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 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.

Whole Exome Sequencing in Patients With Ossification of the Spinal Ligaments

2021 ◽  
Author(s):  
Jiliang Zhai ◽  
Jiahao Li ◽  
Yu Zhao ◽  
Xing Wei
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Vital Role ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Whole Exome ◽  
Clinical Presentations ◽  
Spinal Ligaments ◽  
Neurological Pathology

Abstract Background The clinical presentations of ossification of spinal ligament (OSL) are majorly myelopathy and/or radiculopathy, with serious neurological pathology resulting in paralysis of extremities and disturbances of motility (motor function) lowering the quality of life. Currently, studies find that missense single nucleotide polymorphisms (SNPs) play a vital role in the susceptibility for complex diseases. Methods In the present study, we used whole exome sequencing (WES) method to explore variants in exomes and found out novel potential responsible genes for OSL. Genomic DNA was extracted from ligamentum flavum collected from 5 OSL patients and 5 control patients. Whole-exome sequencing was then performed, while variation forecasts and conservation examination were subsequently assessed. Results 8 common SNP variants were exhibited in all 5 subjects of OSL, presented in the genes of GRHL2, CUL3, WHAMM, IL17RD, POM121L12, SLC26A8 and PTPN23. After screened with numbers of samples and additional screenings with deleterious Polyphen2_HDIV_score, Polyphen2_HVAR_score and SIFT, 4 common SNP variants were displayed in 4 subjects of OSL, presented in the genes of KRT84, KIF1B, NRAP and CETN1. 7 common SNP variants were existed in 3 subjects of OSL, presented in the genes of CCT3, ANLN, ESRRB, SRBD1, ODF3L1, BRAT1 and RBP3. Conclusion We found out novel potential variants in several genes, especially WHAMM, KIF1B and ESRRB, which represented potentially pathogenic mutations in patients with OSL.

scholarly journals Whole-exome sequencing indicates FLG2 variant associated with leg ulcers in Brazilian sickle cell anemia patients

2019 ◽  
Vol 244 (11) ◽  
pp. 932-939 ◽  
Author(s):  
Gabriela Queila de Carvalho-Siqueira ◽  
Galina Ananina ◽  
Bruno Batista de Souza ◽  
Murilo Guimarães Borges ◽  
Mirta Tomie Ito ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Sickle Cell ◽  
Sickle Cell Anemia ◽  
Leg Ulcer ◽  
Leg Ulcers ◽  
Whole Exome ◽  
Extreme Phenotypes

Although sickle cell anemia results from homozygosity for a single mutation at position 7 of the β-globin chain, the clinical aspects of this condition are very heterogeneous. Complications include leg ulcers, which have a negative impact on patients’ quality of life and are related to the severity of the disease. Nevertheless, the complex pathogenesis of this complication has yet to be elucidated. To identify novel genes associated with leg ulcers in sickle cell anemia, we performed whole-exome sequencing of extreme phenotypes in a sample of Brazilian sickle cell anemia patients and validated our findings in another sample. Our discovery cohort consisted of 40 unrelated sickle cell anemia patients selected based on extreme phenotypes: 20 patients without leg ulcers, aged from 40 to 61 years, and 20 with chronic leg ulcers. DNA was extracted from peripheral blood leukocytes and used for whole-exome sequencing. After the bioinformatics analysis, eight variants were selected for validation by Sanger sequencing and TaqMan® genotyping in 293 sickle cell anemia patients (153 without leg ulcers) from two different locations in Brazil. After the validation, Fisher’s exact test revealed a statistically significant difference in a stop codon variant (rs12568784 G/T) in the FLG2 gene between the GT and GG genotypes ( P = 0.035). We highlight the importance of rs12568784 in leg ulcer development as this variant of the FLG2 gene results in impairment of the skin barrier, predisposing the individual to inflammation and infection. Additionally, we suggest that the remaining seven variants and the genes in which they occur could be strong candidates for leg ulcers in sickle cell anemia. Impact statement To our knowledge, the present study is the first to use whole-exome sequencing based on extreme phenotypes to identify new candidate genes associated with leg ulcers in sickle cell anemia patients. There are few studies about this complication; the pathogenesis remains complex and has yet to be fully elucidated. We identified interesting associations in genes never related with this complication to our knowledge, especially the variant in the FLG2 gene. The knowledge of variants related with leg ulcer in sickle cell anemia may lead to a better comprehension of the disease’s etiology, allowing prevention and early treatment options in risk genotypes while improving quality of life for these patients.

scholarly journals Modeling performance of sample collection sites using whole exome sequencing metrics

BioTechniques ◽  
2020 ◽  
Vol 69 (6) ◽  
pp. 420-426
Author(s):  
Natallia Kalinava ◽  
Abraham Apfel ◽  
Robert Cartmell ◽  
Sujaya Srinivasan ◽  
Ming-Shan Chien ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Next Generation ◽  
Sequencing Data ◽  
Sample Collection ◽  
Whole Exome ◽  
Generation Sequencing ◽  
Collection Sites

Although next-generation sequencing assays are routinely carried out using samples from cancer trials, the sequencing data are not always of the required quality. There is a need to evaluate the performance of tissue collection sites and provide feedback about the quality of next-generation sequencing data. This study used a modeling approach based on whole exome sequencing quality control (QC) metrics to evaluate the relative performance of sites participating in the Bristol Myers Squibb Immuno-Oncology clinical trials sample collection. We identified several events for the sample swap. Overall, most sites performed well and few showed poor performance. These findings can increase awareness of sample failure and improve the quality of samples.

Whole Exome Sequencing (WES) in Familien mit linksventrikulärer Ausfluβtraktobstruktion (LVOTO)

2014 ◽  
Vol 62 (S 02) ◽  
Author(s):  
M. Hitz ◽  
S. Al-Turki ◽  
A. Schalinski ◽  
U. Bauer ◽  
T. Pickardt ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

FV 1031. Whole Exome Sequencing for Children with Dyskinetic Movement Disorder

2018 ◽  
Author(s):  
Yasemin Dincer ◽  
Michael Zech ◽  
Matias Wagner ◽  
Nikolai Jung ◽  
Volker Mall ◽  
...  
Keyword(s):  
Movement Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Dyskinetic Movement

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.

Comparative Pharmacognostic, Physicochemical and Phytochemical Studies of Different Samples of Plumbago zeylanica L. Roots

2017 ◽  
Vol 9 (06) ◽  
Author(s):  
Neha Jain ◽  
Mohan Lal Kori
Keyword(s):  
Phytochemical Analysis ◽  
Local Market ◽  
Herbal Drugs ◽  
Disease Treatment ◽  
Organoleptic Evaluation ◽  
Plumbago Zeylanica ◽  
Qualitative And Quantitative ◽  
Crude Drugs ◽  
Phytochemical Studies

The objective of the present study is to evaluate the quality of the marketed and self collected samples of Plumbago zeylanica L. roots on the standardization parameters. This study is planned mainly to confirm changes with quality of drug. Now a day’s more demand of herbal drugs for disease treatment, lack of knowledge of proper methodology and availability are promoting the practices of adulteration and substitution. Thus, the standardization of the plant crude drugs is necessary to maintain their therapeutic efficacy. Comparative studies were carried out to evaluate the standards of P. zeylanica L. with emphasis on organoleptic evaluation, physicochemical and phytochemical analysis. Samples were procured from local market and self collected to determine the qualitative and quantitative variations. The result indicates that self collected sample showed significant results with comparison to marketed sample.

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