Genomics & Proteomics Analysis Chapter 20 Overview of topics to be discussed How to sequence...
-
Upload
corey-stephens -
Category
Documents
-
view
216 -
download
0
Transcript of Genomics & Proteomics Analysis Chapter 20 Overview of topics to be discussed How to sequence...
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 can also be studiedwww.bio.davidson.edu/Courses/genomics/RTPCR/RT_PCR.html :
cDNA:
mRNA Reverse transcriptase
Sanger Method dideoxynucleotides: lack a 3’ OH
But have the 2’ and 3’ have hydrogen
NO DNA EXTENSION
Dideoxy key point!
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
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
Genomic Projects: provide us information about:
Expressed-sequence tags (ESTs)
Single-nucleotide polymorphisms (SNPs) & Haplotypes
Variable Number Tandem Repeats (VNTRs)
Need to understand cDNA
Variable number tandem repeats(VNTRs) in multiple loci
Short stretches of DNA base pairs that are repeated at multiple loci in the chromosomes.
GAGGAGGAG
GAGGAGGAGGAGGAGGAG
GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG
GAGGAGGAGGAGGAGGAG
GAGGAGGAGGAGGAG
GAGGAGGAGGAG
Computational method prediction Paralog
Ortholog
Paralogs: Homologous sequences in same species Orthologs
Homologous Sequences in Different species