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https://www.readbyqxmd.com/read/28924541/the-lrp1-gene-polymorphism-is-associated-with-increased-risk-of-metabolic-syndrome-prevalence-in-the-serbian-population
#1
N Vučinić, E Stokić, I Djan, D Obreht, N Veličković, K Stankov, M Djan
The determination of genetic background in metabolic syndrome (MetS) represents one of the necessary steps to prevent the disorder, thus reducing the cost of medical treatments and helping to design targeted therapy. The study explores the association between individual alleles of the LRP1 gene and the diagnosis of MetS to find correlation between the low-density lipoprotein receptor-related (LRP1) gene polymorphism and each individual anthropometric and biochemical parameter. The study included 93 males and females, aged from 19 to 65, divided into two groups...
June 30, 2017: Balkan Journal of Medical Genetics: BJMG
https://www.readbyqxmd.com/read/28921927/fast-and-cost-effective-single-nucleotide-polymorphism-snp-detection-in-the-absence-of-a-reference-genome-using-semi-deep-next-generation-random-amplicon-sequencing-ramseq
#2
Helmut Bayerl, Robert H S Kraus, Carsten Nowak, Daniel W Foerster, Joerns Fickel, Ralph Kuehn
Biodiversity has suffered a dramatic global decline during the past decades and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and a genetic level. However, in wild species the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in non-model species by semi-deep sequencing of random amplicons...
September 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28921387/analysis-of-24-genes-reveals-a-monogenic-cause-in-11-1-of-cases-with-steroid-resistant-nephrotic-syndrome-at-a-single-center
#3
Weizhen Tan, Svjetlana Lovric, Shazia Ashraf, Jia Rao, David Schapiro, Merlin Airik, Shirlee Shril, Heon Yung Gee, Michelle Baum, Ghaleb Daouk, Michael A Ferguson, Nancy Rodig, Michael J G Somers, Deborah R Stein, Asaf Vivante, Jillian K Warejko, Eugen Widmeier, Friedhelm Hildebrandt
BACKGROUND: Steroid-resistant nephrotic syndrome (SRNS) is the second most frequent cause of end-stage renal disease (ESRD) among patients manifesting at under 25 years of age. We performed mutation analysis using a high-throughput PCR-based microfluidic technology in 24 single-gene causes of SRNS in a cohort of 72 families, who presented with SRNS before the age of 25 years. METHODS: Within an 18-month interval, we obtained DNA samples, pedigree information, and clinical information from 77 consecutive children with SRNS from 72 different families seen at Boston Children's Hospital (BCH)...
September 18, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28917724/backward-genotype-transcript-phenotype-association-mapping
#4
Seunghak Lee, Haohan Wang, Eric P Xing
Genome-wide association studies have discovered a large number of genetic variants associated with complex diseases such as Alzheimer's disease. However, the genetic background of such diseases is largely unknown due to the complex mechanisms underlying genetic effects on traits, as well as a small sample size (e.g., 1000) and a large number of genetic variants (e.g., 1 million). Fortunately, datasets that contain genotypes, transcripts, and phenotypes are becoming more readily available, creating new opportunities for detecting disease-associated genetic variants...
September 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28900436/molecular-resources-from-transcriptomes-in-the-brassicaceae-family
#5
Lua Lopez, Eva M Wolf, J Chris Pires, Patrick P Edger, Marcus A Koch
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28895526/molecular-testing-for-lynch-syndrome-in-people-with-colorectal-cancer-systematic-reviews-and-economic-evaluation
#6
Tristan Snowsill, Helen Coelho, Nicola Huxley, Tracey Jones-Hughes, Simon Briscoe, Ian M Frayling, Chris Hyde
BACKGROUND: Inherited mutations in deoxyribonucleic acid (DNA) mismatch repair (MMR) genes lead to an increased risk of colorectal cancer (CRC), gynaecological cancers and other cancers, known as Lynch syndrome (LS). Risk-reducing interventions can be offered to individuals with known LS-causing mutations. The mutations can be identified by comprehensive testing of the MMR genes, but this would be prohibitively expensive in the general population. Tumour-based tests - microsatellite instability (MSI) and MMR immunohistochemistry (IHC) - are used in CRC patients to identify individuals at high risk of LS for genetic testing...
September 2017: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/28891197/primary-mediastinal-paraganglioma-associated-with-a-familial-variant-in-the-succinate-dehydrogenase-b-subunit-gene
#7
Nardin Samuel, Resham Ejaz, Josh Silver, Shereen Ezzat, Robert J Cusimano, Raymond H Kim
Surgical management is the mainstay of therapy for primary cardiac tumors, yet due to the rarity of these malignancies, their management and workup remains a challenge. Here, we report a unique case of a patient with a primary left ventricular cardiac paraganglioma (PGL) and describe the role of a medical genetics assessment leading to the identification of a rare variant in the SDHB gene to be the causative etiology of this cardiac tumor. Due to decreasing costs and accessibility of molecular genetic analysis, genetic testing may become an emerging diagnostic adjunct in cases of cardiac tumors...
September 10, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28885040/validation-of-next-generation-sequencer-for-24-chromosome-aneuploidy-screening-in-human-embryos
#8
Kabir Sachdeva, Richard Discutido, Firas Albuz, Rawan Almekosh, Braulio Peramo
BACKGROUND: Next-Generation Sequencing (NGS) is the latest approach for preimplantation genetic diagnoses (PGD). AIM: The purpose of this study was to standardize and validate an NGS method for comprehensive chromosome screening and to investigate its applicability to PGD. METHODS: Embryo biopsy, whole-genome amplification, array comparative genomic hybridization (aCGH), and semiconductor sequencing were employed. RESULTS: A total of 204 whole-genome-amplified products were tested with an NGS-based protocol, from which 100 samples were used for standardization and to evaluate the quality of the results produced by this new technique...
September 8, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28879484/acet-an-r-package-for-estimating-dynamic-heritability-and-comparing-twin-models
#9
Liang He, Janne Pitkäniemi, Karri Silventoinen, Mikko J Sillanpää
Estimating dynamic effects of age on the genetic and environmental variance components in twin studies may contribute to the investigation of gene-environment interactions, and may provide more insights into more accurate and powerful estimation of heritability. Existing parametric models for estimating dynamic variance components suffer from various drawbacks such as limitation of predefined functions. We present ACEt, an R package for fast estimating dynamic variance components and heritability that may change with respect to age or other moderators...
September 6, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28878673/review-of-the-reported-measures-of-clinical-validity-and-clinical-utility-as-arguments-for-the-implementation-of-pharmacogenetic-testing-a-case-study-of-statin-induced-muscle-toxicity
#10
REVIEW
Marleen E Jansen, T Rigter, W Rodenburg, T M C Fleur, E J F Houwink, M Weda, Martina C Cornel
Advances from pharmacogenetics (PGx) have not been implemented into health care to the expected extent. One gap that will be addressed in this study is a lack of reporting on clinical validity and clinical utility of PGx-tests. A systematic review of current reporting in scientific literature was conducted on publications addressing PGx in the context of statins and muscle toxicity. Eighty-nine publications were included and information was selected on reported measures of effect, arguments, and accompanying conclusions...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28877177/an-in-vitro-diagnostic-certified-point-of-care-single-nucleotide-test-for-il28b-polymorphisms
#11
Darragh Duffy, Estelle Mottez, Shaun Ainsworth, Tan-Phuc Buivan, Aurelie Baudin, Muriel Vray, Ben Reed, Arnaud Fontanet, Alexandra Rohel, Ventzislava Petrov-Sanchez, Laurent Abel, Ioannis Theodorou, Gino Miele, Stanislas Pol, Matthew L Albert
Numerous genetic polymorphisms have been identified as associated with disease or treatment outcome, but the routine implementation of genotyping into actionable medical care remains limited. Point-of-care (PoC) technologies enable rapid and real-time treatment decisions, with great potential for extending molecular diagnostic approaches to settings with limited medical infrastructure (e.g., CLIA certified diagnostic laboratories). With respect to resource-limited settings, there is a need for simple devices to implement biomarker guided treatment strategies...
2017: PloS One
https://www.readbyqxmd.com/read/28871571/acute-aortic-dissection-pathogenesis-risk-factors-and-diagnosis
#12
Joanna Gawinecka, Felix Schönrath, Arnold von Eckardstein
Acute aortic dissection is a rare but life-threatening condition with a lethality rate of 1 to 2% per hour after onset of symptoms in untreated patients. Therefore, its prompt and proper diagnosis is vital to increase a patient's chance of survival and to prevent grievous complications. Typical symptoms of acute aortic dissection include severe chest pain, hypotension or syncope and, hence, mimic acute myocardial infarction or pulmonary embolism. Advanced age, male gender, long-term history of arterial hypertension and the presence of aortic aneurysm confer the greatest population attributable risk...
September 5, 2017: Swiss Medical Weekly
https://www.readbyqxmd.com/read/28868092/the-spectrum-of-familial-hypercholesterolemia-fh-in-saudi-arabia-prime-time-for-patient-fh-registry
#13
REVIEW
Faisal Alallaf, Fatima Amanullah H Nazar, Majed Alnefaie, Adel Almaymuni, Omran Mohammed Rashidi, Khalid Alhabib, Fahad Alnouri, Mohamed-Nabil Alama, Mohammad Athar, Zuhier Awan
BACKGROUND: Familial hypercholesterolemia (FH) is a life-threatening inherited condition. Untreated patients have the risk to develop raised plasma levels of cholesterol, atherosclerosis and cardiovascular disease (CVD). If diagnosed and treated early in life, the pathological consequences due to atherosclerosis could be avoided and patients with FH can have an anticipated normal life. Mounting evidence suggests that FH is underdiagnosed and undertreated in all populations. The underlying molecular basis of FH is the presence of mutations in one or more genes in the low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB) or proprotein convertase subtilisin/kexin 9 (PCSK9)...
2017: Open Cardiovascular Medicine Journal
https://www.readbyqxmd.com/read/28861226/genetic-sampling-for-estimating-density-of-common-species
#14
Ellen Cheng, Karen E Hodges, Rahel Sollmann, L Scott Mills
Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28860020/triplex-hrm-assay-for-the-simultaneous-assessment-of-il28b-rs12979860-abcb11-rs2287622-and-rnf7-rs16851720-genotypes-in-chronic-hepatitis-c-patients
#15
Elena Luminita Enache, Anca Sin, Liviu Sorin Enache, Ligia Bancu
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IL28B rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classical therapy...
August 28, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28859781/no-261-prenatal-screening-for-fetal-aneuploidy-in-singleton-pregnancies
#16
David Chitayat, Sylvie Langlois, R Douglas Wilson
OBJECTIVE: To develop a Canadian consensus document on maternal screening for fetal aneuploidy (e.g., Down syndrome and trisomy 18) in singleton pregnancies. OPTIONS: Pregnancy screening for fetal aneuploidy started in the mid 1960s, using maternal age as the screening test. New developments in maternal serum and ultrasound screening have made it possible to offer all pregnant patients a non-invasive screening test to assess their risk of having a fetus with aneuploidy to determine whether invasive prenatal diagnostic testing is necessary...
September 2017: Journal of Obstetrics and Gynaecology Canada: JOGC, Journal D'obstétrique et Gynécologie du Canada: JOGC
https://www.readbyqxmd.com/read/28856081/genetic-factors-influencing-drug-induced-liver-injury-do-they-have-a-role-in-prevention-and-diagnosis
#17
REVIEW
Kathleen E Clare, Michael H Miller, John F Dillon
PURPOSE OF REVIEW: The pathogenesis of DILI is currently unknown; however, research has shown strong genetic associations with some DILIs. This paper describes the variant alleles uncovered by GWAS and discusses their potential role as susceptibility biomarkers. RECENT FINDINGS: An association with HLADRB1*15:01 and amoxicillin/clavulanate DILI has been shown by a number of research groups. The presence of the HLA-B*57:01 allele has been associated with an 81-fold increased risk of flucloxacillin DILI...
2017: Current Hepatology Reports
https://www.readbyqxmd.com/read/28852425/evaluation-of-three-read-depth-based-cnv-detection-tools-using-whole-exome-sequencing-data
#18
Ruen Yao, Cheng Zhang, Tingting Yu, Niu Li, Xuyun Hu, Xiumin Wang, Jian Wang, Yiping Shen
BACKGROUND: Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28852181/enrichment-of-viral-nucleic-acids-by-solution-hybrid-selection-with-genus-specific-oligonucleotides
#19
Andrei A Deviatkin, Alexander N Lukashev, Mikhail M Markelov, Larisa V Gmyl, German A Shipulin
Despite recent advances, our knowledge of potential and rare human pathogens is far from exhaustive. Current molecular diagnostic tools mainly rely on the specific amplification of marker sequences and may overlook infections caused by unknown and rare pathogens. Using high-throughput sequencing (HTS) can solve this problem; but, due to the extremely low fraction of pathogen genetic material in clinical samples, its application is only cost-effective in special, rather than routine, cases. In this study, we present a method for the semi-specific enrichment of viral conservative sequences in a HTS library by hybridization in solution with genus-specific degenerate biotinylated oligonucleotides...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851378/in-silico-prediction-of-novel-therapeutic-targets-using-gene-disease-association-data
#20
Enrico Ferrero, Ian Dunham, Philippe Sanseau
BACKGROUND: Target identification and validation is a pressing challenge in the pharmaceutical industry, with many of the programmes that fail for efficacy reasons showing poor association between the drug target and the disease. Computational prediction of successful targets could have a considerable impact on attrition rates in the drug discovery pipeline by significantly reducing the initial search space. Here, we explore whether gene-disease association data from the Open Targets platform is sufficient to predict therapeutic targets that are actively being pursued by pharmaceutical companies or are already on the market...
August 29, 2017: Journal of Translational Medicine
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