scholarly journals PSEA: A phenotypic similarity ensemble approach for prioritizes candidate genes to aid mendelian disease diagnosis

2021 ◽  
Author(s):  
Zhonghua Wang ◽  
Lipei Liu ◽  
Chao Chen ◽  
Xi Liu ◽  
Fei Tang ◽  
...  
Keyword(s):  
Low Cost ◽  
Genetic Disorders ◽  
Disease Diagnosis ◽  
Mendelian Disease ◽  
Evaluation Tool ◽  
Human Phenotype ◽  
Phenotypic Similarity ◽  
Similarity Ensemble Approach ◽  
Massive Number ◽  
Ngs Data

Motivation: Next-generation sequencing is increasingly applied to the molecular diagnosis of genetic disorders. However, challenges for the interpretation of NGS data remain given the massive number of variants produced by NGS. Careful assessment is required to identify the most likely disease-causing variants that best match the patients' clinical phenotypes, which is highly experience-dependent and of low cost-effectiveness. Results: The human phenotype ontology (HPO) together with the information content (IC) are widely used for phenotypic similarity evaluation. Here, we introduce PSEA, a new phenotypic similarity evaluation tool capable of quantifying groups of HPO terms unbiasedly. By comparing with other methods, PSEA show optimal performance and show a higher tolerance to phenotypic noise or incompleteness. We also developed a web server for disease-causing gene prioritization and HPO-gene weighted linkage visualization. Availability: Source code and Web service are free available at https://github.com/zhonghua-wang/psea and https://phoenix.bgi.com/psea, respectively.

scholarly journals Phenotypic homogeneity in childhood epilepsies evolves in gene-specific patterns across 3251 patient-years of clinical data

2021 ◽  
Author(s):  
David Lewis-Smith ◽  
Shiva Ganesan ◽  
Peter D. Galer ◽  
Katherine L. Helbig ◽  
Sarah E. McKeown ◽  
...  
Keyword(s):  
Clinical Data ◽  
Similarity Analysis ◽  
Genetic Studies ◽  
Human Phenotype ◽  
Phenotypic Similarity ◽  
Complex Phenotypes ◽  
Cognitive Framework ◽  
Novel Approach ◽  
Genetic Epilepsies

AbstractWhile genetic studies of epilepsies can be performed in thousands of individuals, phenotyping remains a manual, non-scalable task. A particular challenge is capturing the evolution of complex phenotypes with age. Here, we present a novel approach, applying phenotypic similarity analysis to a total of 3251 patient-years of longitudinal electronic medical record data from a previously reported cohort of 658 individuals with genetic epilepsies. After mapping clinical data to the Human Phenotype Ontology, we determined the phenotypic similarity of individuals sharing each genetic etiology within each 3-month age interval from birth up to a maximum age of 25 years. 140 of 600 (23%) of all 27 genes and 3-month age intervals with sufficient data for calculation of phenotypic similarity were significantly higher than expect by chance. 11 of 27 genetic etiologies had significant overall phenotypic similarity trajectories. These do not simply reflect strong statistical associations with single phenotypic features but appear to emerge from complex clinical constellations of features that may not be strongly associated individually. As an attempt to reconstruct the cognitive framework of syndrome recognition in clinical practice, longitudinal phenotypic similarity analysis extends the traditional phenotyping approach by utilizing data from electronic medical records at a scale that is far beyond the capabilities of manual phenotyping. Delineation of how the phenotypic homogeneity of genetic epilepsies varies with age could improve the phenotypic classification of these disorders, the accuracy of prognostic counseling, and by providing historical control data, the design and interpretation of precision clinical trials in rare diseases.

scholarly journals KNNCNV: A K-Nearest Neighbor Based Method for Detection of Copy Number Variations Using NGS Data

2021 ◽  
Vol 9 ◽  
Author(s):  
Kun Xie ◽  
Kang Liu ◽  
Haque A K Alvi ◽  
Yuehui Chen ◽  
Shuzhen Wang ◽  
...  
Keyword(s):  
Copy Number ◽  
Nearest Neighbor ◽  
Human Cancer ◽  
Gaussian Mixture ◽  
Disease Diagnosis ◽  
Copy Number Variations ◽  
Sequencing Data ◽  
K Nearest Neighbor ◽  
Data Types ◽  
Ngs Data

Copy number variation (CNV) is a well-known type of genomic mutation that is associated with the development of human cancer diseases. Detection of CNVs from the human genome is a crucial step for the pipeline of starting from mutation analysis to cancer disease diagnosis and treatment. Next-generation sequencing (NGS) data provides an unprecedented opportunity for CNVs detection at the base-level resolution, and currently, many methods have been developed for CNVs detection using NGS data. However, due to the intrinsic complexity of CNVs structures and NGS data itself, accurate detection of CNVs still faces many challenges. In this paper, we present an alternative method, called KNNCNV (K-Nearest Neighbor based CNV detection), for the detection of CNVs using NGS data. Compared to current methods, KNNCNV has several distinctive features: 1) it assigns an outlier score to each genome segment based solely on its first k nearest-neighbor distances, which is not only easy to extend to other data types but also improves the power of discovering CNVs, especially the local CNVs that are likely to be masked by their surrounding regions; 2) it employs the variational Bayesian Gaussian mixture model (VBGMM) to transform these scores into a series of binary labels without a user-defined threshold. To evaluate the performance of KNNCNV, we conduct both simulation and real sequencing data experiments and make comparisons with peer methods. The experimental results show that KNNCNV could derive better performance than others in terms of F1-score.

Liquid Metal Ink Enabled Rapid Prototyping of Electrochemical Sensor for Wireless Glucose Detection on the Platform of Mobile Phone

2015 ◽  
Vol 9 (4) ◽  
Author(s):  
Liting Yi ◽  
Jingjing Li ◽  
Cangran Guo ◽  
Lei Li ◽  
Jing Liu
Keyword(s):  
Liquid Metal ◽  
Mobile Phone ◽  
Detection System ◽  
Point Of Care ◽  
Low Cost ◽  
Smart Phone ◽  
Disease Diagnosis ◽  
Glucose Detection ◽  
Sensor Material ◽  
Liquid Metal Ink

Pervasive detection of blood glucose is rather critical for the real-time disease diagnosis which would provide valuable guidance for treatment planning. Here, we established a health care platform for this purpose through incorporating the glucose detection with liquid metal printed sensor and the smart phone monitoring system together. The liquid metal ink composed of bismuth indium stannic (BIS) alloy was identified as an appropriate sensor material to be quickly written or printed on polyvinyl chloride (PVC) substrate at around 59 °C to form desired electrodes. It thus eliminated the complicated procedures as usually required in conventional sensor fabrication strategies. The alloy electrodes were characterized via cyclic voltammetry to demonstrate their practical functionality. Further, unlike using the commonly adopted glucometer, a smart phone was developed as the data acquisition and display center to help improve the portability and ubiquitous virtue of the detection system. Glucose solution in different concentrations was assayed via this platform. It was shown that there is a good linear relationship between the concentration and the integral value of the curve recorded by the mobile phone, which confirms the feasibility of the present method. This quantitative point-of-care system has pervasive feature and is expected to be very useful for future low-cost electrochemical detection.

Label-Free Sickle Cell Disease Diagnosis using a Low-Cost, Handheld Platform

2016 ◽  
Vol 1 (5) ◽  
pp. 1600100 ◽  
Author(s):  
Bekir Yenilmez ◽  
Stephanie Knowlton ◽  
Chu Hsiang Yu ◽  
Matthew M. Heeney ◽  
Savas Tasoglu
Keyword(s):  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Low Cost ◽  
Disease Diagnosis ◽  
Label Free ◽  
Cell Disease

scholarly journals A Review of Carbon Dots Produced from Biomass Wastes

Nanomaterials ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2316
Author(s):  
Chao Kang ◽  
Ying Huang ◽  
Hui Yang ◽  
Xiu Fang Yan ◽  
Zeng Ping Chen
Keyword(s):  
Carbon Dots ◽  
Raw Materials ◽  
Low Cost ◽  
Disease Diagnosis ◽  
Good Choice ◽  
Biomass Waste ◽  
Renewable Raw Materials ◽  
Wide Availability ◽  
Low Cytotoxicity ◽  
Synthetic Approaches

The fluorescent carbon dot is a novel type of carbon nanomaterial. In comparison with semiconductor quantum dots and fluorescence organic agents, it possesses significant advantages such as excellent photostability and biocompatibility, low cytotoxicity and easy surface functionalization, which endow it a wide application prospect in fields of bioimaging, chemical sensing, environmental monitoring, disease diagnosis and photocatalysis as well. Biomass waste is a good choice for the production of carbon dots owing to its abundance, wide availability, eco-friendly nature and a source of low cost renewable raw materials such as cellulose, hemicellulose, lignin, carbohydrates and proteins, etc. This paper reviews the main sources of biomass waste, the feasibility and superiority of adopting biomass waste as a carbon source for the synthesis of carbon dots, the synthetic approaches of carbon dots from biomass waste and their applications. The advantages and deficiencies of carbon dots from biomass waste and the major influencing factors on their photoluminescence characteristics are summarized and discussed. The challenges and perspectives in the synthesis of carbon dots from biomass wastes are also briefly outlined.

scholarly journals Ribosome Display Technology: Applications in Disease Diagnosis and Control

Antibodies ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 28
Author(s):  
Adinarayana Kunamneni ◽  
Christian Ogaugwu ◽  
Steven Bradfute ◽  
Ravi Durvasula
Keyword(s):  
In Vitro Selection ◽  
Low Cost ◽  
Disease Diagnosis ◽  
Single Chain ◽  
Single Chain Antibody ◽  
Ribosome Display ◽  
Technology Applications ◽  
Display Technology ◽  
And Control

Antibody ribosome display remains one of the most successful in vitro selection technologies for antibodies fifteen years after it was developed. The unique possibility of direct generation of whole proteins, particularly single-chain antibody fragments (scFvs), has facilitated the establishment of this technology as one of the foremost antibody production methods. Ribosome display has become a vital tool for efficient and low-cost production of antibodies for diagnostics due to its advantageous ability to screen large libraries and generate binders of high affinity. The remarkable flexibility of this method enables its applicability to various platforms. This review focuses on the applications of ribosome display technology in biomedical and agricultural fields in the generation of recombinant scFvs for disease diagnostics and control.

scholarly journals Recent Developments of Electrochemical and Optical Biosensors for Antibody Detection

2019 ◽  
Vol 21 (1) ◽  
pp. 134 ◽  
Author(s):  
Wei Xu ◽  
Daniel Wang ◽  
Derek Li ◽  
Chung Chiun Liu
Keyword(s):  
Point Of Care ◽  
Low Cost ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Disease Diagnosis ◽  
Antibody Detection ◽  
Recent Developments ◽  
Care Systems ◽  
Point Of Care Systems ◽  
Detection Of Biomarkers

Detection of biomarkers has raised much interest recently due to the need for disease diagnosis and personalized medicine in future point-of-care systems. Among various biomarkers, antibodies are an important type of detection target due to their potential for indicating disease progression stage and the efficiency of therapeutic antibody drug treatment. In this review, electrochemical and optical detection of antibodies are discussed. Specifically, creating a non-label and reagent-free sensing platform and construction of an anti-fouling electrochemical surface for electrochemical detection are suggested. For optical transduction, a rapid and programmable platform for antibody detection using a DNA-based beacon is suggested as well as the use of bioluminescence resonance energy transfer (BRET) switch for low cost antibody detection. These sensing strategies have demonstrated their potential for resolving current challenges in antibody detection such as high selectivity, low operation cost, simple detection procedures, rapid detection, and low-fouling detection. This review provides a general update for recent developments in antibody detection strategies and potential solutions for future clinical point-of-care systems.

Low-Cost Refractometer for Measurement of Protein Concentration and Specific Gravity of Body Fluids

1993 ◽  
Vol 23 (4) ◽  
pp. 171-173 ◽  
Author(s):  
Sarman Singh ◽  
Niti Singh ◽  
M G Karmarkar
Keyword(s):  
Specific Gravity ◽  
Diagnostic Tool ◽  
Protein Concentration ◽  
Low Cost ◽  
Disease Diagnosis ◽  
Body Fluids ◽  
Standard Laboratory ◽  
Standard Methods ◽  
Diagnosis And Prognosis ◽  
Laboratory Techniques

The measurement of protein concentration in serum and other body fluids can be helpful in disease diagnosis and prognosis. It is commonly helpful to know whether a collection of fluid is transudate or exudate. The specific gravity of fluids, including urine, can also be a useful diagnostic tool. The estimation of protein concentration is usually possible only in hospitals where costly chemistry analysers are available. Specific gravity can be measured by standard methods only if large volumes of fluid are available: it is often not possible to measure the specific gravity of cerebrospinal, pleural, pericardial, or pancreatic fluids, or of urine if the volume is less than 50 μl. Recently, we have obtained a small and very handy device by which one can measure both the specific gravity of fluids in small volumes and also their protein content. The method is based on the refraction of light. Both purchase and running costs are very low by comparison with standard laboratory techniques. We describe the use of this instrument and compare its performance with other available methods.

scholarly journals Disease Diagnostics: Label-Free Sickle Cell Disease Diagnosis using a Low-Cost, Handheld Platform (Adv. Mater. Technol. 5/2016)

2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Bekir Yenilmez ◽  
Stephanie Knowlton ◽  
Chu Hsiang Yu ◽  
Matthew M. Heeney ◽  
Savas Tasoglu
Keyword(s):  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Low Cost ◽  
Disease Diagnosis ◽  
Label Free ◽  
Cell Disease ◽  
Disease Diagnostics

scholarly journals Whole exome analysis of primary immunodeficiency

2018 ◽  
Vol 22 (5) ◽  
pp. 620-626
Author(s):  
E. S. Rahmani ◽  
Н. Azarpara ◽  
M. Karimipoor ◽  
Н. Rahimi
Keyword(s):  
Primary Immunodeficiency ◽  
Genetic Disorders ◽  
Single Gene ◽  
Correct Diagnosis ◽  
Severe Combined Immunodeficiency ◽  
Genetic Diagnosis ◽  
Cost Effective ◽  
Mendelian Disease ◽  
Inherited Disorders ◽  
Whole Exome

The human primary immunodeficiency diseases (PIDs) refer to a rare heterogeneous group of single-gene inherited disorders causing malfunctions in the immune system, and thus the affected patients have a predisposition to severe life-threatening infections. The heterogeneous nature of PIDs, which involves at list 300 different genes, makes diagnosis of the disease a complex issue. Although studies revealed that six million people have a kind of PID, but due to a complex diagnosis procedure many affected individuals have not gotten a correct diagnosis. However, thanks to advancing in the DNA sequencing method and availability of sophisticated sequencers molecular characterization of genetic disorders have been revolutionized. The whole exome sequencing (WES) method can help clinicians detect Mendelian disease and other complex genetic disorders. The presented study used WES to investigate two infants with symptoms of primary immunodeficiency including hemophagocytic lymphohistio­cytosis (HLH) and severe combined immunodeficiency (SCID). It has been shown that the HLH patient had a mutation in the UNC13D gene (NM_199242.2:c.627delT), and the SCID patient had a mutation in the RAG1 gene (NM_000448.2:c.322C>G). It has been demonstrated that WES is a fast and cost-effective method facilitating genetic diagnosis in PID sufferers.

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