Gastric Breast Cancer Network Center

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Designing the Future of Medicine

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ABOUT US

CONTACT:

"Centre for BioSystems and Genomic Network Medicine" (CBS.GenNetMed),
University of Ioannina,
Ioannina,
GR 45110,
Greece
Tel: +30 26510 07423
Fax: +30 26510 07094
E-mail.: cbs@gastricbreastcancer.com

THE BEGINNING

The innovative research "Centre for BioSystems and Genomic Network Medicine" (CBS.GenNetMed) joined recently (5/2012) the Network of Research Laboratories at the University of Ioannina . The CBS.GenNetMed aims in innovative biomedical research with integrated genomic analysis of biological samples from patients with cancer and other complex disorders. To assess a genotype-phenotype map, genomic discoveries and clinical data will be analyzed with innovative computational biological approaches and mathematical predictive models. The Centre has a strong patient-oriented strategy to reach personalized medicine through systems science. The future of medicine , i.e.‘ Clinical Innovation ', is now being shaped by research in how to correlate clinical data with genome architecture-based information applying recent network biology and bioinformatics advances aiming in developing innovative therapeutic targets and biomarkers.

«Clinical Innovation»
The term "clinical innovation" [1] was introduced to emphasize the need to choose the most rational research field, from a plethora of available ones, to reach the earliest possible clinical practice.

Revolutionary genome-wide mapping technologies
Innovation is needed to radically improve health care. The innovative high-throughput technologies (HT) and in particular the next generation sequencing (NGS) technologies, in conjunction to microarrays techniques, have revolutionized biomedical research. These modern technologies provide a comprehensive analysis of human genome. The technological advancement and the development of new scientific fields, such as systems computational biology and predictive mathematical models of molecular interactions networks, are dramatically changing biomedical science. In 2012, research efforts have been shifted into how to bring innovative genomic discoveries into clinical practice. These advances in clinical genome and dynamic network biology pave now the way of future network medicine [1-10].
Despite multiple challenges, application of HT-NGS in clinical samples has started [11], aiming to translate genomic data into clinical practice in order to improve the treatment in a variety of diseases including cancer [11-20], diabetes mellitus [21], neurodegenerative diseases such as schizophrenia and autism [22,23] and other complex diseases.

First results - challenges
The first published results of clinical genomics analysis of biological samples [14-16] illustrate that the translation of discoveries from the microscopic fundamental unit of genome (base pair) by using NGS to the patient is much more complicated and difficult than it was initially appreciated [2,3,11].

Publications on genomic network medicine

1. Roukos DH. Disrupting cancer cells' biocircuits with interactome-based drugs: is 'clinical' innovation realistic? Expert Rev Proteomics. 2012 Aug;9(4):349-53. doi: 10.1586/EPR.12.37

2. Roukos DH. Networks medicine: From reductionism to evidence of complex dynamic biomolecular interactions. Pharmacogenomics 2011; 12(5): 695-8.

3. Barabási AL, Gulbahce N, Loscalzo J. Network medicine: A network-based approach to human disease. Nat Rev Genet. 2011; 12:56-68 .

4. Stratton MR. Exploring the genomes of cancer cells: progress and promise. Science. 2011; 331(6024):1553-8.

5. Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol. 2012; 8:565. doi: 10.1038/msb.2011.99

6. Wright DW, Wan S, Shublaq N, Zasada SJ, Coveney PV. From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine. Wiley Interdiscip Rev Syst Biol Med. 2012 Aug 15. doi: 10.1002/wsbm.1186.

7. Metzker, ML Sequencing technologies - the next generation. Nat Rev Genet. 2010;11: 31-46.

8. Roukos DH. Spatiotemporal individual genome code-lifestyle network: revolutionizing personal diagnostics. Expert Rev Mol Diagn. 2012 Apr;12(3):215-8.

9. Roukos DH. Novel clinico-genome network modeling for revolutionizing genotype-phenotype-based personalized cancer care. Expert Rev Mol Diagn. 2010 Jan;10(1):33-48.

10. Roukos DH. Biotechnological, genomics and systems-synthetic biology revolution: redesigning genetic code for a pragmatic systems medicine. Expert Rev Med Devices. 2012 Mar;9(2):97-101.

11. Roukos DH, Ku CS. Clinical Cancer Genome and Precision Medicine. Ann Surg Oncol. 2012 Aug 1. [Epub ahead of print]

12. Ku CS, Cooper DN, Wu M, Roukos DH, Pawitan Y, Soong R, Iacopetta B. Gene discovery in familial cancer syndromes by exome sequencing: prospects for the elucidation of familial colorectal cancer type X. Mod Pathol. 2012 Aug;25(8):1055-68. doi: 10.1038/modpathol.2012.62.

13. Ziogas DE, Roukos DH. Genome diagnostics: next-generation sequencing, new genome-wide association studies and clinical challenges. Expert Rev Mol Diagn. 2011 Sep;11(7):663-6.

14. Katsios CS, Papaloukas C, Tzaphlidou M, Roukos DH. Next-generation sequencing-based testing for cancer mutational landscape diversity: clinical implications? Expert Rev Mol Diagn. 2012; 12(7) : doi:10.1586/erm.12. 6 8 .

15. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10; 486(7403):353-60.

16. Curtis C , Shah SP , Chin SF , Turashvili G , Rueda OM , Dunning MJ , e t a l . The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012 Jun 21; 486(7403):346-352.

17. Ziogas DE, Katsios CS, Tzaphlidou M, Roukos DH. Targeted therapy: overcoming drug resistance with clinical cancer genome. Expert Rev Anticancer Ther. 2012 Jul;12(7):861-4.

18. Cho W, Ziogas DE, Katsios C, Roukos DH. Emerging personalized oncology: sequencing and systems strategies. Future Oncol. 2012 Jun;8(6):637-41.

19. Roukos DH. Next-generation, genome sequencing-based biomarkers: concerns and challenges for medical practice. Biomark Med. 2010 Aug;4(4):583-6.

20. Ku CS, Cooper DN, Roukos DH. The 'sequence everything' approach and personalized clinical decision challenges. Expert Rev Mol Diagn. 2012 May;12(4):319-22.

21. Roukos DH. Dynamics of genome 'iPOP': predicting disease or 'narciss-ome'? Expert Rev Mol Diagn. 2012 Jul;12(6):545-8.

22. Ku CS, Polychronakos C, Tan EK, Naidoo N, Pawitan Y, Roukos DH, Mort M, Cooper DN. A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Mol Psychiatry. 2012 May 29. doi: 10.1038/mp.2012.58

23. Ku CS, Roukos DH. De novo mutations, protein-protein interactions and functional regulatory networks towards novel diagnostics in autism . Expert Rev Proteomics. 2012 ( in press).