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https://www.readbyqxmd.com/read/30004884/protecting-privacy-and-security-of-genomic-data-in-i2b2-with-homomorphic-encryption-and-differential-privacy
#1
Jean Louis Raisaro, Gwangbae Choi, Sylvain Pradervand, Raphael Colsenet, Nathalie Jacquemont, Nicolas Rosat, Vincent Mooser, Jean-Pierre Hubaux
Re-use of patients' health records can provide tremendous benefits for clinical research. Yet, when researchers need to access sensitive/identifying data, such as genomic data, in order to compile cohorts of well-characterized patients for specific studies, privacy and security concerns represent major obstacles that make such a procedure extremely difficult if not impossible. In this paper, we address the challenge of designing and deploying in a real operational setting an efficient privacy-preserving explorer for genetic cohorts...
July 10, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29998600/feasting-on-terrestrial-organic-matter-dining-in-a-dark-lake-changes-microbial-decomposition
#2
Amelia Fitch, Chloe Orland, David Willer, Erik J S Emilson, Andrew J Tanentzap
Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses...
July 11, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29991478/genomic-privacy
#3
REVIEW
Abraham P Schwab, Hung S Luu, Jason Wang, Jason Y Park
BACKGROUND: Genetic information is unique among all laboratory data because it not only informs the current health of the specific person tested but may also be predictive of the future health of the individual and, to varying degrees, all biological relatives. CONTENT: As DNA sequencing has become ubiquitous with decreasing cost, large repositories of genomic data have emerged from the domains of research, healthcare, law enforcement, international security, and recreational consumer interest (i...
July 10, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29990017/fast-and-accurate-detection-of-complex-imaging-genetics-associations-based-on-greedy-projected-distance-correlation
#4
Jian Fang, Chao Xu, Pascal Zille, Dongdong Lin, Hong-Wen Deng, Vince D Calhoun, Yu-Ping Wang
Recent advances in imaging genetics produce large amounts of data including functional MRI images, single nucleotide polymorphisms (SNPs), and cognitive assessments. Understanding the complex interactions among these heterogeneous and complementary data has the potential to help with diagnosis and prevention of mental disorders. However, limited efforts have been made due to the high dimensionality, group structure, and mixed type of these data. In this paper we present a novel method to detect conditional associations between imaging genetics data...
December 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/29989509/advances-in-pathological-understanding-of-high-grade-b-cell-lymphomas
#5
Shaoying Li, Pei Lin, L Jeffrey Medeiros
The designation high-grade B-cell lymphoma (HGBL) has been incorporated into the 2016 Revision of the WHO classification of lymphoid neoplasms and includes two types: (1) HGBL, not otherwise specified; and (2) HGBL with MYC and BCL2 and/or BCL6 rearrangements, also known as double or triple hit lymphoma (DHL/THL). These categories of lymphomas represent 1-2% of non-Hodgkin lymphomas and a considerable portion of DLBCL patients who are primary refractory to R-CHOP therapy. It corresponds to the designation 'B-cell lymphoma, unclassifiable, with features intermediate between DLBCL and Burkitt lymphoma' in the 2008 WHO classification...
July 10, 2018: Expert Review of Hematology
https://www.readbyqxmd.com/read/29985321/candidate-gene-testing-in-clinical-cohort-studies-with-multiplexed-genotyping-and-mass-spectrometry
#6
Sarah E Ashley, Braydon A Meyer, Justine A Ellis, David J Martino
Complex diseases are often underpinned by multiple common genetic variants that contribute to disease susceptibility. Here, we describe a cost-effective tag single nucleotide polymorphism (SNP) approach using a multiplexed genotyping assay with mass spectrometry, to investigate gene pathway associations in clinical cohorts. We investigate the food allergy candidate locus Interleukin13 (IL13) as an example. This method efficiently maximizes the coverage by taking advantage of shared linkage disequilibrium (LD) within a region...
June 21, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29983750/esbl-plasmid-carriage-in-e-coli-enhances-in-vitro-bacterial-competition-fitness-and-serum-resistance-in-some-strains-of-pandemic-sequence-types-without-overall-fitness-cost
#7
Amit Ranjan, Julia Scholz, Torsten Semmler, Lothar H Wieler, Christa Ewers, Stefanie Müller, Derek J Pickard, Peter Schierack, Karsten Tedin, Niyaz Ahmed, Katharina Schaufler, Sebastian Guenther
Background: Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic Escherichia coli infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness...
2018: Gut Pathogens
https://www.readbyqxmd.com/read/29970488/genetic-obesity-next-generation-sequencing-results-of-1230-patients-with-obesity
#8
Lotte Kleinendorst, Maarten P G Massink, Mellody I Cooiman, Mesut Savas, Olga H van der Baan-Slootweg, Roosje J Roelants, Ignace C M Janssen, Hanne J Meijers-Heijboer, Nine V A M Knoers, Hans Kristian Ploos van Amstel, Elisabeth F C van Rossum, Erica L T van den Akker, Gijs van Haaften, Bert van der Zwaag, Mieke M van Haelst
BACKGROUND: Obesity is a global and severe health problem. Due to genetic heterogeneity, the identification of genetic defects in patients with obesity can be time consuming and costly. Therefore, we developed a custom diagnostic targeted next-generation sequencing (NGS)-based analysis to simultaneously identify mutations in 52 obesity-related genes. The aim of this study was to assess the diagnostic yield of this approach in patients with suspected genetic obesity. METHODS: DNA of 1230 patients with obesity (median BMI adults 43...
July 3, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29962324/optimization-of-taylor-spatial-frame-half-pins-diameter-for-bone-deformity-correction-application-to-femur
#9
Pooria Chavoshnejad, Moosa Ayati, Aziz Abbasspour, Morad Karimpur, Daniel George, Yves Rémond, Alireza Heidary Rouchi, Majid Baniassadi
Using external fixtures for bone deformity correction takes advantages of less soft tissue injury, better bone alignment and enhances strain development for bone formation on cutting section, which cause shorter healing time. Among these fixtures, Taylor spatial frame is widely used and includes two rings and six adjustable struts developing 6 degrees of freedom, making them very flexible for this type of application. The current study describes a method to optimize Taylor spatial frame pin-sizes currently chosen from the surgeon's experiences...
July 2018: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/29959827/coordinate-transformation-aided-finite-element-method-for-contour-detection-of-breast-tumors-in-microwave-imaging
#10
Ozlem Ozgun, Mustafa Kuzuoglu
A coordinate transformation based finite element method (called CT-FEM) is presented for detecting contours of breast cancer tissues in the context of microwave imaging. The geometry and location of a single or multiple cancerous tumors inside a breast tissue are identified by constructing an inverse problem based on the genetic optimization algorithm. The expensive forward solution phase during repeated cost function evaluations is accelerated by placing a transformation medium inside the finite element mesh...
June 29, 2018: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/29959382/whole-exome-sequencing-in-intellectual-disability-cost-before-and-after-a-diagnosis
#11
Terry Vrijenhoek, Eline M Middelburg, Glen R Monroe, Koen L I van Gassen, Joost W Geenen, Anke M Hövels, Nine V Knoers, Hans Kristian Ploos van Amstel, Gerardus W J Frederix
Clinical application of whole-exome and whole-genome sequencing (WES and WGS) has led to an increasing interest in how it could drive healthcare decisions. As with any healthcare innovation, implementation of next-generation sequencing in the clinic raises questions on affordability and costing impact for society as a whole. We retrospectively analyzed medical records of 370 patients with ID who had undergone WES at various stages of their diagnostic trajectory. We collected all medical interventions performed on these patients at the University Medical Center Utrecht (UMCU), Utrecht, the Netherlands...
June 29, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29959131/high-throughput-sequencing-and-assessing-disease-risk
#12
Shannon M Rego, Michael P Snyder
High-throughput sequencing has dramatically improved our ability to determine and diagnose the underlying causes of human disease. The use of whole-genome and whole-exome sequencing has facilitated faster and more cost-effective identification of new genes implicated in Mendelian disease. It has also improved our ability to identify disease-causing mutations for Mendelian diseases whose associated genes are already known. These benefits apply not only in cases in which the objective is to assess genetic disease risk in adults and children, but also for prenatal genetic testing and embryonic testing...
June 29, 2018: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/29953415/high-accuracy-determination-of-internal-circadian-time-from-a-single-blood-sample
#13
Nicole Wittenbrink, Bharath Ananthasubramaniam, Mirjam Münch, Barbara Koller, Bert Maier, Charlotte Weschke, Frederik Bes, Jan de Zeeuw, Claudia Nowozin, Amely Wahnschaffe, Sophia Wisniewski, Mandy Zaleska, Osnat Bartok, Reut Ashwal-Fluss, Hedwig Lammert, Hanspeter Herzel, Michael Hummel, Sebastian Kadener, Dieter Kunz, Achim Kramer
BACKGROUND: The circadian clock is a fundamental and pervasive biological program that coordinates 24-hour rhythms in physiology, metabolism and behaviour, and it is essential to health. Whereas time-of-day adapted therapy is increasingly reported to be highly successful, it needs to be personalized since internal circadian time is different for each individual. In addition, internal time is not a stable trait, but is influenced by many factors including genetic predisposition, age, gender, environmental light levels and season...
June 28, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29948840/clinical-application-of-chromosome-microarray-analysis-in-han-chinese-children-with-neurodevelopmental-disorders
#14
Mingyu Xu, Yiting Ji, Ting Zhang, Xiaodong Jiang, Yun Fan, Juan Geng, Fei Li
Chromosome microarray analysis (CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon. We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13...
June 9, 2018: Neuroscience Bulletin
https://www.readbyqxmd.com/read/29946849/cancer-susceptibility-genetic-testing-in-a-high-risk-cohort-of-urban-ashkenazi-jewish-individuals
#15
Sarah M Nielsen, Lenika M De Simone, Olufunmilayo I Olopade
Prior to 2013, genetic testing for Ashkenazi Jewish (AJ) individuals primarily consisted of the three-site BRCA1/BRCA2 AJ panel, full sequencing of BRCA1/2, or the Lynch syndrome mismatch repair genes. Multigene panel testing became more widely available in 2013, but limited data are available regarding the impact of multigene panel testing for AJ individuals. Here, we report the frequency of cancer susceptibility gene mutations in a cohort of 427 AJ individuals seen in the Cancer Risk Clinic at The University of Chicago...
June 26, 2018: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/29946497/surveillance-screening-in-li-fraumeni-syndrome-raising-awareness-of-false-positives
#16
REVIEW
Prerna Kumar, Ryan M Gill, Andrew Phelps, Asmin Tulpule, Katherine Matthay, Theodore Nicolaides
Li-Fraumeni syndrome (LFS) is a rare cancer predisposition syndrome inherited in an autosomal dominant fashion that involves a germline mutation of tumor protein 53 (TP53). With the advent of more accessible and accurate genetic testing methods, along with more widespread knowledge of LFS, asymptomatic carriers can now be more easily identified. No general surveillance protocols were previously recommended other than routine physical exams and breast and colon cancer screening at younger ages, primarily due to questions involving efficacy, cost, and clinical benefits...
April 24, 2018: Curēus
https://www.readbyqxmd.com/read/29945889/chromosomal-analysis-in-ivf-just-how-useful-is-it
#17
REVIEW
Darren K Griffin, Cagri Ogur
Designed to minimize chances of genetically abnormal embryos, preimplantation genetic diagnosis (PGD) involves in vitro fertilization (IVF), embryo biopsy, diagnosis and selective embryo transfer. Preimplantation genetic testing for aneuploidy (PGT-A) aims to avoid miscarriage and live born trisomic offspring and to improve IVF success. Diagnostic approaches include fluorescence in situ hybridization (FISH) and more contemporary comprehensive chromosome screening (CCS) including array comparative genomic hybridization (aCGH), quantitative polymerase chain reaction (PCR), next-generation sequencing (NGS) and karyomapping...
July 2018: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29939475/reconstructing-phylogeny-from-reduced-representation-genome-sequencing-data-without-assembly-or-alignment
#18
Huan Fan, Anthony R Ives, Yann Surget-Groba
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data...
June 25, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29938706/hot-news-hepatitis-b-gene-therapy-coming-to-age
#19
Vicente Soriano
The major pandemics caused by chronic viral infections is produced by HIV, hepatitis C virus (HCV), and hepatitis B virus (HBV), with estimates of 38, 70, and 250 million people worldwide, respectively (Fig. 1). During the last couple of years, the advent of direct oral antivirals has allowed pursuing global HCV eradication. In an unprecedented manner, these drugs cure more than 95% of hepatitis C patients when given for only 2-3 months. The enthusiasm on HCV has renewed the interest for curative strategies for both HIV and HBV...
April 2018: AIDS Reviews
https://www.readbyqxmd.com/read/29937236/universal-screening-at-age-1-2-years-as-an-adjunct-to-cascade-testing-for-familial-hypercholesterolaemia-in-the-uk-a-cost-utility-analysis
#20
Ailsa J McKay, Helen Hogan, Steve E Humphries, Dalya Marks, Kausik K Ray, Alec Miners
BACKGROUND AND AIMS: Familial hypercholesterolaemia (FH) is widely underdiagnosed. Cascade testing (CT) of relatives has been shown to be feasible, acceptable and cost-effective in the UK, but requires a supply of index cases. Feasibility of universal screening (US) at age 1-2 years was recently demonstrated. We examined whether this would be a cost-effective adjunct to CT in the UK, given the current and plausible future undiagnosed FH prevalence. METHODS: Seven cholesterol and/or mutation-based US ± reverse cascade testing (RCT) alternatives were compared with no US in an incremental analysis with a healthcare perspective...
June 4, 2018: Atherosclerosis
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