AACC Workshop #2215 Genomics, Proteomics and New Opportunities for Clinical Diagnostics Monday,July 26,2004,

1. DNA Protein mRNA AACC Workshop #2215Genomics, Proteomics and New Opportunities for Clinical DiagnosticsMonday,July 26,2004,Los Angeles,CA,USA Faculty:Eleftherios P. Diamandis(Session Leader: ediamandis@mtsinai.on.ca)Daniel W. Chan(dchan@jhmi.edu)Darryl E. Palmer-Toy (dpalmertoy@partners.org)

2. Genomics, Proteomics and New Opportunities for Clinical Diagnostics2:00 - 2:30 PM - Genome Projects - Overview [E.P. Diamandis]2:30 - 3:30 PM - Technologies: Microarrays and Applications, Single Nucleotide Polymorphisms [E.P. Diamandis]3:30 - 3:45 PM - BREAK3:45 - 4:30 PM - Introduction to Proteomics [D. Palmer-Toy]4:30 - 5:15 PM - Potential Clinical Diagnostics Using Proteomic Technologies [Daniel W. Chan]5:15 - 5:45 PM - Discussion [All Faculty] AACC 2004

3. How to Find PowerPoint Presentations on the WebGo to: http://www.acdclab.org* Click on item #14, Workshops* Follow the instructions on how to download the files AACC 2004

4. Genomics and ProteomicsThese fields are driven by Technological Advances • Some Critical Technologies Cloning vectors (YAC,PAC,BAC) Automated DNA sequencingBioinformatics Expressed sequence tags (ESTs) Mass spectrometry (Protein analysis) DNA and protein microarrays Single nucleotide polymorphisms • Practical Applications Therapeutics Diagnostics AACC 2004

5. Terminology (…Omics)DNA Genomics mRNA Transcriptomics Protein Proteomics Metabolites Metabolomics Functional genomics, proteomics ----- etc. AACC 2004

6. HistoryOn June 26, 2000, at The White House, it was announced that the Human Genome Project was essentially completed by:Celera Genomics(private company)The National Human Genome Research Initiative and its International Partners (publicly funded)Work is now published:Nature 2001;409:860-921 Science 2001;291:1304-1351 AACC 2004

7. Human Genome Project Completion J.Craig Venter, Ari Patrinos, Francis Collins

8. The Official (Reference) Sequence of the Human GenomeThe highly accurate sequence of the human genome and the essential completion of the project were announced in the Spring of Year 2003. Sequence covers 99% of human genome 99.99% accurate (< 1 error per 10,000 bases)You can find the human genome sequence at: The University of California at Santa Cruz Websitehttp://genome.ucsc.eduOr at  The National Center for Biotechnology Informationhttp://www.ncbi.nih.gov/ AACC 2004

9. Some Completed Genomes • E. Coli • S. Cerevisiae (yeast) • C. Elegans (worm) • Drosophila (fly) • Arabidopsis • Human • Mouse (Nature 2002;420:520-562) • Rat (Nature April 2004) • Chimp (Nature May 2004) AACC 2004

10. Human Genome• 3 x 109 base pairs• Approximately 30,000-40,000 genes• <10% of DNA encodes for genes; the rest represents introns/repetitive elements• Importance of non-coding sequences currently not understood AACC 2004

11. Critical Protein Technologies • Make pure (recombinant) form • Solve crystal structure • Develop specific reagents (antibodies) • Identification (sequencing;Mass spectrometry) • Identify post-translational modifications (glycation, phosphorylation, etc.) • Identify protein-protein interactions (physiological function) • Gene ® protein knockout / transgene AACC 2004

12. Annotation of the Human GenomeWhat is Annotation?Characterize a linear DNA sequence® identify genes, intron/exon boundaries, regulatory sequences, predict protein sequence, identify motifs, predict function, etcAnnotation will likely go on for a few years [ongoing now]Major annotation tool Þ BIOINFORMATICS AACC 2004

14. Predicting the FutureWhat is going to happen now that the human and other genomes are completed?How quickly the next steps will happen?What are the potential difficulties? AACC 2004

15. Grand PlanFind all the genesTranslate genes to proteins“Compute” function by similarity search and comparison to known proteins“Compute” structureExperimentally verify structure/function (pathways)

16. Prediction of Function What is function? This is not a simple term. Function may be related to one or all of the following • a biological process (e.g. serine protease activity) • a molecular event (e.g. proteolysis of a specific substrate) • a cellular structure e.g. membrane; chromatin; mitochondrion; etc • a whole pathway (e.g. cell cycle) • an event of the whole organism (e.g. ovulation) Some scientists have now initiated projects to “compute” function of whole organisms (Systems Biology). AACC 2004

17. A “new” buzzword Aims to explain biological phenomena by combining: * Biology/Medicine * Mathematics * Physics * Engineering * Chemistry * Computer Science See: http://www.systemsbiology.org/ http://systems-biology.org/ Systems Biology AACC 2004

18. Systems Biology

19. Systems Biology • Many major Universities (including Harvard) have now created Departments of “Systems Biology” • Lots of jobs for qualified scientists AACC 2004

20. Structure Prediction • How proteins fold in 3D space • We still cannot reliably “compute” structures of >100 amino acid proteins (ab initio methods) • Experiment and computation: Crystallography  NMR AACC 2004

21. Future • Lots of rigorous work needs to be done • Holistic view • regulation of gene expression • metabolic pathways • signaling cascades Remember: Proteins do not work in isolation but within integrated networks. AACC 2004

22. The Impact of the Human Genome Project in MedicineHopes•Once all genes are known, we will start understanding their function ® Protein Pathways•We will then be able to correlate disease states to certain genes (Pathobiology)DISEASE®GENE (S)GENE (S)®DISEASE•We will then find ways forrational treatments(designer drugs),rational prevention, rational diagnostics AACC 2004

23. Genomics and Drug DiscoveryGenomic technologies are involved in all aspects of the drug discovery process from target validation though to the marketed drug, which include:•Molecular target identification•Drug target characterization and validation•Lead discovery•Lead optimization•Clinical candidate to marketed drug AACC 2004

24. Diagnostics / Prognostics• Does my DNA predispose me to a specific disease?•Do I want to know? (Ethics)•Genetic mutations®disease®cancer®diabetes®Alzheimer’s®heart disease•Whole genome scans for identification of mutations/polymorphisms (SNPs)? AACC 2004

25. Venter Re-Enters SequencingCraig Venter will create an…experimental laboratory dedicated to evaluating breakthrough sequencing technology with the goal of sequencing a person’s genome in a single day for only $1,000 - a fraction of current costs.Nature Biotechnology 2002;20:965 AACC 2004

26. Models of Human Disease • Identify natural human knockouts • Develop mice with every gene (or gene combinations) being knocked out (this project is now underway) AACC 2004

27. Pharmacogenetics (Pharmacogenomics)Goal is to associate human sequence polymorphisms with:•Drug metabolism•Adverse effects•Therapeutic efficacyß*Decrease drug development cost*Optimize selection of clinical trial participants*Increase patient benefit AACC 2004

28. Pharmacogenetics & Pharmacogenomics in Drug Discovery AACC 2004

29. Conclusions • The complete sequence of the Human Genome and its annotation will likely bring about accelerated and important discoveries related to • Disease understanding • Disease prevention • Disease treatment • Out of these discoveries we will likely see a new era of clinical diagnostics with more sensitivity and specificity. AACC 2004