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https://www.readbyqxmd.com/read/28212287/big-data-analytics-for-genomic-medicine
#1
REVIEW
Karen Y He, Dongliang Ge, Max M He
Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28211938/establishment-and-validation-of-a-microfluidic-capillary-gel-electrophoresis-platform-method-for-purity-analysis-of-therapeutic-monoclonal-antibodies
#2
Michael T Smith, Shu Zhang, Troy Adams, Byron DiPaolo, Jennifer Dally
Capillary and microfluidic chip electrophoresis technologies are heavily utilized for development, characterization, release, and stability testing of biopharmaceuticals. Within the biopharmaceutical industry, CE-SDS and M-CGE are commonly used for purity determination by separation and quantitation of size-based variants. M-CGE is used primarily as a R&D tool for product and process development, while cGMP release and stability testing applications are commonly reserved for CE-SDS. This paper describes the establishment of a M-CGE platform method to be used for R&D and cGMP applications, including release and stability testing, for monoclonal antibodies...
February 17, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28211093/gsskat-rapid-gene-set-analysis-and-multiple-testing-correction-for-rare-variant-association-studies-using-weighted-linear-kernels
#3
Nicholas B Larson, Shannon McDonnell, Lisa Cannon Albright, Craig Teerlink, Janet Stanford, Elaine A Ostrander, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan Lange, Johanna Schleutker, John D Carpten, Isaac Powell, Joan E Bailey-Wilson, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Alice S Whittemore, Chih-Lin Hsieh, Fredrik Wiklund, William J Catolona, William Foulkes, Diptasri Mandal, Rosalind Eeles, Zsofia Kote-Jarai, Michael J Ackerman, Timothy M Olson, Christopher J Klein, Stephen N Thibodeau, Daniel J Schaid
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data...
February 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28210099/study-of-polymorphisms-in-the-tp53-and-rb1-genes-in-children-with-retinoblastoma-in-northern-mexico
#4
Edwin J Anaya-Pava, Jesús Nares-Cisneros, Rubén I Cárdenas-Hernández, Yolanda Jaramillo-Rodríguez, Graciela Zambrano-Galván
PURPOSE: To determine the frequency and association of polymorphisms in the TP53 and RB1 genes with clinical characteristics in a group of children with retinoblastoma (RB) in northern Mexico. METHODS: A prospective, longitudinal, and analytical study of 11 patients diagnosed with RB was conducted. Endpoint PCR and high-resolution real-time PCR were performed. Chi-square and Student t tests were used to evaluate associations between variables. Allelic frequencies, as well as genotypic and Hardy-Weinberg equilibriums, were evaluated using Guo and Thompson's method...
2017: Molecular Vision
https://www.readbyqxmd.com/read/28208699/induction-of-syndecan-4-by-organic-inorganic-hybrid-molecules-with-a-1-10-phenanthroline-structure-in-cultured-vascular-endothelial-cells
#5
Takato Hara, Takayuki Kojima, Hiroka Matsuzaki, Takehiro Nakamura, Eiko Yoshida, Yasuyuki Fujiwara, Chika Yamamoto, Shinichi Saito, Toshiyuki Kaji
Organic-inorganic hybrid molecules constitute analytical tools used in biological systems. Vascular endothelial cells synthesize and secrete proteoglycans, which are macromolecules consisting of a core protein and glycosaminoglycan side chains. Although the expression of endothelial proteoglycans is regulated by several cytokines/growth factors, there may be alternative pathways for proteoglycan synthesis aside from downstream pathways activated by these cytokines/growth factors. Here, we investigated organic-inorganic hybrid molecules to determine a variant capable of analyzing the expression of syndecan-4, a transmembrane heparan-sulfate proteoglycan, and identified 1,10-phenanthroline (o-Phen) with or without zinc (Zn-Phen) or rhodium (Rh-Phen)...
February 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208490/geometrical-model-for-martensitic-phase-transitions-understanding-criticality-and-weak-universality-during-microstructure-growth
#6
Genís Torrents, Xavier Illa, Eduard Vives, Antoni Planes
A simple model for the growth of elongated domains (needle-like) during a martensitic phase transition is presented. The model is purely geometric and the only interactions are due to the sequentiality of the kinetic problem and to the excluded volume, since domains cannot retransform back to the original phase. Despite this very simple interaction, numerical simulations show that the final observed microstructure can be described as being a consequence of dipolar-like interactions. The model is analytically solved in 2D for the case in which two symmetry related domains can grow in the horizontal and vertical directions...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208257/hydrophilic-interaction-chromatography-hyphenated-with-mass-spectrometry-a-powerful-analytical-tool-for-the-comparison-of-originator-and-biosimilar-therapeutic-monoclonal-antibodies-at-the-middle-up-level-of-analysis
#7
Valentina D'Atri, Szabolcs Fekete, Alain Beck, Matthew Lauber, Davy Guillarme
The development and approval processes of biosimilar mAbs depend on their comparability to originators. Therefore, analytical comparisons are required to assess structural features and post-translational modifications (PTM) and thereby minimize the risk of being clinically meaningful differences between biosimilar and originator drug products. The glycosylation pattern of mAbs is considered to be an important critical quality attribute (CQA), and several analytical approaches have been proposed that facilitate characterizing and monitoring a glycosylation profile, albeit mainly at a glycan and glycopeptide level of analysis...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28188106/analytical-validation-of-the-next-generation-sequencing-assay-for-a-nationwide-signal-finding-clinical-trial-molecular-analysis-for-therapy-choice-clinical-trial
#8
Chih-Jian Lih, Robin D Harrington, David J Sims, Kneshay N Harper, Courtney H Bouk, Vivekananda Datta, Jonathan Yau, Rajesh R Singh, Mark J Routbort, Rajyalakshmi Luthra, Keyur P Patel, Geeta S Mantha, Savitri Krishnamurthy, Karyn Ronski, Zenta Walther, Karin E Finberg, Sandra Canosa, Hayley Robinson, Amelia Raymond, Long P Le, Lisa M McShane, Eric C Polley, Barbara A Conley, James H Doroshow, A John Iafrate, Jeffrey L Sklar, Stanley R Hamilton, P Mickey Williams
The National Cancer Institute-Molecular Analysis for Therapy Choice (NCI-MATCH) trial is a national signal-finding precision medicine study that relies on genomic assays to screen and enroll patients with relapsed or refractory cancer after standard treatments. We report the analytical validation processes for the next-generation sequencing (NGS) assay that was tailored for regulatory compliant use in the trial. The Oncomine Cancer Panel assay and the Personal Genome Machine were used in four networked laboratories accredited for the Clinical Laboratory Improvement Amendments...
February 3, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28178596/automated-2d-hplc-method-for-characterization-of-protein-aggregation-with-in-line-fraction-collection-device
#9
Abasha Williams, Erik K Read, Cyrus D Agarabi, Scott Lute, Kurt A Brorson
Monoclonal antibodies are mainly produced by mammalian cell culture, which due to its complexity, results in a wide range of product variants/isoforms. With the growing implementation of Quality by Design (QbD) and Process Analytical Technology (PAT) in drug manufacturing, monitoring and controlling quality attributes within a predefined range during manufacturing may provide added consistency to product quality. To implement these concepts, more robust analytical tools could reduce the time needed for monitoring quality attributes during upstream processing...
January 25, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28170479/association-of-sickle-cell-trait-with-hemoglobin-a1c-in-african-americans
#10
Mary E Lacy, Gregory A Wellenius, Anne E Sumner, Adolfo Correa, Mercedes R Carnethon, Robert I Liem, James G Wilson, David B Sacks, David R Jacobs, April P Carson, Xi Luo, Annie Gjelsvik, Alexander P Reiner, Rakhi P Naik, Simin Liu, Solomon K Musani, Charles B Eaton, Wen-Chih Wu
Importance: Hemoglobin A1c (HbA1c) reflects past glucose concentrations, but this relationship may differ between those with sickle cell trait (SCT) and those without it. Objective: To evaluate the association between SCT and HbA1c for given levels of fasting or 2-hour glucose levels among African Americans. Design, Setting, and Participants: Retrospective cohort study using data collected from 7938 participants in 2 community-based cohorts, the Coronary Artery Risk Development in Young Adults (CARDIA) study and the Jackson Heart Study (JHS)...
7, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28164511/application-of-six-sigma-model-to-evaluate-the-analytical-quality-of-four-hba1c-analyzers
#11
Jos Eacute M Maesa, Patricia Fern Aacute Ndez-Riejos, Catalina S Aacute Nchez-Mora, Mar Iacute A De Toro-Crespo, Concepci Oacute N Gonz Aacute Lez-Rodriguez
BACKGROUND: The Six Sigma Model is a global quality management system applicable to the determination of glycated hemoglobin (HbA1c). In addition, this model can ensure the three characteristics influencing the patient risk: the correct performance of the analytical method with low inaccuracy and bias, the quality control strategy used by the laboratory, and the necessary quality of the analyte. The aim of this study is to use the Six Sigma Model for evaluating quality criteria in the determination of glycated hemoglobin HbA1c and its application to assess four different HbA1c analyzers...
January 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28164427/application-of-circulating-tumor-dna-in-prospective-clinical-oncology-trials-standardization-of-pre-analytical-conditions
#12
Lisanne F van Dessel, Nick Beije, Jean C A Helmijr, Silvia R Vitale, Jaco Kraan, Maxime P Look, Ronald de Wit, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens, Martijn P J K Lolkema
Circulating tumor DNA (ctDNA) has emerged as a potential new biomarker with diagnostic, predictive and prognostic applications for various solid tumor types. Before beginning large prospective clinical trials to prove the added value of utilizing ctDNA in clinical practice, it is essential to investigate the effects of various pre-analytical conditions on the quality of cell-free DNA (cfDNA) in general and of ctDNA in particular in order to optimize and standardize these conditions. Whole blood samples were collected from patients with metastatic cancer bearing a known somatic variant...
February 6, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28152060/expression-quantitative-trait-loci-qtl-in-tumor-adjacent-normal-breast-tissue-and-breast-tumor-tissue
#13
Alejandro Quiroz-Zárate, Benjamin J Harshfield, Rong Hu, Nick Knoblauch, Andrew H Beck, Susan E Hankinson, Vincent Carey, Rulla M Tamimi, David J Hunter, John Quackenbush, Aditi Hazra
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array...
2017: PloS One
https://www.readbyqxmd.com/read/28152038/exome-sequencing-covers-98-of-mutations-identified-on-targeted-next-generation-sequencing-panels
#14
Holly LaDuca, Kelly D Farwell, Huy Vuong, Hsiao-Mei Lu, Wenbo Mu, Layla Shahmirzadi, Sha Tang, Jefferey Chen, Shruti Bhide, Elizabeth C Chao
BACKGROUND: With the expanded availability of next generation sequencing (NGS)-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES) when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference...
2017: PloS One
https://www.readbyqxmd.com/read/28149264/serum-insulin-like-growth-factor-i-quantitation-by-mass-spectrometry-insights-for-protein-quantitation-with-this-technology
#15
Richard Kin Ting Kam, Chung Shun Ho, Michael Ho Ming Chan
Liquid chromatography mass spectrometry (LC-MS) is a widely used technique in the clinical laboratory, especially for small molecule quantitation in biological specimens, for example, steroid hormones and therapeutic drugs. Analysis of circulating macromolecules, including proteins and peptides, is largely dominated by traditional enzymatic, spectrophotometric, or immunological assays in clinical laboratories. However, these methodologies are known to be subjected to interfering substances, for example heterophilic antibodies, as well as subjected to non-specificity issues...
December 2016: EJIFCC
https://www.readbyqxmd.com/read/28146185/-community-acquired-staphylococcus-aureus-isolated-from-paraguayan-children-clinical-phenotypic-and-genotypic-characterization
#16
Rosa Guillén, Letizia Carpinelli, Fátima Rodríguez, Héctor Castro, Beatriz Quíñónez, Ana Campuzano, María Macchi, Juana Ortellado, Patricia Almada, Lorena Grau, Mónica Rodríguez, Gladys Velázquez, Carmen Espínola, Gloría Samudio, Gloria Gómez, Wilma Basualdo
INTRODUCTION: The prevalence of Staphylococcus aureus in the community has increased, being the pediatric population the most affected. This fact highlights the need for epidemiological surveillance. AIM: To characterize clinical, phenotypic and genotypic isolates of S. aureus children's samples with community-acquired infections, collected in hospitals of Asuncion and the Central Department, between November 2009 and December 2010. MATERIALS AND METHODS: Descriptive and transverse analysis with analytical component...
December 2016: Revista Chilena de Infectología: órgano Oficial de la Sociedad Chilena de Infectología
https://www.readbyqxmd.com/read/28139890/pharmacogenomics-of-17-alpha-hydroxyprogesterone-caproate-for-recurrent-preterm-birth-a-case-control-study
#17
T A Manuck, W S Watkins, M S Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, U M Reddy, J Ilekis, M Yandell, M W Varner, L B Jorde
OBJECTIVE: To compare maternal genotypes between women with and without significant prolongation of pregnancy in the setting of 17-alpha hydroxyprogesterone caproate (17-P) administration for the prevention of recurrent preterm birth (PTB). DESIGN: Case-control. SETTING: Three tertiary-care centres across the USA. POPULATION: Women (n = 99) with ≥ 1 prior singleton spontaneous PTB, receiving 17-P. METHODS: Women were classified as having successful prolongation of pregnancy during the 17-P treated pregnancy, in two ways: (1) Definition A: success/non-success based on difference in gestational age at delivery between 17-P-treated and untreated pregnancies (success: delivered ≥ 3 weeks later with 17-P) and (2) Definition B: success/non-success based on reaching term (success: delivered at term with 17-P)...
January 31, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28138927/towards-topological-mechanisms-underlying-experience-acquisition-and-transmission-in-the-human-brain
#18
Arturo Tozzi, James F Peters
Experience is a process of awareness and mastery of facts or events, gained through actual observation or second-hand knowledge. Recent findings reinforce the idea that a naturalized epistemological approach is needed to further advance our understanding of the nervous mechanisms underlying experience. This essay is an effort to build a coherent topological-based framework able to elucidate particular aspects of experience, e.g., how it is acquired by a single individual, transmitted to others and collectively stored in form of general ideas...
January 30, 2017: Integrative Psychological & Behavioral Science
https://www.readbyqxmd.com/read/28127742/performance-comparison-of-nextseq-and-ion-proton-platforms-for-molecular-diagnosis-of-clinical-oncology
#19
Fei Cao, Lianju Gao, Longgang Wei, Zhanni Chen, Yan Wang, Xia Ran, Xuehong Meng, Ji Tao
PURPOSE: Next-generation sequencing is a powerful approach to detect genetic mutations with which cancer diagnosis and treatment can be tailored to the individual patient in the era of personalized and precision medicine. Ion Torrent Systems Ion Proton and Illumina NextSeq are 2 major targeted sequencing platforms; however, not much work has been done to compare these platforms' performance for mutation detection in formalin-fixed paraffin-embedded (FFPE) materials. METHODS: We benchmarked the performance by using a collection of FFPE samples from 23 patients with different cancers for NextSeq and Ion Proton platforms...
January 25, 2017: Tumori
https://www.readbyqxmd.com/read/28121008/shared-familial-risk-factors-between-attention-deficit-hyperactivity-disorder-and-overweight-obesity-a-population-based-familial-coaggregation-study-in-sweden
#20
Qi Chen, Ralf Kuja-Halkola, Arvid Sjölander, Eva Serlachius, Samuele Cortese, Stephen V Faraone, Catarina Almqvist, Henrik Larsson
BACKGROUND: Despite meta-analytic evidence for the association between attention-deficit/hyperactivity disorder (ADHD) and overweight/obesity, the mechanisms underlying the association are yet to be fully understood. METHODS: By linking multiple Swedish national and regional registers, we identified 472,735 index males born during 1973-1992, with information on body weight and height directly measured before they were conscripted for military service. We further identified 523,237 full siblings born during 1973-2002 for the index males...
January 25, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
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