2. Genomics & Proteomics Analysis Chapter 20

4. Overview of topics to be discussed  How to sequence genomic DNA (we will have to touch briefly on polymerase chain reaction—a topic from the upcoming “PCR” lab). cDNA  Microarray Analysis  The Human Genome Project  How to use information from any genome sequence: Single Nucleotide Polymorphisms Predicting Function from Sequence

5. cDNA can also be studiedwww.bio.davidson.edu/Courses/genomics/RTPCR/RT_PCR.html :  cDNA: mRNA Reverse transcriptase

6. SEQUENCING DNA Sanger-Dideoxymethod

8.  Sanger Method dideoxynucleotides: lack a 3’ OH  But have the 2’ and 3’ have hydrogen  NO DNA EXTENSION Dideoxy key point!

9. DNA PCR amplification is performed prior to sequence analysis

12. Autoradiogram

14. Can you sequence without using radioactivity? Radioactive!

15. Yes: Example of Labelled Probes  ddGTP  ddATP  ddTTP  ddCTP  Orange  Black  Red  Blue

19. Microarray Analysis

20. Microarray Protocol  DNA or cDNA is added robotically to chip  Chips exposed to labeled cDNA  Label monitored by laser

23. Example of: Microarrays from breast tumors  cDNA from breast tumors from 2 groups of patients Metastatic CancerDisease Free

24. Microarrays of 70 genes Metastatic cancers (row is a patient’s tumor, a column a gene)

25. Genomic DNA Transcriptome Proteome DATA BASE

26. Human Genome Project June, 2002 Dr. Craig Venter President Clinton Dr. Francis Collins

27. The initial draft of the Human Genome 3.4 billion base pairs 32,000 genes Average gene 27,000 bases Chromosome 17, 19, 22 high density May encode 96,000 proteins

28. Mouse: Mus musculus  2.6 billion bp  99% in common with human genome

29. Genomic Projects: provide us information about:  Expressed-sequence tags (ESTs)  Single-nucleotide polymorphisms (SNPs) & Haplotypes  Variable Number Tandem Repeats (VNTRs) Need to understand cDNA

30. Haplotype: A set of SNPs and other variants on the same chromosome

31. Variable number tandem repeats (VNTRs) in multiple loci Short stretches of DNA base pairs that are repeated at multiple loci in the chromosomes. GAG GAGGAG GAGGAGGAG GAGGAGGAGGAG GAGGAGGAG GAGGAGGAGGAGGAGGAG GAGGAGGAGGAGGAG GAGGAGGAGGAG

32. VNTR’s

33. Predicting Function from  Homology Search

34. Computational method prediction  Paralog  Ortholog Paralogs: Homologous sequences in same species Orthologs Homologous Sequences in Different species