WP4 – Building capacity in genetic diagnosis of EE through NGS

Visit exchanges and training activities between SU and both French and Belgium consortium partners will be organized to balance the scientific background and research skills of high-throughput DNA sequencing applications and bridge the gap in genetic diagnostics of EE.

T4.1: Lectures and training on high-throughput DNA sequencing (M3-M18)

Task leader: AMU, participants: SU, UA

To improve the know-how and field of expertise of the SU researchers in different high throughput sequencing technologies, one lecture, 4 short stays and 2 workshops (WS1, WS2) will be offered during the duration of the project in the three project partner institutions (SU, AMU, UA). The two days lecture will be considered for molecular biologists, medical doctors, and technical assistants to acquire theoretical and practical information in the available nextgeneration sequencing (NGS) systems and those on the near horizon. Within the scope of the course, the advantages and disadvantages of current sequencing technologies and their implications on data generation will be discussed. Half of short stays and workshops will be organized to enrich the team of SU researchers with the fundamentals for the design of the genes panel, preparation and validation of the library. At the end of this training, participants will be able to optimize and personalize parameters to fit the needs of the study like coverage of the target region sequencing, number of samples and quality of data output.

T4.2: Training on bioinformatics M10-M21

Task leader: AMU, particpants: SU, UA

In addition to the molecular analysis skills, knowledge of bioinformatics will be highly required for clinical interpretation of the variants. Bioinformatics skills are highly required to assess and analyze the large volumes of sequencing data that are generated by high throughput sequencers. Therefore, two workshops will be convening for junior and senior research staff. Bioinformatics training on NGS data will be considered to build a strong background in current tools focusing on genome analysis and diagnostics. The first organized workshop in SU will be adapted to the needs of beginners in the field of NGS bioinformatics and to allow scientists with no or little background in computer science to get a first hands-on experience in this new research topic. In the second workshop, ten participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally performing their first downstream analysis. This practical training on own data allows participants to learn more about data-integration in conjunction with high throughput applications in order to meet the project goals and objectives.

T4.3: Short term secondments to drive the design of conceptual data modelling and the setup up of biological database: (M19-M30)

Task leader: SU, participants: AMU, UA

Four short term secondments between SU and European partners staffs will be planned to exchange of knowledge, ideas and experience, and to conceive data modelling, to create and to share a database system for bioinformatics. An adaptation of databases already developed by AMU for other projects will be considered (e.g. https://epilepsnps.net/). All of the generated data and the variants identified in SU will be included in this database. Database features include basic variant information (chromosome location, nucleotide change,), detailed annotation at the transcript and protein levels, severity scores, frequency, validation status, and the main associated clinical characteristics. In addition, a web-based application will be developed to facilitate and to control access to the biological database. This later will be shared and remotely accessed by SEED partners in a secure and ubiquitous manner.

Description of Deliverable :

D4.1: A guideline for classification of sequence variants in EE Bioinformatics pipeline for NGS EE data analysis (M 21)
D4.2: A database model (M30)

Relevant Milestones :

MS1 Training objectives and teachning tools available for starting training
MS3 Gene panel design

First investigator:

Laurent VILLARD
Laurent VILLARD
Research director, head of the CNS/NET department of MMG. With a PhD in human genetics, and post-doctoral research work on Down syndrome at...