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 or map units 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. Map-Based Sequencing Approach for the Human Genome Project Contig=uninterrupted stretch of genome derived from two or more partially overlapping cloned DNAs

9. Whole-Genome Shotgun Sequencing Approach for the Human Genome Project

10. Other Sequencing Discoveries Single-Nucleotide PolymorphismsSingle-Nucleotide Polymorphisms –Single-base-pair differences between individuals of the same species –Can be inherited together in a specific set or haplotype –Used to study disease-causing genes

11. Other Sequencing Discoveries Expressed-Sequence TagsExpressed-Sequence Tags –Small sequences derived from cDNA fragments produced from RNA of a specific cell type –Act as markers to identify a larger DNA fragment –Used to study gene activity

12. 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.

13. Genomic DNATranscriptome Proteome DATABASE

14. 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

15. 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.

17. 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

18. Building specific oligonucleotides for microarray analysis

19. 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

20. 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

22. 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

23. 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? There are mRNA sequences of different sizes produced from the same DNA sequence?There are mRNA sequences of different sizes produced from the same DNA sequence? 1.Southern Blot 2.Sanger DNA Sequencing 3.Northern Blot 4.Microarray Analysis

25. Bioinformatics Bioinformatics is an information science focused on -storage of genetic data -organization of data -indexing sequence information

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

27. Databases DNAGenBank (links to protein sequences, scientific literature and genetic information) http://www.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/ ExonsGenScan http://genes.mit.edu/GENSCAN.html http://genes.mit.edu/GENSCAN.html TranscriptomeUnigene http://www.ncbi.nlm.nih.gov/sites/entrez?d b=unigene 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/