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Costs genetic testing

Lauren M Schiebelhut, Sarah S Abboud, Liza E Gómez Daglio, Holly F Swift, Michael N Dawson
The inclusion of next-generation sequencing technologies in population genetic and phylogenetic studies has elevated the need to balance time and cost of DNA extraction without compromising DNA quality. We tested eight extraction methods - ranging from low- to high-throughput techniques - and eight phyla: Annelida, Arthropoda, Cnidaria, Chordata, Echinodermata, Mollusca, Ochrophyta, and Porifera. We assessed DNA yield, purity, efficacy, and cost of each method. Extraction efficacy was quantified using the proportion of successful polymerase chain reaction (PCR) amplification of two molecular markers for metazoans (mitochondrial COI and nuclear Histone 3) and one for Ochrophyta (mitochondrial nad6) at four time points - 0...
October 21, 2016: Molecular Ecology Resources
Christina Mitropoulou, Vasilios Fragoulakis, Ljiljana B Rakicevic, Mirjana M Novkovic, Athanassios Vozikis, Dragan M Matic, Nebojsa M Antonijevic, Dragica P Radojkovic, Ron H van Schaik, George P Patrinos
INTRODUCTION: Clopidogrel, which is activated by the CYP2C19 enzyme, is among the drugs for which all major regulatory agencies recommend genetic testing to be performed to identify a patient's CYP2C19 genotype in order to determine the optimal antiplatelet therapeutic scheme. The CYP2C19*2 and CYP2C19*3 variants are loss-of-function alleles, leading to abolished CYP2C19 function and thus have the risk of thrombotic events for carriers of these alleles on standard dosages, while the CYP2C19*17 allele results in CYP2C19 hyperactivity...
October 21, 2016: Pharmacogenomics
Yang Liu, Saad M Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V Maldonado Dos Santos, Babu Valliyodan, Prasad P Calyam, Nirav Merchant, Henry T Nguyen, Dong Xu, Trupti Joshi
BACKGROUND: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS)...
October 6, 2016: BMC Bioinformatics
Ashraf Dallol, Kamal Daghistani, Aisha Elaimi, Wissam A Al-Wazani, Afaf Bamanie, Malek Safiah, Samira Sagaty, Layla Taha, Rawabi Zahed, Osama Bajouh, Adeel Gulzar Chaudhary, Mamdooh Abdullah Gari, Rola Turki, Mohammed Hussein Al-Qahtani, Adel Mohammed Abuzenadah
BACKGROUND: Hearing Impairment (HI) can have genetic or environmental causes and in some cases, an interplay of both. Genetic causes are difficult to determine as mutations in more than 90 genes have been shown recently to be responsible for HI. Providing a genetic diagnostic test for HI is therefore a challenge especially for ethnic groups where GJB2 mutations are shown to be rare. RESULTS: Here we show the design and implementation of an amplicon-based targeted sequencing panel that allows the simultaneous sequencing of 87 HI genes...
October 10, 2016: BMC Medical Genetics
Chin B Eap
The use of pharmacogenetic tests was already being proposed in psychiatry in the early 2000s because genetic factors were known to influence drug pharmacokinetics and pharmacodynamics. However, sufficient levels of evidence to justify routine use have been achieved for only a few tests (eg, major histocompatibility complex, class I, B, allele 1502 [HLA-B*1502] for carbamazepine in epilepsy and bipolar disorders); many findings are too preliminary or, when replicated, of low clinical relevance because of a small effect size...
September 2016: Dialogues in Clinical Neuroscience
Joseph P Kitzmiller, Eduard B Mikulik, Anees M Dauki, Chandrama Murkherjee, Jasmine A Luzum
Statins are a cornerstone of the pharmacologic treatment and prevention of atherosclerotic cardiovascular disease. Atherosclerotic disease is a predominant cause of mortality and morbidity worldwide. Statins are among the most commonly prescribed classes of medications, and their prescribing indications and target patient populations have been significantly expanded in the official guidelines recently published by the American and European expert panels. Adverse effects of statin pharmacotherapy, however, result in significant cost and morbidity and can lead to nonadherence and discontinuation of therapy...
2016: Pharmacogenomics and Personalized Medicine
Angelo Alonzo, Scott Aaronson, Marom Bikson, Mustafa Husain, Sarah Lisanby, Donel Martin, Shawn M McClintock, William M McDonald, John O'Reardon, Zeinab Esmailpoor, Colleen Loo
Transcranial Direct Current Stimulation (tDCS) is a new, non-invasive neuromodulation approach for treating depression that has shown promising efficacy. The aim of this trial was to conduct the first international, multicentre randomised controlled trial of tDCS as a treatment for unipolar and bipolar depression. The study recruited 120 participants across 6 sites in the USA and Australia. Participants received active or sham tDCS (2.5mA, 20 sessions of 30min duration over 4weeks), followed by a 4-week open label active treatment phase and a 4-week taper phase...
October 15, 2016: Contemporary Clinical Trials
Andrew Turner, Jurgen Sasse, Aniko Varadi
OBJECTIVES: Inherited disorders of haemoglobin are the world's most common genetic diseases, resulting in significant morbidity and mortality. The large number of mutations associated with the haemoglobin beta gene (HBB) makes gene scanning by High Resolution Melting (HRM) PCR an attractive diagnostic approach. However, existing HRM-PCR assays are not able to detect all common point mutations and have only a very limited ability to detect larger gene rearrangements. The aim of the current study was to develop a HBB assay, which can be used as a screening test in highly heterogeneous populations, for detection of both point mutations and larger gene rearrangements...
October 19, 2016: BMC Medical Genetics
Mark D Mathew, Neal D Mathew, Angela Miller, Mike Simpson, Vinci Au, Stephanie Garland, Marie Gestin, Mark L Edgley, Stephane Flibotte, Aruna Balgi, Jennifer Chiang, Guri Giaever, Pamela Dean, Audrey Tung, Michel Roberge, Calvin Roskelley, Tom Forge, Corey Nislow, Donald Moerman
BACKGROUND: The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes...
October 2016: PLoS Neglected Tropical Diseases
Ivain Martinossi-Allibert, Göran Arnqvist, David Berger
Sexual selection can increase rates of adaptation by imposing stronger selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions, and tested them in seed beetles by manipulating either larval host plant or rearing temperature...
October 17, 2016: Journal of Evolutionary Biology
Paul M Hime, Scott Hotaling, Richard E Grewelle, Eric M O'Neill, S Randal Voss, H Bradley Shaffer, David W Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions...
October 17, 2016: Molecular Ecology
Kostja Renko, Carolin S Hoefig, Corinne Dupuy, Lisbeth Harder, Christian Schwiebert, Josef Köhrle, Lutz Schomburg
Iodotyrosine deiodinase (DEHAL1) is a crucial enzyme in iodine homeostasis. Unbound mono- and diiodotyrosines are indispensable byproducts of thyroid hormone biosynthesis. Their iodine needs to be recovered to avoid iodine deficiency, as observed in genetic defects in DEHAL1. Despite its importance, the enzyme is rarely studied. The deiodination process can be monitored by radioactive tracers or via techniques involving mass spectrometry (MS). However, isotope-labeled molecules are expensive, not always commercially available, and their use is legally restricted, while MS requires sophisticated, costly and sensitive instrumentation...
October 12, 2016: Endocrinology
Dan Holmberg, Karin Ruikka, Petter Lindgren, Mats Eliasson, Sofia Mayans
BACKGROUND: T1D and AITD are autoimmune disorders commonly occurring in the same family and even in the same individual. The genetic contribution to these disorders is complex making uncovering of susceptibility genes very challenging. The general aim of this study was to identify loci and genes contributing to T1D/AITD susceptibility. Our strategy was to perform linkage and association studies in the relatively genetically homogenous population of northern Sweden. We performed a GWLS to find genomic regions linked to T1D/AITD in families from northern Sweden and we performed an association study in the families to test for association between T1D/AITD and variants in previously published candidate genes as well as a novel candidate gene, CD247...
October 4, 2016: BMC Medical Genetics
Erik R Mohlhenrich, Rachel Lockridge Mueller
Salamanders have the largest nuclear genomes among tetrapods and, excepting lungfishes, among vertebrates as a whole. Lynch and Conery (2003) have proposed the mutational-hazard hypothesis to explain variation in genome size and complexity. Under this hypothesis, non-coding DNA imposes a selective cost by increasing the target for degenerative mutations, i.e. the mutational hazard. Expansion of non-coding DNA, and thus genome size, is driven by increased levels of genetic drift and/or decreased mutation rates; the former determines the efficiency with which purifying selection can remove excess DNA, while the latter determines the level of mutational hazard...
October 7, 2016: Evolution; International Journal of Organic Evolution
L Zhang, Q Cai, R S Wiederkehr, M Fauvart, P Fiorini, B Majeed, M Tsukuda, T Matsuno, T Stakenborg
Pharmacogenetics has often been touted as a cornerstone for precision medicine as detailed knowledge of a specific genetic makeup may allow for accurate predictions of a patient's individual drug response. Still, the widespread use of genetic tests is limited as they remain expensive and cumbersome, requiring sophisticated tools and highly trained personnel. In order for pharmacogenetics to reach its full potential, more cost-effective and easily accessible genotyping methods are desired. To meet these challenges, we present a silicon-based integrated microsystem for the detection of multiple single nucleotide polymorphisms (SNPs) directly from human blood...
October 5, 2016: Lab on a Chip
Di Dong, Semra Ozdemir, Yong Mong Bee, Sue-Anne Toh, Marcel Bilger, Eric Finkelstein
OBJECTIVES: To investigate patient preferences and willingness to pay (WTP) for a genetic test that can reduce the risk of life-threatening adverse drug reactions (ADRs). We hypothesize that test features (risk of developing the adverse reaction with and without testing, test cost, and treatment cost) and the choice context (physician recommendation and the most common choice made by peer patients) will influence choices. METHODS: A discrete choice experiment was conducted in which 189 patients at high risk for gout were asked to choose between treatment options that varied along key attributes...
September 2016: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
Dominic A Carone
Cerebral autosomal dominant arteriopathy and subcortical ischemic leukoencephalopathy (CADASIL) is sometimes misdiagnosed as multiple sclerosis (MS). MS and CADASIL are not known to co-occur and brain magnetic resonance imagining (MRI) findings can help with differential diagnosis. Despite the availability of this information, a case report is presented of a 61-year-old woman who was misdiagnosed with MS at age 50, tested positive for CADASIL at age 56, described incorrectly as having both conditions simultaneously, and continued on MS disease-modifying medications, resulting in financial and physical hardship...
August 11, 2016: Applied Neuropsychology. Adult
T Aykanat, M Lindqvist, V L Pritchard, C R Primmer
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%)...
October 6, 2016: Journal of Fish Biology
Ana L Salgado, Tomasz Suchan, Loïc Pellissier, Sergio Rasmann, Anne-Lyse Ducrest, Nadir Alvarez
Elevation gradients impose large differences in abiotic and biotic conditions over short distances, in turn, likely driving differences in gene expression more than would genetic variation per se, as natural selection and drift are less likely to fix alleles at such a narrow spatial scale. As elevation increases, the pressure exerted on plants by herbivores and on arthropod herbivores by predators decreases, and organisms spanning the elevation gradient are thus expected to show lower levels of defence at high elevation...
September 2016: Royal Society Open Science
Qi Shi, Nanbo Sun, Tao Sun, Jing Wang, Shan Tan
The exposure of normal tissues to high radiation during cone-beam CT (CBCT) imaging increases the risk of cancer and genetic defects. Statistical iterative algorithms with the total variation (TV) penalty have been widely used for low dose CBCT reconstruction, with state-of-the-art performance in suppressing noise and preserving edges. However, TV is a first-order penalty and sometimes leads to the so-called staircase effect, particularly over regions with smooth intensity transition in the reconstruction images...
September 1, 2016: Biomedical Optics Express
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