1. 17th European Congress of Pathology Biochips and related Bioinformatics areas applied to Pathology Barcelona September 18, 1999 Dr. Fernando Martín-Sánchez Head of the Bioinformatics Unit SGLSSP - ISCIII

2. Contents Presentation New data: – genome structure and function New technologies: – bioinformatics – DNA chips Applications in Pathology – protein chips – tissue chips

3. Presentation

4. Bioinformatics Unit http://biotic.isciii.es

5. Bioinformatics Unit BIOTIC OBJECTIVE To facilitate knowledge about new technologies for processing genetic information and its application in biomedical research and clinical practice Genetic Information Technologies in Health

6. New data

7. Human Genome Project Approx. 100.000 genes, 3.000 millions of base pairs 9000 genes identified, 5400 associated with diseases, 500 used in genetic tests Will be finished in year 2003 “consensus” sequence

8. Post-Genomics Era Structural Genómics (DNA sequences) Functional Genomics (mRNAs) Individual Genomics (mutations, SNPs) Comparative Genomics (homology, evolution) Proteomics (proteins)

9. New technologies: bioinformatics

10. Bioinformatics  Biomedical research is an information- based discipline  New experimental approaches generate huge amounts of information  Research and development of tools that are useful to understand the information flow: genes --- molecular structures --- biochemical function --- biological behaviour --- influence in diseases and health.

11. Genomics Biochips Clinical data Proteomics Bioinformatics Tools for genetic information processing GENETIC INFORMATION Research & Clinical applications Knowledge on molecular basis of diseases

12. Bioinformatic Applications Biological information databases Sequence alignment and analysis Prediction of protein structure and function Genetic and metabolic maps Expression and polimorphism data management

13. New technologies: Biochips

14.  Biochips arise from the combination of concepts and techniques of biotechnolgy and microelectronics  In microchips - High density of integration of electronic circuits on a silicon wafer  In biochips - High density of integration of genetic material on a silicon, glass or plastic wafer Biochips. Basic technology

15. Biochips. Manufacturing Photolitography: A silica wafer is alternately illuminated through a lithographic mask in defined patterns and washed with a solution of synthetic nucleotides

16. BIOCHIP Design Fabrication Biochips. Technology SAMPLE Isolate Amplify Tag Incubate (hybridise) Stain Wash Scan Data Analysis

17. Biochips: process Differential gene expression 1. Selection of samples 2. Extract mRNA y RT 3. Gluorescent tagging of cDNA 4. Hibridization with the microarray 5. Scanning 6. Image data analysis

18. Biochips. Limitations New technology –Limited accesibility –High costs Poor interoperability Commercial kits are difficult to customize for the researcher Data interpretation

19. Biochips and Bioinformatics High-throughput techniques are generating huge amounts of information BIOINFORMATICS represents a fundamental set of tools for analysing all of this information

20. Biochips and Bioinformatics BiochipsBioinformatics Data Management and analysis Tools Data Bases Data Mining Visualization Internet Data Polimorphism Gene expression Genotype-Phenotype relationships

21. Biochips and Bioinformatics More and more labs are adquiring the technology Explossion of data from arrays Need of standarization for annotation and storing data Public repository at the EBI XML and TIFF images Genes Experiments Expression data + image

22. Applications

23.  Transcript imaging (differential gene expression)  Drug profiling  Toxicogenomics  DNA sequencing and re- sequencing  SNP´s detection  Detection of drug resistance in pathogens  Histopathology Biochips. Applications

24. Applications in Pathology Histopathology - study of pathological processes in tissues - has to benefit from the information yielded by new genomic technologies Research tools for high-throughput molecular characterization of tumor and other tissue specimens

25. Genetic material analysis: –DNA, RNA: (in situ PCR and Hybridization) Haematoxylin, eosin sections –Fresh tissue –Archived, parafine-embebbed material Samples –surgery –biopsy –cytopathology –necropsy –PROTEINS: (inmunocytochemistry) Applications in Pathology

26. In a single experiment: –Measuring the expression of hundreds or thousands of genes in a tumor. SAGE (Serial Analysis of Gene Expression) DNA microarrays –Measuring the expression of several genes in hundreds of tumors. (different pacients, different stages) Applications in Pathology

27. Micro Array technology could be classified in three main groups: –Nucleic acid Microarrays (DNA, RNA) –Protein Microarrays –Tissue Microarrays Applications in Pathology

28. Protein chips Evolution of the DNA chips High-throughput approach for gene expression and receptor-ligand interactions Protein Microarrays are the next step forward in the analysis for gene expression. Are complementary with gene expression DNA arrays

29. Protein chips ProteinChip (Ciphergen):

30. Tissue chips Tissue chips are array-based high- throughput techniques that allow to work in a parallel way. The array provides targets for parallel analysis of proteins, DNA and RNA by In Situ detection of targets

31. Tissue chips Select the regions of interest form paraffin embedded tissue blocks to be used as samples Extract the material with a needle that takes a small cylinder of sample Samples are arrayed in a new paraffin block

32. Cut the paraffin block with the arrayed samples in slices that will become the tissue chips Analyse the tissue chips by Immunohistochemistr y DNA ISH, mRNA ISH, In Situ PCR Tissue chips

33. The advantages of Tissue Chips are: –Rapid molecular profiling of large number of samples in a single experiment –Reduce the time of analysis –Facilitates the standardised analysis of multiple genes in the same sample with the same technology, same probes and same criteria –FISH in these devices is as good as in ethanol fixed frozen samples Tissue chips

34. Nat Med. 4 (7) 844-7 Jul 98 –NHGRI, Pathology Basel, Tampere Hosp. –1000 biopsies, breast cancer –200 sections (4-8 microns) –6 gene amplifications –p53 and estrogen receptor expression Tissue chips 0,6 mm 3-4 mm

35. Cancer Res. 59 803-6 Feb 99 –Different stages of prostate cancer –371 tumors, 5 genes –FISH –Survey method to pinpoint most important genes for detailed studies with conventional techniques –Identification of patterns and interrelationships between gene amplifications Tissue chips

36. Am. J. Path. 154 (4) 981-6 Apr 99 –Combination of DNA arrays and Tumor Arrays to identify and evaluate genes implied in renal cell carcinoma –1º - cDNA array 5184 cDNA clones. Different expression of 89 genes in normal kidney cells and cancer cell line CRL-1933 –2º - Tissue array with 532 RCC specimen to measure vimentin expression by IHC. Tissue chips

37. Virtual Tumor Databank Molecular Pathology Program - CNIO Intranet C.N.I.O.Intranet Hospitals Clinical Records Anatomical Pathology Extranet Genetic Analysis of the tumor Shared Databases Genetic public and private databases

38. Contacting us:  E-mail: biotic@isciii.es  Web: http://biotic.isciii.es  Mailing list: lista.biotic@isciii.es  News Bulletin: BIOTIC - News  Phone: +34 91 509 70 27  Fax: +34 91 509 79 17