Download The Human Genome Analysis Variable Number Tandem Repeats


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
Overview
Genomic DNA
Transcriptome
DATA BASE
Proteome
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/conte
nt/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.
GAGGAG
GAGGAGGAG
GAGGAGGAG
GAGGAGGAGGAGGAG
GAGGAGGAGGAG
GAG
GAGGAGGAG
GAGGAGGAGGAG
GAGGAGGAGGAGGAGGAG
GAGGAGGAGGAGGAGGAG
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 Analysis
http://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 have
recurring cancer. Now return to the original microarrays and compare these
two groups of women (disease-free and recurring cancer).
Is gene expression different?
The composite microarray
Can you see any differences?
(Each row is a patient’s tumor, a column a gene)
Cancer free
Recurring
cancers
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