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Genomics Analysis
Chapter 20
Overview of topics to be discussed
The Human Genome Analysis
Variable Number Tandem Repeats
Short Tandem Repeats
Single Nucleotide Polymorphisms and Haplotypes
Expressed sequence tags (ESTs)
Predicting Protein Function
BLAST searches (in lab) Homlogous genes
Orthologs versus paralogs
Microarray Analysis and an example of its application
Genomic DNA Transcriptome Proteome
DATA BASE
Overview
The Human Genome Project
June 2002
Methods to used include:
The two strategies used:
Bac-to-Bac Sequencing (Map Based Sequencing)
Shot-Gun Method
http://www.sciencemag.org/content/291/5507/1304.full
Map-based Cloning of Human Genome
“Partial Restriction Digests”
Smaller pieces for sequencing
Time Consuming Process whereby: Areas of overlap
between identifies the sequence of DNA
http://www.hhmi.org/biointeractive/dna/DNAi_human_genome_seq.html
Shot-Gun Sequencing of the human genome
http://bcs.whfreeman.com/thelifewire/content/chp17/1702002.html
Human Genome approximated:
3.4 billion base pairs
32,000 genes
Average gene 27,000 bases
Chromosome 17, 19, 22 high density
May encode 96,000 proteins
Ongoing data bases from human genome project: Variable Number Tandem Repeats (VNTRs)
Short Tandem Repeats (STRs)
Single-nucleotide polymorphisms (SNPs) SNP Maps and haplotypes
http://www.ncbi.nlm.nih.gov/pubmed/11029002 http://www.fruitfly.org/SNP/
Expressed-sequence tags (ESTs)Oops! Need to understand cDNA
Haplotype:A set of SNPs and other varians on the same chromosome
http://hapmap.ncbi.nlm.nih.gov/
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
Forensic Analysis: STRs FBI: Combined DNA
Index System
13 loci
STRs (4-5 nucleotide repeats)
Example of D1S80 STR Distance migrated on
gel electrophoresis corresponds to size of repeating nucleotide sequence.
cDNA mRNA
Reverse transcriptase
cDNA
Predicting Function from Homology Search
Phylogenetic Profile
Computational method prediction Paralog
Ortholog
Microarray Analysishttp://www.youtube.com/watch?v=VNsThMNjKhM
Microarray Protocol DNA or cDNA is added
robotically to chip
Chips exposed to labeled cDNA
Label monitored by laser
Microarrays from breast tumors cDNA from breast tumors breast cancer patients
EACH patient has a chip and microarray containing “candidate” genes
Time passes and some women remain “cancer-free” while other women haverecurring cancer. Now return to the original microarrays and compare thesetwo groups of women (disease-free and recurring cancer). Is gene expression different?
The composite microarray Can you see any differences?
Recurring cancers
(Each row is a patient’s tumor, a column a gene)
Cancer free
Expression patterns varies between patients
Those “genes” that are green from “normal” tissue genes
Those “genes” that are red are associated with cancer!
BLAST searches Unknowns and examples of how to search
database provided tomorrow in lab.
Mouse: Mus musculus 2.6 billion bp
99% in common with human genome