Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics

Periodic Reporting for period 2 - TrainMALTA (Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics)

Reporting period: 2017-04-01 to 2018-12-31

High throughput sequencing (HTS) is poised to play an ever increasingly central role in the elucidation of the causes of disease. Developments in recent years have revolutionised the approach to genetic studies making it possible to query the entire genome, transcriptome and epigenome. Coupled with falling costs and accessibility to HTS technologies, this has made it easier for researches to generate vast data sets. The bottleneck is data processing: analysis, integration and validation of the data; and the availability of trained professionals equipped with the necessary skill sets to analyse HTS data in a meaningful way. Thus, the TrainMALTA project was specifically designed to address these shortcomings by providing scientists at the University of Malta with training in basic programming, statistics, HTS data processing, analysis, visualisation, interpretation and validation. The overall aim is to enable scientists to transition HTS findings from the research lab to the clinic by:

• Acquiring a solid understanding of the basis of data analysis thus enabling life scientists to analyse and interpret HTS data within a biological and clinical context
• Appreciating the limitations of each technique and analysis pipeline
• Enhancing collaborations between life scientists, bioinformaticians and statisticians
• Developing the skill set necessary to validate HTS data using model systems (the zebrafish model and induced Pluripotent Stem Cells; iPSCs).

To this end, the TrainMALTA action focused on the transfer and exchange of knowledge between expert groups from two internationally-leading research institutions, the University of Cambridge (UCAM) and the Katholieke Universiteit Leuven (KU Leuven), and researchers from the University of Malta (UoM).
This was achieved through a series of training events (summer schools, workshops and short courses), creation of online repositories of training material, exchanges and expert visits, networking and collaborations.
These activities have significantly strengthened the knowledge base at UoM and, together with participation at international meetings, have helped increase the research profile of UoM, helping to promote the participation of Malta in future EU research programmes. Furthermore, there are also advancements in science and technology which will benefit regional and European socio-economic development.

1. To provide training on best-practices in bioinformatics analysis, integration of HTS data, and robust quantitative analytical methods:
A detailed bioinformatics survey was designed to assess the needs of UoM researchers so as to tailor the TrainMALTA activities. Based on these results, the following activities were organised:
i. Two summer schools held at UoM on Bioinformatics for HTS and the integrated analysis of genomic, transcriptomic and epigenomic data.
ii. Seven workshops hands on workshops were organised and researchers had the opportunity to attend international bioinformatics courses.
iii An exchange visit by a post-graduate researcher to the UCAM research group for intensive training in bioinformatic pipeline development and anlaysis of data.

2. Training in the use of model systems: zebrafish and iPSCs for validation of HTS data
Validation of HTS data is an essential part of data interpretation. Model organisms such as the zebrafish and patient derived iPSC lines are useful models amenable to laboratory manipulation for functional confirmation. Training in this area included:
i. A dedicated summer school held at the UoM where participants had the opportunity to use CRISPR for genome editing, complemented by a series of seminars on the use of zebrafish and iPSCs in resarch.
ii. Six intensive exchange visits were also organised on the handling, maintenance and manipulation of zebrafish with a special focus on the setting up and running of a zebrafish facility; training in the use and maintenance of iPSC lines, differentiation and characterisation; and the generation of epigenomic libraries.

3. To enhance collaborations between life scientists, bioinformaticians and statisticians
The training activities contributed towards building links between the three partner institutions and scientists and bioinformaticians within the UoM:
i. Three annual TrainMALTA networking events were held one in each partner institution. This networking events brought together scientists and bioinformaticians from the 3 partners and participants had the opportunity to present their ongoing work and discuss opportunities for future collaborations.
ii. A genomics in medicine policy meeting was also held at the UoM bringing together leading academics, researchers, medical consultants and policy makers to explore the future of genomics in Malta
iii. The TrainMALTA project also brought together research academics from various fields at UoM who have together developed a new MSc in Bioinformatics which will ensure that the knowledge gained through the project will be passed on to a new researchers in this area. The development of the MSc course is also a first step towards the continued expansion of Bioinformatics in Malta.
v. A number of ongoing collaborations have also been set-up which will extend beyond the end of the project.

4. To strengthen the knowledge base at the UoM and increase the research profile of the University of Malta
All training activities have been very well attended. In addition, staff and students at the UoM were funded by TrainMALTA to participate in international courses and conferences:
i. Three summer schools and seven hands-on training workshops were organised.
ii. Seven researchers benefited from exchange visits for intensive training at UCAM and KULeuven. These researchers are now training others in the techniques.
iii. More than 50 researchers have attended international conferences, presenting their research findings at the majority of the meetings attended.
iv. A number of research grant applications have also been submitted. Two have been awarded and an imminent reply is expected on four others.

The training activities organised through the TrainMALTA action have helped contribute towards achieving the expected impacts:

1. Acquiring new skill sets in the area of Bioinformatics for the analysis of HTS data sets has been made possible for a number of researchers (both faculty and students)
2. The knowledge acquired has helped develop a new MSc course in Bioinformatics as well as smaller teaching modules within a number of already established BSc and MSc courses
3. A number of publications are currently in preparation and some are under review. Findings have already been presented in a number of national and international fora
4. Attendance (and presentation) at leading international conferences has increased over the past 36 months helping to increase the scientific profile of the University of Malta
5. There has been an increase in the number of grant applications submitted for both local and international funding
6. The TrainMALTA action has also aided in the setting up of iPSC research at the UoM
7. Ongoing collaborations have been set-up which are expected to survive beyond the end of the project
8. Researchers from the UoM have been approached by other leading institutions with the aim of submitting new joint H2020 and HorizonEurope applications

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Periodic Reporting for period 2 - TrainMALTA (Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics)

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