WG2: Integration of omics data
Description
Integration of omics data will consider the following aspects: (i) Optimization and standardization of methods for the omics analysis of pancreas tumoral and normal tissue samples; (ii) Establishment of standardized approaches for omics data deposit. To this end, the Web-Based Platform for Mining Pancreatic Expression Datasets will be used as a model and its potential extension to other omics data will be assessed; and (iii) Identifying and documenting the available algorithms for omics data integration.
Issues to be considered include: the data high dimensionality - small sample size problem, the inherently noisy nature of the data, the stability and reproducibility of the models, the incorporation of domain knowledge into the knowledge discovery process using innovative statistical and bioinformatics approaches.
WG2 prioritized the identification of pancreas cancer omics databases and omics-related data standardization or optimization and the evaluation of confidentiality issues and issues related to data sharing (WG2-1), and the integrated omics analysis (WG2-2).
| Coordinator | Kristel Van Steen ([email protected]) |
| Co-leaders | Joerg Hoheisel, Nuria López-Bigas |
| Members | Fentaw Abegaz Yarew, Azmi Adawi, Sinead Aherne, Fátima Al-Shahrour Núñez, Laufey Amundadottir, Peter Bailey, Maria-Antonietta Bali, Claudio Bassi, Dave Beare, Hilmar Berger, Kirill Bessonov, Andrew Biankin, Nidhi Bindal, Ewan Birney, Erik Bongcam, Alvis Brazma, Markus Büchler, Christiane Bruns, Peter Bühlmann, Kridsadakorn Chaichoompu, David K. Chang, Claude Chelala, Tatjana Crnogorac-Jurcevic, Isabel Cuesta, Ahmed Debit, Octavio Espinosa, Irene Esposito, Joan Frigola, Mario Fernandez Fraga, Simon Forbes, Patrick Forde, Ramouna Fouladi, Fieke Froeling, François Fuks, Francesco Gadaleta, Darlene Goldstein, Eduardo González Couto, David González Pisano, Abel González-Pérez, Elena Gusareva, Ivo Gut, Ralf Herwig, Manuel Hidalgo, Joerg Hoheisel, Elin Kure, Núria López-Bigas, Evangelina López de Maturana, Meritxell Rovira Loris, Teresa Macarulla, Núria Malats, José Carlos Martínez, John McPherson, Matthias Merkenschlager, Esther Molina-Montes, Yves Moreau, Loris Mularoni, Steven Olde Damink, Veronique Orian-Rousseau, Sandra Orchard, Stephan Ossowski, Lorenzo Pasquali, Bernard Peers, Silvia Pineda, Sabarina Radhakrishnan, Marta Rava, Anwar Rayan, Francisco X. Real, Pablo Riesgo, Vandana Sandhu, Tamara Sauri Nadal, Alain Sauvanet, Aldo Scarpa, Carl Johann Simon-Gabriel, Euan Stronach, Ahmed Tawfik, Dayem Ullah, Alfonso Valencia, Eric Van Cutsum, Jean-Luc Van Laethem, Kristel Van Steen, Harpreet Wasan. |
Research Lines
Optimization and standardization of methods for the omics analysis of pancreas tumoral and normal tissue samples
Establishment of standardized approaches for omics data deposit
Identifying and documenting the available algorithms for omics data integration
Issues to be considered include: the data high dimensionality - small sample size problem, the inherently noisy nature of the data, the stability and reproducibility of the models, the incorporation of domain knowledge.
Activities
CAPITA SELECTA IN COMPLEX DISEASE ANALYSIS
The third edition of Capita Selecta in Complex Disease Analysis took place in Liège on 24-26 November 2014. The focus of CSCDA2014 was on:
- population and patient heterogeneity
- data fusion and omics integration for rare diseases.
Two book chapters on the Action and WG2 scientific-related interests have been published in 2014:
- (1) Kristel Van Steenand Núria Malats, on behalf of the COST Action BM1204 participants. Perspectives on Data Integration in Human Complex Disease Analysi. In: Big data analytics in Bioinformatics and Healthcare. Pages: 284-322. Available at Irma International.
- (2) Enrique Carrillo-de Santa Pau, Francisco X. Real, Alfonso Valencia. Bioinformatics analysis of pancreas cancer genome in high-throughput genomic Technologies. In Molecular Diagnostics and Treatment of pancreatic cancer. Pages: 93-131.
CANCER GENOMICS AND PERSONALISED MEDICINE WORKSHOP: FOCUS ON PANCREAS CANCER.
1st July 2015. Barcelona, Spain.
In this workshop examples of the application of omics in pancreatic cancer research where presented. Several groups working on omics data analysis shared ideas and experiences on this subject.
TRAINING SCHOOL ON INTERACTIONS IN COMPLEX DISEASE ANALYSIS
This training school was held in Antwerp, Belgium, during April 27-29, 2016.
+ More information at training school section
Resources identified
Biostatistics, bioinformatics, machine learning, functional genomics,biomedicine, informatics, oncology, pathology, transcriptomics, epigenomics,computational cancer, molecular oncology, data management, genomics,guidelines development, statistics, epidemiology, statistical genetics,computational biology, visualization, digestive oncology, computer science,integrative biology.
Networking
ELIXIR (https://elixir-europe.org/)
PED (https://pancreasexpression.org/home/)
COSMIC (https://cancer.sanger.ac.uk/cosmic/)
EORTC
Meetings
- Madrid, November 2013
- Heidelberg, February 2014
- Liege, November 2014
- Toledo, June 2015
- Barcelona. July 2015
- Cluj-Napoca, November 2015