Genomic Analysis Chapter 19

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Presentation transcript:

Genomic Analysis Chapter 19

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

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

SEQUENCING DNA Sanger-Dideoxymethod

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

DNA PCR amplification is performed prior to sequence analysis

Autoradiogram

Can you sequence without using radioactivity? Radioactive!

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

Microarray Analysis

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

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

Microarrays of 70 genes Metastatic cancers (row is a patient; column a gene) Metastatic cancers

Genomic DNA Transcriptome Proteome DATA BASE

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

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

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

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

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

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

Predicting Function from Homology Search

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