2. ď Background
ď History
ď Introduction
ď Types of microarrays
ď DNA microarray
ď Principle
ď Types of DNA microarray
ď Steps involved in DNA microarray
ď Applications
ď Advantages
ď Limitations and disadvantages
ď Future of microarrays
ď Take home message
3. Background
ď A human organism has over 250 different cell types
(e.g., muscle, skin, bone, neuron), most of which
have identical genomes, yet they look different and
have different activities
ď Less than 20% of the genes are expressed in a typical
cell type
ď Apparently the differences in gene expression is what
makes the cells look and function differently
4.
5.
6.
7. History
⢠Once the human genome sequence was completed
in 2001, it paved the way for many experiments
and researches;
⢠one such area was identifying the regions of DNA
which control normal and disease states.
⢠Functional genomics is the study of gene function
through parallel expression measurements of a
genome.
8. History
⢠Microarray ď analyzes large amount of samples which
have either been recorded previously or from new
samples
⢠History: Microarray technology evolved from Southern
blotting, where fragmented DNA is attached to a
substrate and then probed with a known DNA
sequence
⢠Use of miniaturized microarrays for gene expression
profiling first reported in 1995, and a complete
eukaryotic genome (Saccharomyces cerevisiae) on a
microarray was published in 1997
9. Microarray
⢠It is a 2D array on a solid
substrate (usually a glass
slide or silicon thin-film
cell) that assays large
amounts of biological
material using high-
throughput screening,
miniaturized,
multiplexed and parallel
processing and detection
methods.
10. Types
ď DNA microarrays, such as cDNA microarrays,
oligonucleotide microarrays, BAC microarrays and SNP
microarrays
ď MMChips, for surveillance of microRNA populations
ď Protein microarrays
ď Peptide microarrays, for detailed analyses or optimization
of proteinâprotein interactions
ď Tissue microarrays
ď Cellular microarrays(also called transfection microarrays)
ď Chemical compound microarrays
ď Antibody microarrays
11. DNA microarray
⢠A DNA microarray (also commonly known as
genome chip, DNA chip, or gene array) is a
collection of microscopic DNA spots, commonly
representing single genes, arrayed on a solid
surface by covalent attachment to a chemical
matrix.
⢠Each spot of DNA, called a probe, represents a
single gene.
12. Principle
⢠Hybridization : The property of complementary
nucleic acid sequences is to specifically pair
with each other by forming hydrogen bonds
between complementary nucleotide base pairs.
⢠The principle of DNA microarrays lies on the
hybridization between the nucleotide. Using this
technology the presence of one genomic or cDNA
sequence in 1,00,000 or more sequences can be
screened in a single hybridization.
13. Types of DNA microarrays
⢠Based on different technologies and probe types,
and intended application it can be:
ďź Bacterial artificial chromosome arrays
ďź cDNA microarrays
ďź Oligonucleotide microarrays
ďź In-situ synthesized microarrays
ďź Bead microarrays
14.
15. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
17. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Collecting tissue
18. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating RNA
19. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating RNA
20. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating RNA
21. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating RNA
22. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating RNA
23. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating mRNA
24. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating mRNA
25. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating mRNA
26. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
⢠Isolating mRNA
27. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Make labeled DNA copy
28. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Make labeled DNA copy
29. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Make labeled DNA copy
30. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Make labeled DNA copy
31.
32. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Apply DNA
33. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Apply DNA
34. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Apply DNA
35. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Apply DNA
36. Steps involved
In microarray
I. Collect tissue
II. Isolate RNA
III. Isolate mRNA
IV. Make labeled DNA
copy
V. Apply DNA
VI. Scan microarray
VII. Analyze data
Scan microarray
37. Analyzing data
⢠GREEN represents Control DNA, where either DNA
or cDNA derived from normal tissue is hybridized to
the target DNA.
⢠RED represents Sample DNA, where either DNA or
cDNA is derived from diseased tissue hybridized to
the target DNA.
⢠YELLOW represents a combination of Control and
Sample DNA, where both hybridized equally to the
target DNA.
⢠BLACK represents areas where neither the Control
nor Sample DNA hybridized to the target DNA.
40. Some questions for the age of
genomics
⢠How gene expression differs in different cell types?
⢠How gene expression differs in a normal and diseased (e.g.,
cancerous) cell?
⢠How gene expression changes when a cell is treated by a
drug?
⢠How gene expression changes when the organism develops
and cells are differentiating?
41. Applications
ďą In cancer
ďźTumor formation involves simultaneous changes in
hundreds of cells and variations in genes.
ďźIdentification of single-nucleotide polymorphisms
(SNPs) and mutations, classification of tumors,
identification of target genes of tumor suppressors,
42. Applications
ďą In cancer
ďź Identification of cancer biomarkers, identification
of genes associated with chemoresistance
ďą Early detection of precancerous lesions
ďź Identification of gene expression profiles or
âgenomic fingerprintsâ will allow clinicians to
differentiate harmless lesions from precancerous
lesions or from very early cancer
43. Applications
ďą Antibiotic treatment
ďą Gene expression profiling
ď In different cells/tissues
ď During the course of development
ď Under different environmental or chemical stimuli
ď In disease state versus healthy
ďą Molecular diagnosis
ď Molecular classification of disease
ďą Drug development
ď Identification of new targets
ďą Pharmacogenomics
ď Individualized medicine
44. Advantages
ďź Provides data for thousands of genes.
ďź One experiment instead of many.
ďź Fast and easy to obtain results.
ďź Huge step closer to discovering cures for diseases
and cancer.
ďź Different parts of DNA can be used to study gene
expresion
45. Limitations of DNA microarrays
ď First, arrays provide an indirect measure of relative
concentration.
However, due to the kinetics of hybridization, the
signal level at a given location on the array is not
linearly proportional to concentration of the species
hybridizing to the array.
ď For complex mammalian genomes, it is often difficult
to design arrays in which multiple related DNA/RNA
sequences will not bind to the same probe on the
array.
46. Disadvantages
ď The biggest disadvantage of DNA chips is that they are
expensive to create.
ď The production of too many results at a time requires
long time for analysis, which is quite complex in
nature.
ď The DNA chips do not have very long shelf life, which
proves to be another major disadvantage of the
technology
47. The Future of DNA arrays
ď When the cost is similar, sequencing has many advantages
relative to microarrays.
Sequencing is a direct measurement of nucleic acids
present in solution. One need only count the number of a
given type of sequences present to determine itâs
abundance.
ď Unlike DNA arrays, sequencing is not dependent on prior
knowledge of which nucleic acids may be present.
48. The Future of DNA arrays
ď Sequencing is also able to independently detect closely
related gene sequences, novel splice forms or RNA
editing that may be missed due to cross hybridization
on DNA microarrays
ď As a result of these advantages and the decreasing cost
of sequencing, DNA arrays are being rapidly replaced by
sequencing for nearly every assay
49. Take home message
ď Microarrays are a powerful tool and holds much
promise for the analysis of diseases.
ď Classifications of disease by DNA, RNA, or protein
profiles will greatly enhance our ability to diagnose,
prevent, monitor and treat our patients.
ď Microarrays promise a more biologically based,
individualized treatment