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  • Periodic Reporting for period 1 - TrainMALTA (Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics)
H2020

TrainMALTA Report Summary

Project ID: 692041
Funded under: H2020-EU.4.b.

Periodic Reporting for period 1 - TrainMALTA (Interdisciplinary Training in High-Throughput Sequencing, Bioinformatics and Model Systems: Moving towards Clinical applications of Genomics)

Reporting period: 2016-01-01 to 2017-03-31

Summary of the context and overall objectives of the project

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 focuses 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 scientists, postgraduate students and academics from the University of Malta (UoM).
This is being 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 will significantly strengthen the knowledge base at UoM and, together with participation at international meetings, will help increase the research profile of UoM, helping to promote the participation of Malta in future EU research programmes. Furthermore, there will also be advancements in science and technology which will benefit regional and European socio-economic development.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

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 to the specific needs of the scientific community at the UoM. Forty-six (46) researchers from the UoM completed the survey. The results highlighted the different areas in which training was required. Based on these results, the following activities were organised:

i. A 2-day Data Carpentry Workshop was held on the 16th and 17th May 2016 at the UoM, streamed live from UCAM to thirty-one (31) participants at the UoM.
ii. [R]efresh, a 3-day refresher course for R was held between 31st August and 2nd September at the UoM and was attended by 15 participants.
iii. Genetics for IT Professionals, an introductory course on Genetics for IT scientists was held on 9th September 2016 and was attended by 4 participants.
iv. The first summer school (D2.3, MS1) was held between the 12th and 16th September 2016 at the University of Malta (UoM). Thirty-four (34) researchers from the UoM, UCAM, and KULeuven took part in the training.
v. TrainMALTA hosted an EMBL-EBI roadshow session in Malta on the 2nd and 3rd February 2017. Three (3) expert trainers delivered the training to twenty-seven (27) researchers at the UoM.
vi. A bioinformatician at the UoM was funded through TrainMALTA to attended the course “Complex Trait Analysis of Next Generation Sequence Data” at the Max Delbruck Center for Molecular Medicine, Berlin, Germany.



2. Training in the use of model systems: zebrafish and iPSCs for validation of HTS data

This second objective will be mostly addressed during the second part of the project. To date:

i. The third project meeting held between all three beneficiaries focused on the organisation of the second summer school and various training visits by postgraduates or staff of UoM to UCAM and KULeuven to train in these techniques.
ii. Through this training initiative, one (1) postgraduate student at the UoM attended the international training course 'Derivation and Culture of Human Induced Pluripotent Stem Cells (hiPSCs)' at the Wellcome Genome Campus, Cambridge, UK.
iii. The second annual summer school is currently being planned for September 2017. This will be held at the UoM and is centred on Model Systems: an introduction to iPSCs and the Zebrafish (Danio rerio) for functional work.



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. The first annual TrainMALTA networking event was held on the 25th and 26th April 2016 at the University of Malta (UoM) and was open to all and research staff, postgraduate students and other researchers. This networking event brought together thirty-seven (37) scientists from the field of genetics, molecular biology, IT, computer science and bioinformatics from the UoM, UCAM, and KULeuven.
ii. The second annual TrainMALTA networking event is currently being planned. It will be held at the University of Cambridge on 1st and 2nd June 2017.



4. To strengthen the knowledge base at the UoM and increase the research profile of the University of Malta

The organised training activities have been very well attended and have contributed towards strengthening the knowledge base at UoM. In addition, staff and students at the UoM were funded by TrainMALTA to participate in international courses and conferences:

i. Online mentoring (D3.1) was carried out via email queries and responses. Specific requests on HTS data analysis, experimental design, building of pipelines and parameters for analysis were either directly answered by the UCAM trainers or forwarded to other specialists in the field.
ii. Twelve (12) researchers attended two international conferences: Genomics of Rare diseases: Beyond the Exome and the European Society of Human Genetics (D1.9).
iii. Five (5) researchers presented their research findings at the major European Society of Human Genetics (ESHG) conference.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

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. 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.
3. Attendance (and presentation) at leading international conferences has increased over the past 15 months helping to increase the scientific profile of the University of Malta.
4. To date 65 researchers from the UoM have benefited from the 6 locally organised training activities.

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