ASSIGNMENT II

MICROARRAY ANALYSIS OF GENE

EXPRESSION OF CANCER TO GUIDE THE USE
OF CHEMOTHERAPEUTICS

Submitted by: Sagar N

Roll number: 14BBT045
Kumaraguru College of Technology
Department of Biotechnology
 Abstract

A microarray is a multiple lab on a chip ,2D array on a solid substrate. Microarray analysis of
gene expression (MAGE) is that it can be used to identify the some genes that were
previously thought to be unrelated to a pathologic or physiologic event. During the past
years, The molecular profiling is a source of investigating the applications of MAGE in
cancer, identifying the undiscovered cancer types, to guiding the use of therapeutics. The
roles of cancer genomic signatures have three phases. In the first phase, genomic
signatures were described in stored cancer specimens and dubbed as molecular portraits of
cancer. Whenever gene expression profiles were carefully correlated with sufficient clinical
information of cancer patients, new subgroups of cancers with distinct outcomes were
revealed. In second phase, validation of cancer signatures were emphasized and commonly
performed with independent groups of cancer specimens or independent data set. In the
third phase, cancer genomic signatures have been further expanded beyond depicting the
molecular portrait of cancer to predicting patient outcomes and guiding the use of cancer
therapeutics. microarray technologies has provides genome-wide strategies for searching
tens of thousands of genes simultaneously

Keywords :MAGE , profiling, genomic signatures, therapeutics.

INTRODUCTION
A DNA microarray is an orderly arrangement of DNA on solid support, providing a medium
for matching samples of known and unknown DNA. The types of DNA microarrays and
relevant methodologies are reviewed by Chao et al [1]. Cancer is a complex and prevalent
disease, has become a prime target for the application of novel technologies of genomics,
proteomics, and functional genomics, since intensive research may help in the development
of a predictive, individualized approach to cancer care and can facilitate the selection of the
best treatment method for each individual patient .Microarrays gives the opportunity to
analyze tens of thousands of genes on single assay. Functional genomics focuses on
genome-wide patterns of gene expression and the mechanisms by which gene expression
are coordinated. The use of microarrays has spread rapidly throughout the research
community since the 1990s when it was first introduced [2]. The completion of the human
genome project as well as the current availability of high-throughput technologies have
enabled us to move from the study of single molecules to the simultaneous analysis of 24
thousand human genes in the complex biological systems of human life.

The development of microarray-based multigene prognostic gene signatures been pursued

by many groups in the last decade with the aim of defining which patients would have such
a good prognosis that they could forgo chemotherapy. Microarray-based gene expression
profiling studies undoubtedly have contributed to understanding of the heterogeneity and
complexity of breast cancer behavior.[3]

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Overview of Microarray Analysis of Gene Expression
(MAGE)

A microarray or DNA chip is an orderly arrangement of DNA molecules that have

been chemically bonded to a fine grid of surfaces. The purpose of MAGE is to analyze the
expression states of genes in complementary DNA prepared from mRNA in which the
hybridization takes place on the array via the Watson Crick duplex formation method. A
probe is the tethered nucleic acid of known sequence on the fine grid surface, whereas a
target is the free nucleic acid in the biological samples to be determined [4]. The power of a
microarray is its large-scale ability to analyze the expression of thousands of genes
simultaneously.
The two basic types of DNA microarrays are oligonucleotide microarrays and cDNA
microarrays, For the majority of oligonucleotide microarrays, the oligonucleotides are directly
synthesized and arrayed in a discrete regular grid on silicon or glass chip surfaces. . cDNA
microarrays are previously prepared DNA clones which are immobilized to a glass slide.
In the late 1980s, Stephen Fodor and his colleagues adopted the process of
photolithography to make microarrays with chemically synthesized oligonucleotides [5].
Affymetrix microarrays contain between 11 -20 pairs of oligonucleotide probes for each
target RNA, in which one of the pair is the reverse complement to a unique 25-mer in the
RNA and the other contains a mutated middle base pair and serves as a measure of stray
signal . The chip is arrayed with oligonucleotides that are individually synthesized directly on
the chip by automatic procedures until four nucleotides occupy the place. This cycle of
reproduction and addition of a nucleotide is repeated until the array carries oligonucleotides
that are 2025 nucleotides in length.
In the mid-1990s, Pat Brown and his colleagues developed the dot blot microarray.
The array is made in three steps: (1) preparing the plasmid cDNA clones to be put on the
array, using PCRs to amplify the cDNA inserts (2) spotting the DNA onto the glass surface of
the array with a spotting robot(3) postspotting processing of the glass slide [6]. During gene
expression analysis with cDNA microarrays, four steps are involved: (1) sample preparation
and labeling, (2) hybridization, (3) washing, and (4) image acquisition. With these two-color
arrays, two different sets of mRNA samples are used, each labeled separately with different
fluorescent tags and the other is the test sample for which the gene expression pattern is to
be determined.

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Advanced Microarray Data Analyses

To evaluate how MAGE can help to make a diagnosis or choose a therapy, it requires one
set of patients to identify a gene-expression pattern called a genetic signature .The response
to a treatment,or the induction of side effects by a drug. The power of microarray technology
is its ability to use changes in multiple genes as the pattern of gene expression rather than to
choose thresholds of individual markers [7].

During the investigation period, it is critical that understand find the minimization of
expression noise and bias through effective design. Expression noise can be defined as
gene expression variation that does not correlate with the biology or behavior being studied
and is introduced by both the technology itself and/or during tissue processing

An unsupervised analysis does not use any a priori class definition, but it simply seeks to
determine what structure is inherent in the data A commonly used example of unsupervised
analysis is hierarchical clustering, i.e. letting the data define its own patterns by clustering
genes that are most similar in expression profile[8]. A supervised analysis is more likely to
reveal putative associations between genes and the cytogenetic class, but it may bias the
outcome by forcing a model onto the data, i.e. the overfitting risk

MAGE in Clinical Cancer Investigation

As a proof , cDNA microarrays is used to identify genes of differential expression between
in vitro cultured human mammary epithelial cells and breast tumor specimens . Their results
supported the feasibility and usefulness of this systematic approach for studying variations in
gene expression patterns in human cancers as a means to dissect and classify solid tumors
[7]. 64 surgical specimens of human breast tumors from 42 patients were analyzed for gene
expression profiles . They identified a set of co-expressed genes for which variation in mRNA
levels could be related to specific features of physiologic variation. Molecular portraits of
cancer with gene expression profiles were thus proposed

Ramaswamy et al compared gene expression patterns between primary tumors and

metastases [8]. They identified a gene expression signature that distinguished primary from
metastatic adenocarcinomas
.

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CONCLUSION
Cancer being a very complex and multi-factorial disease leaves us with many unmapped
questions. Curing cancer to its root requires intensive treatment, but due to deficient in-
terruption of multi-signaling oncogenic pathways and drug-induced adverse effects, still
complications develop owing to the side effects of the therapy. Microarray technology has
been used in the search for gene profiles that are associated with different histologic types,
responses to radiation, and prognostic outcomes

However, there is advancement in the field of cancer etiology, diagnostics, therapeutics,

prognosis and other alternative translational applications to achieve the practical feasibility,
microarray technology would need to address a range of quality-control issues. Every aspect
of the process should be so robust that it can be considered to be foolproof.

PLAGIARISM REPORT

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Bibliography

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[4] Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA
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[5] Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL. Multiplexed
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