scholarly journals Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

2018 ◽  
Author(s):  
J Budis ◽  
J Gazdarica ◽  
J Radvanszky ◽  
M Harsanyova ◽  
I Gazdaricova ◽  
...  
Keyword(s):  
Large Scale ◽  
High Reliability ◽  
Low Cost ◽  
Variant Calling ◽  
Prenatal Testing ◽  
Data Set ◽  
Gold Standard Method ◽  
Non Invasive ◽  
Scale Population ◽  
Low Coverage

AbstractLow-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1,548 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world.

Micromolding Fabrication of Biocompatible Dry Micro-Pyramid Array Electrodes for Wearable Biopotential Monitoring

2021 ◽  
Author(s):  
Marco Vinicio Alban ◽  
Haechang Lee ◽  
Hanul Moon ◽  
Seunghyup Yoo
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Skin Irritation ◽  
Electrode Impedance ◽  
Non Invasive ◽  
Solution Processes ◽  
Dry Electrodes ◽  
Array Electrode ◽  
Low Cost Manufacturing ◽  
Electromyography Signals

Abstract Thin dry electrodes are promising components in wearable healthcare devices. Assessing the condition of the human body by monitoring biopotentials facilitates the early diagnosis of diseases as well as their prevention, treatment, and therapy. Existing clinical-use electrodes have limited wearable-device usage because they use gels, require preparation steps, and are uncomfortable to wear. While dry electrodes can improve these issues and have demonstrated performance on par with gel-based electrodes, providing advantages in mobile and wearable applications; the materials and fabrication methods used are not yet at the level of disposable gel electrodes for low-cost mass manufacturing and wide adoption. Here, a low-cost manufacturing process for thin dry electrodes with a conductive micro-pyramidal array is presented for large-scale on-skin wearable applications. The electrode is fabricated using micromolding techniques in conjunction with solution processes in order to guarantee ease of fabrication, high device yield, and the possibility of mass production compatible with current semiconductor production processes. Fabricated using a conductive paste and an epoxy resin that are both biocompatible, the developed micro-pyramidal array electrode operates in a conformal, non-invasive manner, with low skin irritation, which ensures improved comfort for brief or extended use. The operation of the developed electrode was examined by analyzing electrode-skin-electrode impedance, electroencephalography, electrocardiography, and electromyography signals and comparing them with those measured simultaneously using gel electrodes.

scholarly journals Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions

PLoS ONE ◽  
2020 ◽  
Vol 15 (8) ◽  
pp. e0238245 ◽  
Author(s):  
Marcel Kucharik ◽  
Andrej Gnip ◽  
Michaela Hyblova ◽  
Jaroslav Budis ◽  
Lucia Strieskova ◽  
...  
Keyword(s):  
Detection Limits ◽  
Prenatal Testing ◽  
Genomic Sequencing ◽  
Non Invasive ◽  
Low Coverage

scholarly journals Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ngoc Hieu Tran ◽  
Thanh Binh Vo ◽  
Van Thong Nguyen ◽  
Nhat-Thang Tran ◽  
Thu-Huong Nhat Trinh ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Frequency Distribution ◽  
Genetic Variants ◽  
Large Scale ◽  
Genomic Analysis ◽  
Prenatal Testing ◽  
Allele Frequency Distribution ◽  
Genetic Studies ◽  
Non Invasive ◽  
Vietnamese Population

Abstract The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.

scholarly journals Technologies for Distributed Generation: key performance factors for industrial application

2018 ◽  
pp. 80-87 ◽  
Author(s):  
G. G. Nalbandyan ◽  
S. S. Zholnerchik
Keyword(s):  
Distributed Generation ◽  
Electricity Market ◽  
Smart Grids ◽  
Large Scale ◽  
High Efficiency ◽  
High Reliability ◽  
Low Cost ◽  
Retail Trade ◽  
Economic Effects ◽  
The Cost

The reduction in the cost of technologies for distributed generation involves an increasing decentralization of power generation and large-scale development of distributed sources around the world. This trend is a key change in both the characteristics of electricity consumption: it is becoming increasingly flexible and mobile, and the patterns of consumer behavior in the electricity market. Electricity consumers are becoming at the same time its suppliers and require revision of traditional regulation standards of the electricity market. The purpose of the article is to assess the influence of distributed generation on the economy of both enterprises and the country as a whole. To identify the effects of the introduction of distributed generation technologies, the method of case study analysis is used. The empirical analysis was carried out on the basis of twelve Russian companies that use their own energy sources. The selected companies belong to the following industries: industrial production, housing and communal services, retail trade, construction, agriculture. Technological and economic effects are revealed. Technological ones include: improving consumer reliability, energy security, involving local energy resources, optimizing load management and redundancy, providing the flexibility of smart grids (in terms of generation), reducing the load on the environment, including CO2 emissions. Economic effects: optimization of the load schedule, reduction of losses in the process of transmission/distribution of energy, expansion of cogeneration, etc., providing the consumer with the electricity of a given quality, saving losses in networks, reducing the cost of energy. The identified effects of the introduction of distributed generation technologies make it possible to highlight the advantages of regeneration facilities: high efficiency and the possibility of cogeneration and trigeneration, individual maneuvering capacity loading, high reliability of equipment, low cost of transportation of electricity, fuel usage of the by-products and the main production waste. In conclusion, recommendations are formulated on a set of measures for the development of industrial distributed generation in Russia at the Federal level.

scholarly journals A predictive model to diagnose pregnancy in guanacos (Lama guanicoe) using non-invasive methods

2020 ◽  
Vol 98 (1) ◽  
pp. 13-20
Author(s):  
A. Marozzi ◽  
V.I. Cantarelli ◽  
F.M. Gomez ◽  
A. Panebianco ◽  
L.R. Leggieri ◽  
...  
Keyword(s):  
Predictive Model ◽  
Large Scale ◽  
Population Studies ◽  
Lama Guanicoe ◽  
Non Invasive ◽  
Pregnant Females ◽  
Metabolite Concentrations ◽  
Scale Population ◽  
Pregnancy Status ◽  
Free Ranging

Pregnancy status is usually not included in ecological studies because it is difficult to evaluate. The use of non-invasive methods to determine pregnancy, without physically restraining individuals, would enable pregnancy to be included in population studies. In this study, we evaluated sex steroid hormones in plasma and fecal samples from pregnant and non-pregnant females to develop a pregnancy predictive model for guanacos (Lama guanicoe (Müller, 1776)). Samples were obtained during live-shearing management (i.e., capture, shear, and release) of guanacos. Enzyme immunoassays were used to evaluate progesterone (P4) and estradiol (E2) concentrations in plasma and pregnanediol glucuronides (PdG) and conjugated estrogens (EC) in feces. Mean hormonal and fecal metabolite concentrations were significantly higher in pregnant females than in non-pregnant females. A linear relationship was found between each hormone and its fecal metabolite. Finally, hormonal data were combined with an independent source of pregnancy diagnosis such as abdominal ballottement to develop a logistic regression model to diagnose pregnancy in non-handled individuals. The use of predictive models and non-invasive methods might be suitable to incorporate pregnancy information in large-scale population studies on guanaco and other free-ranging ungulates.

scholarly journals Dynamic Fault-Tolerant Workflow Scheduling with Hybrid Spatial-Temporal Re-Execution in Clouds

Information ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 169 ◽  
Author(s):  
Na Wu ◽  
Decheng Zuo ◽  
Zhan Zhang
Keyword(s):  
Large Scale ◽  
Fault Tolerant ◽  
Critical Path ◽  
High Reliability ◽  
Low Cost ◽  
Cost Effective ◽  
Scientific Workflow ◽  
Workflow Scheduling ◽  
Workflow Execution ◽  
Computing Environments

Improving reliability is one of the major concerns of scientific workflow scheduling in clouds. The ever-growing computational complexity and data size of workflows present challenges to fault-tolerant workflow scheduling. Therefore, it is essential to design a cost-effective fault-tolerant scheduling approach for large-scale workflows. In this paper, we propose a dynamic fault-tolerant workflow scheduling (DFTWS) approach with hybrid spatial and temporal re-execution schemes. First, DFTWS calculates the time attributes of tasks and identifies the critical path of workflow in advance. Then, DFTWS assigns appropriate virtual machine (VM) for each task according to the task urgency and budget quota in the phase of initial resource allocation. Finally, DFTWS performs online scheduling, which makes real-time fault-tolerant decisions based on failure type and task criticality throughout workflow execution. The proposed algorithm is evaluated on real-world workflows. Furthermore, the factors that affect the performance of DFTWS are analyzed. The experimental results demonstrate that DFTWS achieves a trade-off between high reliability and low cost objectives in cloud computing environments.

Non-invasive prenatal testing in detecting sex chromosome aneuploidy: A large-scale study in Xuzhou area of China

2018 ◽  
Vol 481 ◽  
pp. 139-141 ◽  
Author(s):  
Feng Suo ◽  
Chuangxia Wang ◽  
Tianya Liu ◽  
Yuan Fang ◽  
Qin Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Sex Chromosome ◽  
Prenatal Testing ◽  
Sex Chromosome Aneuploidy ◽  
Non Invasive ◽  
Chromosome Aneuploidy ◽  
Large Scale Study

scholarly journals Can Bibliographic Pointers for Known Biological Data Be Found Automatically? Protein Interactions as a Case Study

2001 ◽  
Vol 2 (4) ◽  
pp. 196-206 ◽  
Author(s):  
Christian Blaschke ◽  
Alfonso Valencia
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Biological Data ◽  
Positive Finding ◽  
Data Set ◽  
Large Scale Assessment ◽  
Low Coverage ◽  
Standard Protein

The Dictionary of Interacting Proteins(DIP) (Xenarioset al., 2000) is a large repository of protein interactions: its March 2000 release included 2379 protein pairs whose interactions have been detected by experimental methods. Even if many of these correspond to poorly characterized proteins, the result of massive yeast two-hybrid screenings, as many as 851 correspond to interactions detected using direct biochemical methods.We used information retrieval technology to search automatically for sentences in Medline abstracts that support these 851 DIP interactions. Surprisingly, we found correspondence between DIP protein pairs and Medline sentences describing their interactions in only 30% of the cases. This low coverage has interesting consequences regarding the quality of annotations (references) introduced in the database and the limitations of the application of information extraction (IE) technology to Molecular Biology. It is clear that the limitation of analyzing abstracts rather than full papers and the lack of standard protein names are difficulties of considerably more importance than the limitations of the IE methodology employed. A positive finding is the capacity of the IE system to identify new relations between proteins, even in a set of proteins previously characterized by human experts. These identifications are made with a considerable degree of precision.This is, to our knowledge, the first large scale assessment of IE capacity to detect previously known interactions: we thus propose the use of the DIP data set as a biological reference to benchmark IE systems.

scholarly journals Reveel: large-scale population genotyping using low-coverage sequencing data

2015 ◽  
Vol 32 (11) ◽  
pp. 1686-1696 ◽  
Author(s):  
Lin Huang ◽  
Bo Wang ◽  
Ruitang Chen ◽  
Sivan Bercovici ◽  
Serafim Batzoglou
Keyword(s):  
Large Scale ◽  
Sequencing Data ◽  
Scale Population ◽  
Low Coverage
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