1. Genomic Analysis Chapter 19-20

2. Overview of topics to be discussed
How to sequence genomic DNA (pp )
(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

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

4. SEQUENCING DNA
Sanger-Dideoxymethod

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

7. DNA PCR amplification is performed prior to sequence analysis

10. Autoradiogram

11. Can you sequence without using radioactivity?
Radioactive!

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

14. Microarray Analysis

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

18. Example of: Microarrays from breast tumors
cDNA from breast tumors from 2 groups of patients
Metastatic Cancer Disease Free

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

20. Genomic DNA
Transcriptome
Proteome
DATA BASE

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

22. 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

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

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

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

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

27. Predicting Function from
Homology Search

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