Download Genomics

Genomics
Study of the Functions and
Interactions of Many Genes at Once
Goal of the Human Genome Project: To Determine the
Sequence of All of the DNA in a Human Cell
Per haploid
genome
Now estimated
at 30,000 genes
How Can We Use Human Genome Information?
Cytogenetic
map or
Distances: 1 base
Distances: 10,000 bases
Distances: 100,000 bases
Distances: 5,000,000 bases
Chromosomal Maps
From
A
B
A
B
D
C
B
B
E
To
B
D
D
E
E
E
C
F
F
Distance in cM
20
8
12
6
14
9
15
28
22
Determining the
Human Genome Sequence
Sequencing: The order
of DNA nucleotides is
determined for
fragments produced by
restriction enzymes
Assembly: Computer
analysis determines
the order of fragments
by aligning overlapping
regions
Assembly: Using Overlapping
Regions to Arrange Sequences
Determining the
Human Genome Sequence
Annotation:
Computer analysis
locates possible gene
regions and identifies
potential functions
Gene Expression:
Studying RNA
production by
Microarray Analysis to
identify protein-coding
sequences in specific
cell types
DNA Sequencing by
the Sanger Method
Relies on Chain Termination during
replication due to incorporation of
Dideoxynucleotides
OH H
H
H
deoxyribose dideoxyribose
Replicate unknown DNA using dideoxynucleotides
to terminate growing chains at various positions
Unknown Sequence
3’-A-G-C-C-C-A-G-A-T-T-5’
Complementary Products
Black= dideoxynucleotide
5’-T-3’
5’-T-C-G-G-G-3’
5’-T-C-G-3’
5’-T-C-G-G-G-T-C-T-3’
5’-T-C-3’
5’-T-C-G-G-G-T-C-T-A-3’
5’-T-C-G-G-G-T-C-T-A-A-3’
5’-T-C-G-G-G-T-C-3’
5’-T-C-G-G-G-T-3’
5’-T-C-G-G-3’
Use gel electrophoresis to separate replicated
fragments that differ by one base
A
Dideoxynucleotide
T
C
G
Size of DNA on gel shows distance from start of replication
Labeling of dideoxynucleotide shows complementary
sequence
Determine unknown sequence from complementary
sequence with base-pairing rules
A
Dideoxynucleotide
T
C
G
Complementary
Sequence
5’-T-C-G-G-G-T-C-T-A-A
5’-T-C-G-G-G-T-C-T-A
5’-T-C-G-G-G-T-C-T
5’-T-C-G-G-G-T-C
5’-T-C-G-G-G-T
5’-T-C-G-G-G
5’-T-C-G-G
5’-T-C-G
5’-T-C
5’-T
Complementary Sequence
Unknown Sequence
5’-T-C-G-G-G-T-C-T-A-A-3’
3’-A-G-C-C-C-A-G-A-T-T-5’
Use of Fluorescent Dideoxynucleotides
in Sanger Sequencing
Microarray Analysis
• Microarray
• DNA sequences arranged in a matrix
• Tests for binding to complementary sequences
• Steps in Microarray Analysis
• Arrange DNA or cDNA in an ordered array on a
glass slide
• Incubate array with fluorescently-labeled probe
• Detect probe hybridization using a laser
• Record and store data with computers
Array of 1046 cDNAs probed with bone
marrow based cDNA probe
Using Human Genome Information
Pharmacogenomics Using DNA Microarrays
to select individual drug
treatments
Mutations in Gene for
Affect the following disease conditions
Glutathione-STransferase (GST)
Detoxification of environmental toxins
Susceptibility to some cancers
Cytochrome P450
Affects rate of metabolizing 30-40 drugs
5-10% of Caucasians and African
Americans have low rates
Apo E4
Gene dose affects
Age of onset for Alzheimer's disease
Response to drug Tacrine