1. PrognoChip Mediator, FORTH-ICS 1 Integrating Clinical and Genomic Information through the PrognoChip Mediator Implemented by Manos Kalaitzakis, Dimitris Manakanatas, Haridimos Kondylakis, Manolis Nikoloudakis, and Maria Michou Under the guidance of Anastasia Analyti & Dimitris Plexousakis Institute of Computer Science, FORTH-ICS, Greece Department of Computer Science, University of Crete, Greece Medical Doctors Elias Sanidas, Efstathios Stathopoulos, Maria Kafousi Medical School, University of Crete, Greece Stamatis Vassilaros Prolipsis Diagnostic Breast Center, Athens, Greece

2. PrognoChip Mediator, FORTH-ICS 2 The aim of PrognoChip is: –the identification of molecular markers for the classification and prognosis of Breast Cancer, based on: the correlation of patient’s clinicohistopathological parameters and therapy response with their tumor gene expression profiles

3. PrognoChip Mediator, FORTH-ICS 3 Tumor Tissue Route SurgeryTumor sample liquid nitrozen or ice Histopathologist Sample 1 Paraffin cuts Microscope paraffin coloring report biopsis PAGNH: University Hospital PROLIPSIS: Breast Cancer Center Sample 2 Tissue Bank Microarray experiment RNA later extraction FORTH-IMBB: Molecular Biology Lab

4. PrognoChip Mediator, FORTH-ICS 4 The Integrated Clinico-Genomics Environment of PrognoChip Consists of: (a)a Clinical Information System to keep patient clinical information (i.e., clinical, laboratory, and histopathological information), (b)a Genomic Information System to manage DNA microarray experiments, analyze raw hybridization data, and store gene expression profiles, (c)a middleware layer, called PrognoChip Mediator, for the integration of the Clinical and Genomic Information Systems, and (d)a Data Mining layer, for the intelligent processing of the retrieved clinico-genomic data, knowledge extraction, and visualization.

5. PrognoChip Mediator, FORTH-ICS 5 Three Databases to Integrate  Genomic Information System (extension of BASE v1.2.16, developed by Lund Univ.) microarray design, samples, hybridizations, etc.  Clinical Information System (extension of Integrated Care Solutions, developed by FORTH-ICS.) patient medical history, current findings, diagnostic test results, tumor histopathologic diagnosis, etc.  Gene Ontology (GO) Database ontology terms for the annotation of gene products

6. PrognoChip Mediator, FORTH-ICS 6 Mediator Findings Repository Clinical IS Data Mining Tools Query Engine metadata findings Submit/search/ update medical doctor (web-based) Genomic IS Normalization Plug-ins Submit/search/ update biologist (client-server based) GO database biomedical investigator (web-based) Visualization Tools virtual query Specify parameters (local access) output XML file store/query findings local installation store administration & temporary data Mediator DB PrognoChip: The Integrated Clinico-Genomics Environment

7. PrognoChip Mediator, FORTH-ICS 7 The PrognoChip Mediator  The authorized biomedical investigator can form clinico-genomic queries through a web-based graphical user interface.  Specifically, the user can specify criteria for selecting tumors: (i)excised from patients with a clinical profile of interest, (ii)having histopathologic characteristics of interest, and (iii)participating in a PrognoChip microarray experiment of specified quality and characteristics.  Returned tumors are accompanied with desirable clinico-genomic information (e.g., gene expression profiles).

8. PrognoChip Mediator, FORTH-ICS 8 Clinical Criteria Patient past breast diseases Gynecological history (e.g. age of menarche, menopausal status, etc.) Total duration of hormone intake Other risk factors (e.g. smoking habits, etc. ) Family history of malignancy Current findings and blood tumor markers Therapies before and after surgery Effectiveness of therapies

9. PrognoChip Mediator, FORTH-ICS 9 Clinical Query Forms

10. PrognoChip Mediator, FORTH-ICS 10

11. PrognoChip Mediator, FORTH-ICS 11 1011

12. PrognoChip Mediator, FORTH-ICS 12

13. PrognoChip Mediator, FORTH-ICS 13

14. PrognoChip Mediator, FORTH-ICS 14

15. PrognoChip Mediator, FORTH-ICS 15

16. PrognoChip Mediator, FORTH-ICS 16

17. PrognoChip Mediator, FORTH-ICS 17

18. PrognoChip Mediator, FORTH-ICS 18

19. PrognoChip Mediator, FORTH-ICS 19

20. PrognoChip Mediator, FORTH-ICS 20 Tumor Histopathologic Criteria Tumor histological type Diameter Grade Lymphatic, Veinous, Perineural, Skin, Nipple, and Lymph node invasion Histological TMN Immunohistochemical tumor markers (ER, HER-2, etc.)

21. PrognoChip Mediator, FORTH-ICS 21 Histopathologic Query Forms

22. PrognoChip Mediator, FORTH-ICS 22

23. PrognoChip Mediator, FORTH-ICS 23

24. PrognoChip Mediator, FORTH-ICS 24

25. PrognoChip Mediator, FORTH-ICS 25

26. PrognoChip Mediator, FORTH-ICS 26 Genomic Criteria  The channel of the cancerous tissue  Hybridization quality indicators  Dates of hybridizations  The name of the desired normalization procedure  Reporter/Gene filtering criteria –GO annotations and evidence code Molecular Function, Biological Process, and Cellular Location ontology terms

27. PrognoChip Mediator, FORTH-ICS 27 Genomic Query Forms

28. PrognoChip Mediator, FORTH-ICS 28

29. PrognoChip Mediator, FORTH-ICS 29

30. PrognoChip Mediator, FORTH-ICS 30 Select Page After patient/tumor criteria specification, the user selects the clinical, histopathologic, and genomic fields of interest that will accompany the cancerous sample in the output.

31. PrognoChip Mediator, FORTH-ICS 31 Select Page: Part 1

32. PrognoChip Mediator, FORTH-ICS 32

33. PrognoChip Mediator, FORTH-ICS 33 Select Page: Part 2

34. PrognoChip Mediator, FORTH-ICS 34

35. PrognoChip Mediator, FORTH-ICS 35 Query Processing 1.When a Query Form is saved, part of the related subquery is formed. 2.When the Select Page is filled out, final clinical subqueries are formed. 3.Clinical subqueries are submitted to Clinical IS and results are composed. 4.Based on the tumor names returned in 3), final genomic queries are formed and submitted to Genomic IS. 5.Results from Clinical IS and Genomic IS are joined based on tumor name. 6.Output XML file is formed, based on a predetermined schema.

36. PrognoChip Mediator, FORTH-ICS 36 Output XML File Schema For the full Output XML File schema, see: http://www.ics.forth.gr/~analyti/PrognoChip/ OutputXMLFileSchema.jpg Description is provided in: http://www.ics.forth.gr/~analyti/PrognoChip/ OutputXMLFileDescription.pdf

37. PrognoChip Mediator, FORTH-ICS 37 Result Page In the Result Page, the user can: download the complete set of output files to his/her machine, view the output XML file, and download previous results.

38. PrognoChip Mediator, FORTH-ICS 38

39. PrognoChip Mediator, FORTH-ICS 39 Output XML File

40. PrognoChip Mediator, FORTH-ICS 40 Data Mining Layer  It supports decision making operations, on output XML files.  Examples: Retrieve the tumor gene expression profiles of patients that meet clinical profile A and clinical profile B. Then, find the genes that best discriminate between these two groups. Cluster patients based on their tumor gene expression profiles. Then, identify indicative patient clinical profiles, for these clusters.

41. PrognoChip Mediator, FORTH-ICS 41 Details on the PrognoChip Mediator can be found in:  Anastasia Analyti, Haridimos Kondylakis, Dimitris Manakanatas, Manos Kalaitzakis, Dimitris Plexousakis, George Potamias, Integrating Clinical and Genomic Information through the PrognoChip Mediator, Procs. of the 7th International Symposium on Biological and Medical Data Analysis (ISBMDA-2006), 250-261, 2006. Springer-Verlag

42. PrognoChip Mediator, FORTH-ICS 42 PrognoChip Mediator Web Site  http://www.ics.forth.gr/isl/projects/PrognoChip/

43. PrognoChip Mediator, FORTH-ICS 43 Acknowledgements The development of PrognoChip Mediator was supported by National funds within the context of:  the PrognoChip project (GSRT-EPAN).PrognoChip 2004-2007

44. PrognoChip Mediator, FORTH-ICS 44 Thank you !!!