-Rosalina Andrinopoulou, Harm A W M Tiddens
BACKGROUND: The dawn of precision medicine and CFTR modulators require more detailed assessment of lung structure in cystic fibrosis (CF) clinical studies. Various imaging markers have emerged and are measurable, but clarity is needed to identify what markers should count for clinical studies. High-resolution chest computed tomography (CT) scoring has yielded sensitive markers for the study of CF disease progression. Once completed, CT scores from ongoing randomized controlled trials can be used to examine relationships between imaging endpoints and therapeutic effectiveness...
December 28, 2016: Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society
https://www.readbyqxmd.com/read/27997169/rapid-accurate-precise-and-reliable-relative-free-energy-prediction-using-ensemble-based-thermodynamic-integration
#8
Agastya P Bhati, Shunzhou Wan, David W Wright, Peter V Coveney
The accurate prediction of the binding affinities of ligands to proteins is a major goal in drug discovery and personalized medicine. The time taken to make such predictions is of similar importance to their accuracy, precision, and reliability. In the past few years, an ensemble based molecular dynamics approach has been proposed that provides a route to reliable predictions of free energies based on the molecular mechanics Poisson-Boltzmann surface area method which meets the requirements of speed, accuracy, precision, and reliability...
December 20, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27975230/discovery-of-candidate-biomarkers
#9
John E Wiktorowicz, Kizhake V Soman
Properly performed, biomarker discovery can lead to effective candidates that can ultimately serve as predictors of disease, medical condition, define therapeutic parameters, and many other applications in medicine. Preferably, biomarkers comprise a panel of indicators, e.g. proteins and/or peptides that can be predictive or diagnostic of the medical condition of interest. Emphasis here is placed on "panel," as single candidates are rarely sufficient to provide the necessary sensitivity and specificity. To develop an effective panel that survives the development process described in Chap...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27882571/a-note-on-statistical-repeatability-and-study-design-for-high-throughput-assays
#10
George Nicholson, Chris Holmes
Characterizing the technical precision of measurements is a necessary stage in the planning of experiments and in the formal sample size calculation for optimal design. Instruments that measure multiple analytes simultaneously, such as in high-throughput assays arising in biomedical research, pose particular challenges from a statistical perspective. The current most popular method for assessing precision of high-throughput assays is by scatterplotting data from technical replicates. Here, we question the statistical rationale of this approach from both an empirical and theoretical perspective, illustrating our discussion using four example data sets from different genomic platforms...
November 24, 2016: Statistics in Medicine
https://www.readbyqxmd.com/read/27870452/sex-hormones-and-genotype-interact-to-influence-psychiatric-disease-treatment-and-behavioral-research
#11
REVIEW
Aarthi R Gobinath, Elena Choleris, Liisa A M Galea
Sex differences exist in the vulnerability, incidence, manifestation, and treatment of numerous neurological and psychiatric diseases. Despite this observation prominent in the literature, little consideration has been given to possible sex differences in outcome in both preclinical and clinical research. This Mini-Review highlights evidence supporting why studying sex differences matter for advances in brain health as well as improving treatment for neurological and psychiatric disease. Additionally, we discuss some statistical and methodological considerations in evaluating sex differences as well as how differences in the physiology of the sexes can contribute to sex difference in disease incidence and manifestation...
January 2, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27869223/insight-into-the-metabolic-mechanism-of-scoparone-on-biomarkers-for-inhibiting-yanghuang-syndrome
#12
Heng Fang, Aihua Zhang, Jingbo Yu, Liang Wang, Chang Liu, Xiaohang Zhou, Hui Sun, Qi Song, Xijun Wang
Scoparone (6,7-dimethoxycoumarin) is the representative ingredient of Yinchenhao (Artemisia capillaris Thunb.) which is a famous Chinese medicinal herb and shows favorable efficacy for all kinds of liver disease, specifically for the treatment of Yanghuang syndrome (YHS). The precise molecular mechanism concerning the action of scoparone on YHS is yet to be fully elucidated. The aim of the present study was to determine the mechanism of scoparone and evaluate its efficacy on metabolite levels. The differential expression of metabolites responsible for the pharmacological effects of scoparone was characterized and the protection effect of scoparone against this disease...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27866835/over-using-chemotherapy-in-the-adjuvant-setting
#13
Giuseppe Curigliano, Carmen Criscitiello, Angela Esposito, Giancarlo Pruneri
Avoidance of unnecessary or ineffective treatment should be one of the main goals in adjuvant breast oncology today. Unfortunately, both patients and doctors hunt for tiny statistical differences in survival curves. This search could not only lead to an oncological approach of unlimited addition that we will not be able to afford, but would also end inevitably in indeterminate overtreatment with substantial risks of unexpected toxic effects eating away whatever progress we might make. "Do not harm" remains the main principle in medicine...
February 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/27853751/quantitative-mri-radiomics-in-the-prediction-of-molecular-classifications-of-breast-cancer-subtypes-in-the-tcga-tcia-data-set
#14
Hui Li, Yitan Zhu, Elizabeth S Burnside, Erich Huang, Karen Drukker, Katherine A Hoadley, Cheng Fan, Suzanne D Conzen, Margarita Zuley, Jose M Net, Elizabeth Sutton, Gary J Whitman, Elizabeth Morris, Charles M Perou, Yuan Ji, Maryellen L Giger
Using quantitative radiomics, we demonstrate that computer-extracted magnetic resonance (MR) image-based tumor phenotypes can be predictive of the molecular classification of invasive breast cancers. Radiomics analysis was performed on 91 MRIs of biopsy-proven invasive breast cancers from National Cancer Institute's multi-institutional TCGA/TCIA. Immunohistochemistry molecular classification was performed including estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and for 84 cases, the molecular subtype (normal-like, luminal A, luminal B, HER2-enriched, and basal-like)...
2016: NPJ Breast Cancer
https://www.readbyqxmd.com/read/27853465/epigenetic-dna-methylation-profiling-with-msre-a-quantitative-ngs-approach-using-a-parkinson-s-disease-test-case
#15
Adam G Marsh, Matthew T Cottrell, Morton F Goldman
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27830252/findings-from-the-section-on-bioinformatics-and-translational-informatics
#16
H Dauchel, T Lecroq
OBJECTIVES: To summarize excellent current research and propose a selection of best papers published in 2015 in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD: We provide a synopsis of the articles selected for the IMIA Yearbook 2016, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27826610/identification-of-long-bone-fractures-in-radiology-reports-using-natural-language-processing-to-support-healthcare-quality-improvement
#17
Robert W Grundmeier, Aaron J Masino, T Charles Casper, Jonathan M Dean, Jamie Bell, Rene Enriquez, Sara Deakyne, James M Chamberlain, Elizabeth R Alpern
BACKGROUND: Important information to support healthcare quality improvement is often recorded in free text documents such as radiology reports. Natural language processing (NLP) methods may help extract this information, but these methods have rarely been applied outside the research laboratories where they were developed. OBJECTIVE: To implement and validate NLP tools to identify long bone fractures for pediatric emergency medicine quality improvement. METHODS: Using freely available statistical software packages, we implemented NLP methods to identify long bone fractures from radiology reports...
November 9, 2016: Applied Clinical Informatics
https://www.readbyqxmd.com/read/27825144/genetic-variants-associated-with-gastrointestinal-symptoms-in-fabry-disease
#18
Maria Teresa Di Martino, Francesca Scionti, Simona Sestito, Angela Nicoletti, Mariamena Arbitrio, Pietro Hiram Guzzi, Valentina Talarico, Federica Altomare, Maria Teresa Sanseviero, Giuseppe Agapito, Antonio Pisani, Eleonora Riccio, Osvaldo Borrelli, Daniela Concolino, Licia Pensabene
Gastrointestinal symptoms (GIS) are often among the earliest presenting events in Fabry disease (FD), an X-linked lysosomal disorder caused by the deficiency of α-galactosidase A. Despite recent advances in clinical and molecular characterization of FD, the pathophysiology of the GIS is still poorly understood. To shed light either on differential clinical presentation or on intervariability of GIS in FD, we genotyped 1936 genetic markers across 231 genes that encode for drug-metabolizing enzymes and drug transport proteins in 49 FD patients, using the DMET Plus platform...
November 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27818668/an-approach-based-on-hplc-fingerprint-and-chemometrics-to-quality-consistency-evaluation-of-matricaria-chamomilla-l-commercial-samples
#19
Agnieszka Viapiana, Wiktoria Struck-Lewicka, Pawel Konieczynski, Marek Wesolowski, Roman Kaliszan
Chamomile has been used as an herbal medication since ancient times and is still popular because it contains various bioactive phytochemicals that could provide therapeutic effects. In this study, a simple and reliable HPLC method was developed to evaluate the quality consistency of nineteen chamomile samples through establishing a chromatographic fingerprint, quantification of phenolic compounds and determination of antioxidant activity. For fingerprint analysis, 12 peaks were selected as the common peaks to evaluate the similarities of commercial samples of chamomile obtained from different manufacturers...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27807752/bayesian-computation-methods-for-inferring-regulatory-network-models-using-biomedical-data
#20
Tianhai Tian
The rapid advancement of high-throughput technologies provides huge amounts of information for gene expression and protein activity in the genome-wide scale. The availability of genomics, transcriptomics, proteomics, and metabolomics dataset gives an unprecedented opportunity to study detailed molecular regulations that is very important to precision medicine. However, it is still a significant challenge to design effective and efficient method to infer the network structure and dynamic property of regulatory networks...
2016: Advances in Experimental Medicine and Biology
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