scholarly journals Bioinformatics workflows for clinical applications in precision oncology

Author(s):  
Natalie Jäger
2019 ◽  
Author(s):  

AbstractClinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from errors introduced at each step of next generation sequencing (NGS). For NGS to successfully improve patient lives, discriminating between true mutations and artifacts is crucial.We systematically interrogated somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy. Different types of samples with varying input amount and tumor purity were processed using multiple library construction protocols. Whole-genome and whole-exome sequencing were carried out at six sequencing centers followed by processing with nine bioinformatics pipelines to evaluate their reproducibility. We identified artifacts due to sample and library processing and evaluated the capabilities and limitations of bioinformatics tools for artifact detection and removal.By examining the interaction and effect of various wet lab and computational parameters concomitantly, here we recommend actionable best practices for mutation detection in clinical applications using NGS technologies.


Author(s):  
Mark Pernik ◽  
Cylaina Bird ◽  
Jeffrey Traylor ◽  
Diana Shi ◽  
Timothy Richardson ◽  
...  

The emergence of three-dimensional human organoids has opened the door for development of patient-derived cancer organoid (PDO) models, which closely recapitulate parental tumor tissue. Mainstays of preclinical cancer modeling include in vitro cell lines and patient-derived xenografts, but these models lack the cellular heterogeneity seen in human tumors. Moreover, xenograft establishment is resource- and time-intensive, rendering these models difficult to use to inform clinical trials and decisions. PDOs, however, can be created efficiently and retain tumor-specific properties such as cellular heterogeneity, cell-cell and cell-stromal interactions, tumor microenvironment, and therapeutic responsiveness. PDO models and drug screening protocols have been described for several solid tumors and, more recently, for gliomas. Since PDOs can be developed in clinically relevant timeframes and share many characteristics of parent tumors, they may enhance the ability to provide precision oncologic care for patients. This review explores the current literature on cancer organoids, highlighting the history of PDO development, organoid models of glioma, and potential clinical applications of PDOs.


Author(s):  
J.D. Shelburne ◽  
G.M. Roomans

Proper preparative procedures are a prerequisite for the validity of the results of x-ray microanalysis of biological tissue. Clinical applications of x-ray microanalysis are often concerned with diagnostic problems and the results may have profound practical significance for the patient. From this point of view it is especially important that specimen preparation for clinical applications is carried out correctly.Some clinical problems require very little tissue preparation. Hair, nails, and kidney and gallbladder stones may be examined and analyzed after carbon coating. High levels of zinc or copper in hair may be indicative of dermatological or systemic diseases. Nail clippings may be analyzed (as an alternative to the more conventional sweat test) to confirm a diagnosis of cystic fibrosis. X-ray microanalysis in combination with scanning electron microscopy has been shown to be the most reliable method for the identification of the components of kidney or gallbladder stones.A quantitatively very important clinical application of x-ray microanalysis is the identification and quantification of asbestos and other exogenous particles in lung.


Author(s):  
A. LeFurgey ◽  
P. Ingram ◽  
L.J. Mandel

For quantitative determination of subcellular Ca distribution by electron probe x-ray microanalysis, decreasing (and/or eliminating) the K content of the cell maximizes the ability to accurately separate the overlapping K Kß and Ca Kα peaks in the x-ray spectra. For example, rubidium has been effectively substituted for potassium in smooth muscle cells, thus giving an improvement in calcium measurements. Ouabain, a cardiac glycoside widely used in experimental and clinical applications, inhibits Na-K ATPase at the cell membrane and thus alters the cytoplasmic ion (Na,K) content of target cells. In epithelial cells primarily involved in active transport, such as the proximal tubule of the rabbit kidney, ouabain rapidly (t1/2= 2 mins) causes a decrease2 in intracellular K, but does not change intracellular total or free Ca for up to 30 mins. In the present study we have taken advantage of this effect of ouabain to determine the mitochondrial and cytoplasmic Ca content in freeze-dried cryosections of kidney proximal tubule by electron probe x-ray microanalysis.


1976 ◽  
Vol 40 (2) ◽  
pp. 106-106
Author(s):  
DL Torney ◽  
HD Espinosa

1994 ◽  
Vol 3 (1) ◽  
pp. 79-88 ◽  
Author(s):  
Theresa A. Kouri

Lexical comprehension skills were examined in 20 young children (aged 28–45 months) with developmental delays (DD) and 20 children (aged 19–34 months) with normal development (ND). Each was assigned to either a story-like script condition or a simple ostensive labeling condition in which the names of three novel object and action items were presented over two experimental sessions. During the experimental sessions, receptive knowledge of the lexical items was assessed through a series of target and generalization probes. Results indicated that all children, irrespective of group status, acquired more lexical concepts in the ostensive labeling condition than in the story narrative condition. Overall, both groups acquired more object than action words, although subjects with ND comprehended more action words than subjects with DD. More target than generalization items were also comprehended by both groups. It is concluded that young children’s comprehension of new lexical concepts is facilitated more by a context in which simple ostensive labels accompany the presentation of specific objects and actions than one in which objects and actions are surrounded by thematic and event-related information. Various clinical applications focusing on the lexical training of young children with DD are discussed.


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