scholarly journals System analysis of the sequencing quality of human whole exome samples on BGI NGS platform

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Vera Belova ◽  
Anna Pavlova ◽  
Robert Afasizhev ◽  
Viktoriya Moskalenko ◽  
Margarita Korzhanova ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
System Analysis ◽  
Classical Method ◽  
Region Of Interest ◽  
Genomic Region ◽  
Pcr Duplicates ◽  
Sequencing Quality ◽  
Chinese Company ◽  
The Cost

AbstractHuman exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia. The reliability and quality of the obtained data are already beyond any doubt. However, only a few kits compatible with these sequencers can be used for such specific tasks as exome sequencing. We developed our own solution for library pre-capture pooling and exome enrichment with Agilent probes. In this work, using a set of the standard benchmark samples from the Platinum Genome collection, we demonstrate that the qualitative and quantitative parameters of our protocol which we called “RSMU_exome” exceed those of the MGI Tech kit. Our protocol allows for identifying more SNV and indels, generates fewer PCR duplicates, enables pooling of more samples in a single enrichment procedure, and requires less raw data to obtain results comparable with the MGI Tech's protocol. The cost of our protocol is also lower than that of MGI Tech's solution.

scholarly journals System Analysis of the Sequencing Quality of Human Whole Exome Samples on Bgi Ngs Platform

2021 ◽  
Author(s):  
Vera Belova ◽  
Anna Pavlova ◽  
Robert Afasizhev ◽  
Viktoria Moskalenko ◽  
Margarita Korzhanova ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
System Analysis ◽  
Regions Of Interest ◽  
Qualitative And Quantitative ◽  
Whole Exome ◽  
Pcr Duplicates ◽  
Sequencing Quality ◽  
Chinese Company ◽  
Chinese Manufacturer

AbstractHuman whole exome sequencing (WES) is now the standard for most medical genetics applications worldwide. The leaders are manufacturers of enrichment kits that base their protocols on a hybridization approach using cRNA or cDNA biotinylated samples specific to regions of interest in the genome. Recently, platforms from the Chinese company MGI Tech have been successfully promoted in the markets of many countries in Europe and Asia. There is no longer any question about their reliability and the quality of the data obtained. However, very few task-specific kits for WES, in particular, are presented for these sequencers. We have developed our solution for library pre-capture pooling and exome enrichment using Agilent probes. In this work, we demonstrate on a set of standard benchmark samples from the Platinum Genome Collection that our protocol, called “RSMU_exome”, is superior to the kit from MGI Tech in qualitative and quantitative terms. It allows detecting more SNVs and CNVs with superior sensitivity and specificity values, generates fewer PCR duplicates, allows more samples to be pooled in a single enrichment, and requires less raw data to produce results comparable to the MGI Tech solution. Also, our protocol is significantly cheaper than the kit from the Chinese manufacturer.

scholarly journals OFCS: Optimized Framework of Compressive Sensing for Medical Images in Bottleneck Network Condition

2018 ◽  
Vol 8 (5) ◽  
pp. 2829
Author(s):  
Lakshminarayana M ◽  
Mrinal Sarvagya
Keyword(s):  
Compressive Sensing ◽  
Medical Image ◽  
Medical Images ◽  
Region Of Interest ◽  
Lossless Compression ◽  
Cost Effective ◽  
Signal Quality ◽  
Effective Solution ◽  
The Cost

Compressive sensing is one of teh cost effective solution towards performing compression of heavier form of signals. We reviewed the existing research contribution towards compressive sensing to find that existing system doesnt offer any form of optimization for which reason the signal are superiorly compressed but at the cost of enough resources. Therefore, we introduce a framework that optimizes the performance of the compressive sensing by introducing 4 sequential algorithms for performing Random Sampling, Lossless Compression for region-of-interest, Compressive Sensing using transform-based scheme, and optimization. The contribution of proposed paper is a good balance between computational efficiency and quality of reconstructed medical image when transmitted over network with low channel capacity. The study outcome shows that proposed system offers maximum signal quality and lower algorithm processing time in contrast to existing compression techniuqes on medical images.

Managing the effectiveness of the regional health system

2020 ◽  
Vol 26 (3) ◽  
pp. 698-720
Author(s):  
E.V. Lobkova ◽  
A.S. Petrichenko
Keyword(s):  
Public Health ◽  
Health System ◽  
System Analysis ◽  
Health Indicators ◽  
Krasnoyarsk Krai ◽  
Regional Health ◽  
Luenberger Observer ◽  
Efficiency Assessment ◽  
Public Health Indicators

Subject. This article studies the mechanism of State health regulation and methods of management of efficiency of regional healthcare institutions. Objectives. The article aims to analyze the territorial health system in the context of the urgent need to optimize budget expenditures and address public health problems, as well as develop directions to improve the effectiveness of the regional health system of the Krasnoyarsk Krai. Methods. For the study, we used the method of index numbers and calculation of dynamics indicators using official statistics data. Results. We have developed and now present a system of indicators of regional health efficiency assessment, focused mainly on public health indicators and quality of medical services. We also offer our own version of the Luenberger observer modification adapted to the objectives of the regional health system analysis. Conclusions and Relevance. The article concludes that it is necessary to optimize the regional health system using the parameters of medical and social efficiency of the system. The proposed approach to assessing the effectiveness of regional health system can be used as a mechanism to develop recommendations for the management of the network of medical and prophylactic institutions of the region.

Pengaruh Kompetensi Coder terhadap Keakuratan dan Ketepatan Pengkodean Menggunakan ICD 10 di Rumah Sakit X Pekanbaru Tahun 2016

2018 ◽  
Vol 1 (1) ◽  
pp. 31-43
Author(s):  
Nur Maimun ◽  
Jihan Natassa ◽  
Wen Via Trisna ◽  
Yeye Supriatin
Keyword(s):  
Medical Record ◽  
Human Error ◽  
Medical Personnel ◽  
Quality Of Data ◽  
Accuracy And Precision ◽  
Result Show ◽  
Study Implementation ◽  
Icd 10 ◽  
The Cost

The accuracy in administering the diagnosis code was the important matter for medical recorder, quality of data was the most important thing for health information management of medical recorder. This study aims to know the coder competency for accuracy and precision of using ICD 10 at X Hospital in Pekanbaru. This study was a qualitative method with case study implementation from five informan. The result show that medical personnel (doctor) have never received a training about coding, doctors writing that hard and difficult to read, failure for making diagnoses code or procedures, doctor used an usual abbreviations that are not standard, theres still an officer who are not understand about the nomenclature and mastering anatomy phatology, facilities and infrastructure were supported for accuracy and precision of the existing code. The errors of coding always happen because there is a human error. The accuracy and precision in coding very influence against the cost of INA CBGs, medical and the committee did most of the work in the case of severity level III, while medical record had a role in monitoring or evaluation of coding implementation. If there are resumes that is not clearly case mix team check file needed medical record the result the diagnoses or coding for conformity. Keywords: coder competency, accuracy and precision of coding, ICD 10

ABOUT NECESSITY OF MATHEMATICAL MODELING OF THE BUSINESS PROCESS OF COST ESTIMATE CALCULATIONS IN THE CONSTRUCTION OF OIL AND GAS FACILITIES

2017 ◽  
pp. 139-145
Author(s):  
R. I. Hamidullin ◽  
L. B. Senkevich
Keyword(s):  
Mathematical Modeling ◽  
Quality Assessment ◽  
Business Process ◽  
Oil And Gas ◽  
Oil And Gas Industry ◽  
Gas Industry ◽  
Construction Organizations ◽  
The Cost ◽  
Cost Of Construction

A study of the quality of the development of estimate documentation on the cost of construction at all stages of the implementation of large projects in the oil and gas industry is conducted. The main problems that arise in construction organizations are indicated. The analysis of the choice of the perfect methodology of mathematical modeling of the investigated business process for improving the activity of budget calculations, conducting quality assessment of estimates and criteria for automation of design estimates is performed.

Return on Invesment (ROI) of Software Product: A Systematic Literature Review

2015 ◽  
Vol 6 (1) ◽  
pp. 50-57
Author(s):  
Rizqa Raaiqa Bintana ◽  
Putri Aisyiyah Rakhma Devi ◽  
Umi Laili Yuhana
Keyword(s):  
Return On Investment ◽  
Assessment Criteria ◽  
Software Product ◽  
And Performance ◽  
Rational Consideration ◽  
Actual Return ◽  
The Cost ◽  
Investment Models ◽  
The Impact

The quality of the software can be measured by its return on investment. Factors which may affect the return on investment (ROI) is the tangible factors (such as the cost) dan intangible factors (such as the impact of software to the users or stakeholder). The factor of the software itself are assessed through reviewing, testing, process audit, and performance of software. This paper discusses the consideration of return on investment (ROI) assessment criteria derived from the software and its users. These criteria indicate that the approach may support a rational consideration of all relevant criteria when evaluating software, and shows examples of actual return on investment models. Conducted an analysis of the assessment criteria that affect the return on investment if these criteria have a disproportionate effort that resulted in a return on investment of a software decreased. Index Terms - Assessment criteria, Quality assurance, Return on Investment, Software product

OSTEOPOROSIS AND RISK FACTORS IN THE PATIENTS ON CHRONIC HEMODIALYSIS

2015 ◽  
pp. 50-58
Author(s):  
Thi Dung Nguyen ◽  
Tam Vo
Keyword(s):  
Quality Of Life ◽  
Risk Factors ◽  
Bone Density ◽  
Region Of Interest ◽  
Cross Sectional Study ◽  
Chronic Hemodialysis ◽  
Cross Sectional ◽  
X Ray ◽  
Density Reduction

Background: The patients on hemodialysis have a significantly decreased quality of life. One of many problems which reduce the quality of life and increase the mortality in these patients is osteoporosis and osteoporosis associated fractures. Objectives: To assess the bone density of those on hemodialysis by dual energy X ray absorptiometry and to examine the risk factors of bone density reduction in these patients. Patients and Method: This is a cross-sectional study, including 93 patients on chronic hemodialysis at the department of Hemodialysis at Cho Ray Hospital. Results: Mean bone densities at the region of interest (ROI) neck, trochanter, Ward triangle, intertrochanter and total neck are 0.603 ± 0.105; 0.583 ± 0.121; 0.811 ± 0.166; 0.489 ± 0.146; 0.723 ± 0.138 g/cm2 respectively. The prevalences of osteoporosis at those ROI are 39.8%, 15.1%; 28%; 38.7%; and 26.9% respectively. The prevalences of osteopenia at those ROI are 54.8%; 46.3%; 60.2%; 45.2% and 62.7% respectively. The prevalence of osteopososis in at least one ROI is 52.7% and the prevalence of osteopenia in at least one ROI is 47.3%. There are relations between the bone density at the neck and the gender of the patient and the albuminemia. Bone density at the trochanter is influenced by gender, albuminemia, calcemia and phosphoremia. Bone density at the intertrochanter is affected by the gender. Bone density at the Ward triangle is influenced by age and albuminemia. Total neck bone density is influenced by gender, albuminemia and phosphoremia. Conclusion: Osteoporosis in patients on chronic hemodialysis is an issue that requires our attention. There are many interventionable risk factors of bone density decrease in these patients. Key words: Osteoporosis, DEXA, chronic renal failure, chronic hemodialysis

Strategy for Protecting the North Sea: A Chemical Industry Perspective

1991 ◽  
Vol 24 (10) ◽  
pp. 269-276
Author(s):  
J. R. Lawrence ◽  
N. C. D. Craig
Keyword(s):  
North Sea ◽  
Chemical Industry ◽  
Important Research ◽  
The Public ◽  
The North ◽  
Anthropogenic Inputs ◽  
Seven Principles ◽  
The North Sea ◽  
The Cost

The public has ever-rising expectations for the environmental quality of the North Sea and hence of everreducing anthropogenic inputs; by implication society must be willing to accept the cost of reduced contamination. The chemical industry accepts that it has an important part to play in meeting these expectations, but it is essential that proper scientific consideration is given to the potential transfer of contamination from one medium to another before changes are made. A strategy for North Sea protection is put forward as a set of seven principles that must govern the management decisions that are made. Some areas of uncertainty are identified as important research targets. It is concluded that although there have been many improvements over the last two decades, there is more to be done. A systematic and less emotive approach is required to continue the improvement process.

Phamacognostical and Pharmaceutical Evaluation of Chandrashakaladi Vataka - A herbal formulation

2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Dr. Akash S Changole ◽  
Mandip Goyal ◽  
Harish CR
Keyword(s):  
Classical Method ◽  
Raw Materials ◽  
Herbal Medicines ◽  
Vital Role ◽  
Published Data ◽  
Herbal Formulation ◽  
Physico Chemical ◽  
Good Manufacturing Practices ◽  
Solvent Systems

Background: Quality control and the standardization of herbal medicines involve steps like standard source and quality of raw materials, good manufacturing practices and adequate analytical screening. These practices play a vital role in guaranting the quality and stability of herbal preparations. Chandrashakaladi Vataka is an Ayurvedic herbal formulation mentioned to be beneficial in Kushtha. Till date no published data is available on its analytical profile. Aim: To develop the Pharmacognostical and Phyto-chemical profile of Chandrashakaladi Vataka. Material and Methods: Chandrashakaladi Vataka was prepared as per classical method and analytical findings were recorded. Samples were subjected to organoleptic analysis, physico-chemical analysis and HPTLC examination by optimizing the solvent systems. Results and Conclusions: Pharmacognostical profile of Chandrashakaladi Vataka was established. Loss on drying, Ash value, Acid insoluble extract, Methanol soluble extract, Chandrashakaladi Vataka was found within prescribed limits. HPTLC profile of Chandrashakaladi Vataka revealed 12 spots at 254 nm and 13 spots at 366 nm.

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