1. Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once

2. Structural Structural Genomics Genomics characterizes the  Organization  Organization and sequence of the DNA in the whole genome Functional Functional Genomics characterizes the  Transcriptome:  Transcriptome: mRNA production as an indicator of gene expression  Proteome:  Proteome: protein production Comparative Comparative Genomics compares the structure and functions of genomes of different organisms Genomics Overview

3. Size of the Human Genome Per haploid genome New estimate 32,000 genes

4. Structural Genomics: Maps GeneticGenetic Maps (Linkage Maps) –Gene –Gene locations relative to other known genes –Based –Based on recombination, measured in centimorgans PhysicalPhysical Maps –Gene –Gene distances measured in numbers of base pairs –Based –Based on direct analysis of DNA

5. Increasing Resolution of Maps

6. Mapping of Restriction Fragments

7. Solution BamH1 4 kb 9 kb 3 kb 2 kb 8 kb 3 kb 2 kb EcoR1 BamH1 7 kb 1 kb

8. Two Sequencing Approaches for the Human Genome Project Map-based Sequencing Whole-Genome Shotgun Sequencing Contig=uninterrupted stretch of genome derived from two or more partially overlapping cloned DNAs

9. Other Sequencing Discoveries Single-Nucleotide PolymorphismsSingle-Nucleotide Polymorphisms –Single-base-pair differences between individuals of the same species –Used to study disease-causing genes Expressed-Sequence TagsExpressed-Sequence Tags –cDNA fragments produced from RNA of a specific cell type –Used to study gene activity

10. Applying Your Knowledge Which type of map Is based on recombination frequencies?Is based on recombination frequencies? Presents the order of the nucleotides in the DNA?Presents the order of the nucleotides in the DNA? Shows the number of nucleotides between regions on the map?Shows the number of nucleotides between regions on the map? 1.Physical Map 2.Sequence Map 3.Genetic Map 4.None of these is correct.

11. Genomic DNATranscriptome Proteome DATABASE

12. Functional Genomics: Microarray Analysis MicroarrayMicroarray DNA sequences arranged in a matrixDNA sequences arranged in a matrix Tests for binding to complementary sequencesTests for binding to complementary sequences

13. A cDNA microarray containing 19,200 ESTs was used to identify genes that may be involved in colon tumor metastasis (spreading). cDNA from a colon tumor with low metastatic activity is labeled green. This shows genes that are down- regulated during metastasis. cDNA from a colon tumor with high metastatic activity is labeled red. This shows genes that are up-regulated during metastasis.

14. Steps in Microarray Analysis Arrange DNA or cDNA in an ordered array on a glass slideArrange DNA or cDNA in an ordered array on a glass slide (can also build oligonucleotides directly on a slide) Incubate array with fluorescently-labeled probeIncubate array with fluorescently-labeled probe Detect probe hybridization using a laserDetect probe hybridization using a laser Record and store data with computersRecord and store data with computers

15. Building specific oligonucleotides for microarray analysis

16. Array of 1046 cDNAs probed with bone marrow based cDNA probe

17. Applying Structural Genomics: Identifying Genotypes at the Molecular Level BRCA1 Mutations Lane 2: Deletion Mutation affecting codon 39 Lane 3: Insertion Mutation affecting codon 40

18. Functional Genomics: Studying Gene Expression Northern Blotting -separate mRNA from specific cell type by size using gel electrophoresis type by size using gel electrophoresis -transfer mRNA to filter -use DNA probe to detect complementary mRNA sequences

20. Using Human Genome Information Pharmacogenomics  Using DNA Microarrays to select individual drug treatments Mutations in Gene for Affect the following disease conditions Cytochrome P450  Affects rate of metabolizing 30-40 drugs  5-10% of Caucasians and African Americans have low rates Apo E4 Gene dose affects  Age of onset for Alzheimer's disease  Response to drug Tacrine

21. Applying Your Knowledge Which method would be best for determining whether Sequences on two genomic clones overlap?Sequences on two genomic clones overlap? A thyroid cancer cell is producing different proteins from a non-cancerous thyroid cell?A thyroid cancer cell is producing different proteins from a non-cancerous thyroid cell? The size of a mRNA for a specific gene sequence?The size of a mRNA for a specific gene sequence? 1.Southern Blot 2.Sanger DNA Sequencing 3.Northern Blot 4.Microarray Analysis

23. Bioinformatics Bioinformatics is an information science focused on -storage of genetic data -organization of data -indexing sequence information Ask me about summer internships in Bioinformatics at NIST!

24. Applications of Bioinformatics DNADNA - identifying gene sequences -predicting protein sequences -exploring evolutionary relationships ProteinProtein -identifying protein products of genes

25. Databases DNAGenBank (links to protein sequences, scientific literature and genetic information) http://www.ncbi.nlm.nih.gov:80/ http://www.ncbi.nlm.nih.gov:80/ Restriction Sites WebCutter http://www.firstmarket.com/cutter http://www.firstmarket.com/cutter ProteinExPASy= Expert Protein Analysis System http://www.expasy.ch/ http://www.expasy.ch/