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NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science

NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science. Session 1 : Genome Projects. Genome Science Syllabus. 1. Introduction to Genome Projects (PH) 2. Genome Sequencing (PH) 3. SNPs and Variation (GG) 4. Gene Expression Profiling (PH)

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NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science

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  1. NCSU Summer Institute of Statistical Genetics, Raleigh 2004: Genome Science Session 1: Genome Projects

  2. Genome Science Syllabus 1. Introduction to Genome Projects (PH) 2. Genome Sequencing (PH) 3.SNPs and Variation (GG) 4.Gene Expression Profiling (PH) 5. Proteomics and Functional Genomics (GG) 6. Metabolomics and in silico Genomics (PH)

  3. Genomics Timeline

  4. The Central Dogma Replication DNA DNA Transcription mRNA Translation Protein

  5. Gene Structure • Bacteria Gene 1 Gene 2 Gene 3 Promoter Translation Start Translation stop Transcription Start • Eukaryotes Intron 1 Intron 2 Exon 1 Exon 2 Exon 3 Promoter Translation Start Translation stop Transcription Start REGULATORY REGIONS

  6. Gene Regulation • In any given cell type, only 10 - 20% of all genes are “expressed” • Regulation at the transcription level occurs by trans-acting proteins binding to cis-acting regulatory enhancers and repressors • Post-transcriptional regulation includes: - alternate splicing - RNA localization - translational control - protein modification • Maybe 15% - 30% of any genome is dedicated to gene regulation

  7. Big Questions • How can we find genes in the midst of genome sequence ? • Which genes are expressed in which tissues ? • What do all the proteins encoded by the genes do ? • What is the molecular nature of genetic variation ? • What lies beyond reductionist genetics: network genomics ?

  8. Introduction to Genome Projects Aims of Genomics Genetic and Physical Maps The Human Genome Project Animal Genome Projects Plant Genome Projects Microbial and Parasite Genome Projects

  9. General Goals of Genomics (i) Establishment of an integrated web-based database and research interface. (ii) Assembly of physical and genetic maps of the genome. (iii) Generation and ordering of genomic and expressed sequences. (iv) Identification and annotation of the complete set of genes encoded by the genome. (v) Compilation of atlases of gene expression. (vi) Accumulation of functional data, including biochemical and phenotypic properties. (vii) Characterization of DNA sequence diversity. (viii) Provision of resources for online comparison with other genomes.

  10. Assembling a Genetic Map

  11. Radiation Hybrid mapping

  12. Assembly of physical maps

  13. Chromosome painting

  14. Cat-Human Synteny

  15. Cytological, genetic, & physical maps

  16. A Vision for the HGPCollins et al, Nature 422: 835-847 (2003)

  17. 5 Year Plan 2 1. The Human DNA Sequence - complete sequence by end of 2003, 2 years earlier than initially planned - complete one third of sequence by end of 2001 - finish working draft of 90% of genome in mapped clones by end of 2001 2. Sequencing Technology - continue to increase throughput and reduce cost - support research on novel technologies and integration with genome projects 3. Human Genome Sequence Variation - develop technologies for large scale SNP identification and scoring - identify common variants in coding regions of the majority of identified genes - create a SNP map of at least 100,000 markers - develop intellectual foundations for studies of sequence variation - create public resources of DNA samples and cell lines 4. Technology for Functional Genomics - develop cDNA resources - support methods for study of function of non- protein-coding sequences - develop technology for comprehensive analysis of gene expression - improve methods for genome-wide mutagenesis - develop technology for global protein analysis 5. Comparative Genomics - complete sequences of C. elegans and D. melanogaster genomes by 2002 - develop mouse physical and genetic maps and cDNA resources - aim to complete mouse genome sequence by 2005 - identify and start work on other important model organisms 6. Ethical, Legal and Social Implications (ELSI) 7. Bioinformatics and Computational Biology - improve content and utility of databases - develop better tools fo data generation, capture and annotation - develop and improve tools for comprehensive functional studies - improve tools for representing and analyzing sequence similarity and variation - create mechanisms for production of robust, exportable shared software

  18. 5 Year Plan 3 • Genomics to Biology I-1 Comprehensive identification of structural and regulatory components of the human genome I-2 Elucidate the organization of genetic regulatory circuits and pathways in cells and organisms I-3 Develop a detailed understanding of heritable variation in the human genome I-4 Understand evolutionary variation across species and the mechanisms that generate it I-5 Develop policy options for dissemination and use of genome information in research and clinics II.Genomics to Health II-1 Develop robust strategies of identifying genetic components of disease and drug susceptibility II-2 Begin to develop strategies for identifying alleles that contribute to “good health” II-3 Develop molecular taxonomy of disease states and predictive algorithms of progression II-4 Use new understanding of genes and pathways to develop better therapeutics II-5 Investigate how genetic information is used in the clinical setting and how it influences choice II-6 Develop genome-based tools for improve the health of all • Genomics to Society III-1 Develop policy options for use of genomics and medical and non-medical settings III-2 Understand the relationship between genomics, race, and ethnicity III-3 Understand the consequences of uncovering the genetic basis of human traits and behaviors III-4 Assess how to define ethical boundaries for use of genomic information

  19. Who’s genome was sequenced ?

  20. The NCBI websitehttp://www.ncbi.nlm.nih.gov/

  21. Online Mendelian Inheritance in Manhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

  22. The Cancer Genome Anatomy Projecthttp://www.ncbi.nlm.nih.gov/ncicgap/

  23. Mouse Genomicshttp://www.informatics.jax.org/

  24. Mouse-Human Synteny

  25. Online Mendelian Inheritance in Animalshttp://morgan.angis.su.oz.au/Databases/BIRX/omia/

  26. Little Humans with wings

  27. Plant Genome Projects

  28. acedb Plant genetic mapshttp://www.gramene.org/

  29. Arabisopsis segmental duplicationshttp://www.arabidopsis.org/

  30. Defining the minimal genome

  31. A microbial genome at TIGRhttp://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl

  32. The SGD yeast databasehttp://genome-www.stanford.edu/Saccharomyces/

  33. Parasite genomics

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