DNA
Chip, Microarray Revolutionize Genomic Analysis
DNA microarray has
emerged as a prime technology for the performance of gene
expression analyses. Combined with bioinformatics and other
advanced technology, it offers numerous applications with absolute
accuracy.
Availability of whole genomic sequences of many organisms have created
the need for high throughput analysis of gene expression patterns and
the DNA chip and microarray technology have revolutionized functional
and genomic analysis at this level. This technology uses a single chip
to monitor the whole genome so that researchers can have a
better picture of the interactions among thousands of genes
simultaneously. In the past several years, this new technology has
attracted several biologists as it generates large amount of
data in little time and facilitates the quantification of thousands of
genes from many samples
DNA microarrays are used to examine the gene expression changes in
cancer patients. Tumor profiling, using DNA microarrays, allows the
analysis of the development and the progression of complex diseases.
The technology allows scientists to examine targets for drug discovery,
potential diagnostic and prognostic biomarkers for many complex
diseases; detect viruses and other pathogens from blood samples and
thus evolved as a pathogen detection method.
DNA microarrays are recently used to identify inheritable markers, and
therefore used as a genotyping tool. SNP chips based on DNA microarray
technology allow the high throughput profiling of single nucleotide
polymorphisms using a chip or array approach. This has
allowed polymorphisms to be more quickly assayed and also their
relevance to disease to be easily determined. Today, the technology has
emerged as an indispensable research tool for gene expression profiling
and mutation analysis.
The beginning
Microarray technology has evolved from southern blotting, where
fragmented DNA is attached to a substrate and then probed with a known
gene or fragment. The use of a collection of distinct DNAs in arrays
for expression profiling was first described in 1987, and the arrayed
DNAs were used to identify genes whose expression is modulated by
interferon. These early gene arrays were made by spotting cDNAs onto
filter paper with a pin-spotting device. The use of miniaturized
microarrays for gene expression profiling was first reported in 1995,
and a complete eukaryotic genome (Saccharomyces cerevisiae) on a
microarray was published in 1997. Affymetrix further developed DNA
microarrays which were based on high-density 25-mer oligos from human
cDNA sequences. Microarrays were originally designed to measure gene
expression levels of a few genes.
Terminologies that have been used in the literature to describe this
technology include biochip, DNA chip, DNA microarray, and gene
array. Affymetrix, Inc. owns a registered trademark,
GeneChip, which refers to its high density, oligonucleotide-based DNA
arrays.
Today, there are more than 1,000 microarray core facilities are
available and over 100 service companies are offering microarray
processing services worldwide. India is a late entrant to the
microarray world. However, rapid progress in the last few years has
resulted in establishment of over 50 microarray facilities and five
commercial microarray service providers in India.
Application advances
As more information accumulates, scientists could able to use
microarrays to ask increasingly complex questions to perform more
intricate experiments. With new advances, researchers are able to
better understand the functions of new genes based on similarities in
expression patterns with those of known genes. Ultimately, these
studies promise to expand the size of existing gene families, reveal
new patterns of coordinated gene expression across gene families, and
uncover entirely new categories of genes. Furthermore, because the
product of any one gene usually interacts with those of many others,
our understanding of how these genes coordinate will become clearer
through such analyses, and precise knowledge of these
inter-relationships will emerge. The use of microarrays may also speed
up the identification of genes involved in the development of various
diseases as it enables scientists to examine a much larger number of
genes. This technology will also help in the examination of integration
of gene expression and function at the cellular level, reveals how
multiple gene products work together to produce physical and chemical
responses for both static and changing cellular needs.
Developing new protein arrays and constructing miniaturized
flow-through systems, which can potentially take this technology from
the research bench into industrial, clinical and other routine
applications, exemplify the intense developments that are now ongoing
in this field. Recent growth in the field of protein microarray shows
the potential applications of enzyme–substrate,
DNA–protein and different types of protein–protein
interactions. The technology is now more heavily regulated in terms of
the bioinformatics, which has led to the generation of more credible
results.
Rini Mukherjee Saxena, senior product manager, Agilent Technologies
said, ‘’Many studies have focused on the
methylation state of specific genomic sites that are thought to play
important roles in cellular processes. Conventional methods of
analyzing this event are labor intensive, low-throughput and expensive.
Microarray-based methods have evolved as powerful high-throughput
analysis tools capable of detecting and mapping DNA methylation changes
on a previously unachievable genome-wide scale.”
Other researchers in the field expect that DNA chips will enable
clinicians and in some cases even patients to quickly and inexpensively
detect the presence of a whole array of genetically based diseases and
conditions, including AIDS, Alzheimer’s disease, cystic
fibrosis, and some forms of cancer. Moreover, the technology could make
it possible to conduct widespread disease screening
cost-effectively, and to monitor the therapies more effectively. So
far, only a few companies have commercialized DNA-chip products, and
the barriers to market entry remain great.
Challenges
Microarray technology is an expensive technology in terms of cost of
required equipment, reagents and trained manpower. The technology is
rapidly advancing; frequent upgradation of machines and methods becomes
a major bottle neck in maintaining a microarray lab.
The major hurdle in the efficient utilization of microarray technology
is the lack of trained manpower to analyze the microarray data.
Expertise in spread sheet and database operations and analysis packages
are essential for efficient statistical analysis of data and to find
significant patterns.
As DNA-chip companies prepare to bring their products to market, they
have to face major technological, manufacturing and
regulatory challenges. The technology trade-offs involve finding ways
to increase the number of arrays on a single chip, as well as
increasing the rate of production to meet expected demand.
The main challenge involves achieving all these market-oriented
parameters at a cost that supports a commercially acceptable price. In
a tight managed-care marketplace that places a premium on technologies
that can either show quick savings or more-efficient results, some
analysts say that such unit prices will limit the growth of the
DNA-chip market.
Future
Microarray technology offers a ray of hope to personalized drugs and
molecular diagnostics as it enables global views of biological
processes. With technical development that offers increased
sensitivity, microarray technology is expected to become an
indispensable tool in the fields of biology, biotechnology, drug
discovery, and other application areas. If DNA microarray is used for
the development of pharmaceutical products, it can considerably reduce
the cost and time for the entire process of drug discovery and
development, and can also contribute in developing personal drugs.
Although this marketplace is in its infancy, with considerable
challenges remaining to be overcome, the speed with which manufacturers
are progressing toward commercialization will soon make DNA chips a
viable alternatives to traditional chemical assays. Indeed,
manufacturers hope that within a decade they will usher in a new era in
diagnosis and treatment for diseases and conditions that have genetic
origins.
Jahanara Parveen