From September 24th to 28th, experts in omic integration from all over the world traveled to Pamplona to share their knowledge in the 2nd edition of STATegra Summer School on NGS and Data Integration, organized by the Translational Bioinformatics Unit of Navarrabiomed Biomedical Research Centre.
STATegra is a European project funded with 50 billion euros within the FP7 program (7th Framework Programme for Research and Technological Development) and of which David Gómez Cabrero, head of the Translational Bioinformatics Unit and organizer of the summer school, is a member.
The major aim of this project is to develop new statistic methods and bioinformatic resources so that the scientific community can integrate data from different omic technologies into their studies.
The combined analysis of all this information will mean an improvement in the diagnostic and treatment methods of multiple complex diseases, bringing the patient closer to Personalized Medicine. STATegra Summer School was born within this context, his 1st edition being taken place in Valencia in 2015.
Between the collaborating organizations of this proyect are the PRINCIPE FELIPE Research Center from valencia, spain, the Imperial College of London and the University of California.
STATegra project partners. Source: Centro de Investigación Príncipe Felipe.
This 2nd edition was attended by both national and international young researchers from different institutes, including the CIMA of Pamplona, the CNIO of Madrid, the Fundación IVI (IVI-RMA Global) of Valencia, KAUST University of Saudi Arabia, the Karolinska Institute of Sweden, the German Institute of Human Nutrition of Germany or Navarrabiomed itself, of Pamplona.
During 5 days, the assistants followed an intensive program of more tha 12 hours a day, in which they had the opportunity to learn and apply different protocols of omic intefration to their own data. Furthermore, they were asked to form multidisciplinary groups, composed by statisticians, computational scientists and biologists, among other profiles, to work on small integration projects under the supervision of specialists, presenting and discussing the main obtained results as a final activity.
On the 1st day, Sonia Tarrazona, from the Centro de Investigación Príncipe Felipe (Valencia), opened the session with the application of RNA-Seq data analysis methods. After describing the main existing types of NGS (Next Generation Sequencing) technologies, she explained the possible biases and batch effects that must be taken into account for the normalization of this data type, as well as the different types of statistical methods that can be applied to obtain differentially expressed genes between several conditions.
Afterwards, she presented the functional enrichment methods that can help us to understand which are the molecular pathways and cellular functions that might be altered in, for instant, certain type of patients.
The 2nd day was focused on the analysis of ATAC-Seq data by Ricardo N Ramirez, from Harvard Medical School in the USA. In this session, the students learned how to build ATAC-Seq signals using different methods of peak calling, how to visualize these data and how to apply this technology to transcription factor new motif discovery and footprinting. The practical session was devoted to the integration of DNase-Seq, ChIP-Seq and RNA-Seq data.
The specialist David Gómez Cabrero, at one of his lectures on omic data integration. STATegra Summer School 2018. Source: Navarrabiomed, Biomedical Research Centre.
The third day was divided into 3 sessions along with their respective practical workshops.In the first place, David Gómez Cabrero presented the main considerations that must be taken into account when analyzing DNA methylation data and when integrating them with other omics. Next, Narsis A Kiani, from the Karolinska Institute in Sweden, introduced the students to the main concepts in network theory, describing the main parameters to be calculated, how to visualize networks, and the different methods that can be used to analyze and compare them. Finally Vincenzo Lagani of the Ilia State University in Georgia,described the main meta-analysis methods that researchers use to join data from different studies, stressing the importance of carrying out previously an exhaustive systematic review to obtain optimal results.
I already worked with micronome, transcriptome and methylome data during my masters study projects in the institute I currently work at. Since I am going to start a PhD in November at the same place and I will probably work with omics data as well, I wanted to obtain an overview of the different omics and how to combine them. In general, the course met my exectations and it is a good start to discover things in detail. The tight schedule was not bad in terms of extensive work, but in terms of understanding, internalizing and focusing because of the quick topic changes. – Lisa Zellner, Department of Experimental Diabetology, German Institute of Human Nutrition, Germany. STATegra Summer School assistant.
On the 4th day Vicenzo continued his presentation with Non-Parametric Combination methods (NPC, Non-Parametric Combination) for cases in which there is an overlap between samples from different studies and, therefore, these are not independent. After the hands-on, Nuria Planells, from Navarrabiomed, presented a method based on concatenation, omicsPCA, which applied the wellknown Principal Component Analysis (PCA) combining samples to which different omics have been applied.
The day ended again with Narsis, who taught the students the main advances in the construction of multilayer networks, where each layer can be created with data from a different omic.
Finally, it was the turn of the new single cell RNA-Seq technologies. In this lecture, David described the experimental steps to follow in order to obtain single-cell data, and the bioinformatic methods used in their analysis, from the imputation techniques for the recovery of missing values (NA) to the network modeling from this type of information.
The afternoon was filled by two seminars, given by Ricardo N Ramirez and Jasper Tegnér, the latter from KAUST University in Saudi Arabia. The event ended with the discussion of the projects developed during the week by the multidisciplinar groups.
I applied to the summer school with the aim of learning how to analyze epigenomics data to integrate them with the transcriptomics results of my first year of PhD. This experience allowed me to get to know many researchers from the best national and international centers on these techniques. On the 1st day we were told that we were going to be exhausted but with studying material for 3 years. I confirm this statement. I am really looking forward a 3rd edition. – Almudena Devesa Peiró, Departament of Genomics and Systems Reproductive Medicine, Fundación IVI (IVI-RMA Global), Valencia. STATegra Summer School assistant.
STATegra Summer School assistants on the last day, at Navarrabiomed, Pamplona.
Special thanks to Nuria Planell for her help and the Communication and Design Unit of Navarrabiomed, Biomedical Research Centre for providing me with most of the graphic material of this post.
Do you want to know when will take place the next STATegra, and where it is going to celebrate? Or who are going to be the participating experts and on which new tools are going to treat their formations? Write us a comment and we will clarify all your doubts
Image credits: Khoamartin / shutterstock.com