Application of genome analysis strategies in the clinical testing for pediatric diseases

Jin, Yichen; Zhang, Li; Hong, Huasheng; Xiao, Wenming; Tong, Weida; Tao, Yiran; Ni, Xin; Shi, Tieliu; Guo, Yongli

doi:10.1002/ped4.12044

Cited by 13 publications

(13 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…On the other hand, updating gene list every day is, however, impractical, costly and with less sense. Gene panels is at present insufficient for detection and is not recommended by most of the genetics and clinicians (Biesecker and Green, 2014; Wenger et al, 2017; Ewans et al, 2018; Jin et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Wang

Shen²,

Fang

et al. 2019

Front. Pharmacol.

View full text Add to dashboard Cite

Objective: Whole Exome Sequencing (WES) is an effective diagnostic method for complicated and multi-system involved rare diseases. However, annotation and analysis of the WES result, especially for single case analysis still remain a challenge. Here, we introduce a method called phenotype-driven designing “virtual panel” to simplify the procedure and assess the diagnostic rate of this method.Methods: WES was performed in samples of 30 patients, core phenotypes of probands were then extracted and inputted into an in-house software, “Mingjian” to calculate and generate associated gene list of a virtual panel. Mingjian is a self-updating genetic disease computer supportive diagnostic system that based on the databases of HPO, OMIM, HGMD. The virtual panel that generated by Mingjian system was then used to filter and annotate candidate mutations. Sanger sequencing and co-segregation analysis among the family were then used to confirm the filtered mutants.Result: We first used phenotype-driven designing “virtual panel” to analyze the WES data of a patient whose core phenotypes are ataxia, seizures, esotropia, puberty and gonadal disorders, and global developmental delay. Two mutations, c.430T > C and c.640G > C in PMM2 were identified by this method. This result was also confirmed by Sanger sequencing among the family. The same analysing method was then used in the annotation of WES data of other 29 neurological rare disease patients. The diagnostic rate was 65.52%, which is significantly higher than the diagnostic rate before.Conclusion: Phenotype-driven designing virtual panel could achieve low-cost individualized analysis. This method may decrease the time-cost of annotation, increase the diagnostic efficiency and the diagnostic rate.

show abstract

Section: Introductionmentioning

confidence: 99%

Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Wang

Shen²,

Fang

et al. 2019

Front. Pharmacol.

View full text Add to dashboard Cite

show abstract

“…Asimismo, es importante que exista legislación sobre el uso de las tecnologías de secuenciación en el ámbito clínico, con el fin de que se estandaricen los procesos y se promueva la implementación e investigación sobre el tema. Los gobiernos de algunos países, como China y Estados Unidos, han adelantado medidas regulatorias y guías con esta finalidad (56).…”

Section: Perspectivasunclassified

Secuenciación de nueva generación (NGS) de ADN: presente y futuro en la práctica clínica

et al. 2020

View full text Add to dashboard Cite

Introducción: el término secuenciación de nueva generación (NGS) hace referencia a las tecnologías diseñadas para analizar gran cantidad de ADN de forma masiva y paralela. Abordamos en esta revisión los conceptos básicos de estas tecnologías, las consideraciones de su uso clínico actual y perspectivas a futuro. Desarrollo: las pruebas basadas en NGS han revolucionado el estudio de los genomas pues permiten la lectura de millones de secuencias de ADN de forma masiva y paralela en un menor lapso de tiempo y a menor costo por base. Estas pruebas incluyen la secuenciación de panel de genes, la secuenciación completa del exoma y la secuenciación completa del genoma. El análisis de sus resultados es complejo y requiere de un proceso bioinformático y clínico exhaustivo para su adecuada interpretación. Las limitaciones de las pruebas NGS incluyen aspectos técnicos como la cobertura, profundidad y longitud de las secuencias, las cuales se pueden solventar implementando buenas prácticas de laboratorio. Conclusiones: las pruebas basadas en la secuenciación por NGS son herramientas diagnósticas que deben partir de una aproximación clínica adecuada para su uso razonado, correcta interpretación y toma de decisiones acertadas. Es de gran trascendencia que los médicos tengan la información básica para poder solicitar e interpretar estas pruebas dada su relevancia clínica actual.

show abstract

“…According to the Notice, the technology and products related to clinical genetic testing shall be approved and registered by the CFDA and State Health Planning Commission before entering into the market (Lenore et al, 2016). In July 2014, the CFDA approved the second-generation gene sequencing diagnosis, which can be used for non-invasive prenatal examination for fetal chromosomal aneuploidy disease (Jin et al, 2018). Since then, the CFDA has not approved any other genetic sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

Genetic Privacy and Data Protection: A Review of Chinese Direct-to-Consumer Genetic Test Services

Wang

2020

Front. Genet.

View full text Add to dashboard Cite

Background: The existing literature has not examined how Chinese direct-to-consumer (DTC) genetic testing providers navigate the issues of informed consent, privacy, and data protection associated with testing services. This research aims to explore these questions by examining the relevant documents and messages published on websites of the Chinese DTC genetic test providers. Methods: Using Baidu.com, the most popular Chinese search engine, we compiled the websites of providers who offer genetic testing services and analyzed available documents related to informed consent, the terms of services, and the privacy policy. The analyses were guided by the following inquiries as they applied to each DTC provider: the methods available for purchasing testing products; the methods providers used to obtain informed consent; privacy issues and measures for protecting consumers' health information; the policy for third-party data sharing; consumers right to their data; and the liabilities in the event of a data breach. Results: 68.7% of providers offer multiple channels for purchasing genetic testing products, and that social media has become a popular platform to promote testing services. Informed consent forms are not available on 94% of providers' websites and a privacy policy is only offered by 45.8% of DTC genetic testing providers. Thirtynine providers stated that they used measures to protect consumers' information, of which, 29 providers have distinguished consumers' general personal information from their genetic information. In 33.7% of the cases examined, providers stated that with consumers' explicit permission, they could reuse and share the clients' information for non-commercial purposes. Twenty-three providers granted consumer rights to their health information, with the most frequently mentioned right being the consumers' right to decide how their data can be used by providers. Lastly, 21.7% of providers clearly stated their liabilities in the event of a data breach, placing more emphasis on the providers' exemption from any liability. Conclusions: Currently, the Chinese DTC genetic testing business is running in a regulatory vacuum, governed by self-regulation. The government should develop a

show abstract

Application of genome analysis strategies in the clinical testing for pediatric diseases

Cited by 13 publications

References 31 publications

Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease

Secuenciación de nueva generación (NGS) de ADN: presente y futuro en la práctica clínica

Genetic Privacy and Data Protection: A Review of Chinese Direct-to-Consumer Genetic Test Services

Contact Info

Product

Resources

About