Biomedical Engineering Reference
In-Depth Information
occurring per bp within the 3 billion bp of the human DNA. Point mutations can affect
how a human reacts to bacteria, drugs, and chemicals and may also result in genetic
diseases like cystic fi brosis and sickle-cell anemia. Biochips allow the analysis of mul-
tiple SNPs within individuals so that correlations between SNP patterns and disease
susceptibility and/or drug response can be investigated. Drug companies are using
SNP-based studies on gene candidates and will be able to achieve delivery systems
that can provide accurate, inexpensive, and rapid automated genotyping of as many
SNPs as possible. From the Affymetrix family of GeneChips, the p53 GeneChip is
able to detect the SNP of the p53 tumor-suppressor gene. The HIV GeneChip
can be used to detect mutations in the HIV-1 protease as well as the virus's reverse
transcriptase genes.
Apparently, biomedical applications are the main demands of the DNA biochip.
The selected applications are shown in Table 11.5.
TABLE 11.5
Selected DNA arrays applications. Source: 3rd Millennium
Applications
Major goals
Comments
Disease classifi cation
Identify disease subgroups based on
Such classifi cation can shed light on the biological basis
their unique gene expression profi les
for different clinical outcomes. It may be useful for
creating sensitive diagnostic tests, thereby permitting
more effective, targeted treatment. This approach has
been used with several kinds of cancers.
Function prediction
Predict the function of unknown
These experiments require a large database of “known”
genes based on the similarity of their
expression profi les that can be used for comparisons. This
gene expression profi les to those of
approach will become powerful as such databases
known genes
continue to grow over the next several years.
Pathway identifi cation
Find biomolecular pathways that are
This task is crucial for fi nding targets for potential
affected by disease and disease
drugs or for more clearly understanding how existing
treatment
drugs work.
Gene network
Identify prevalent expression patterns
This approach has been used to fi nd regulatory elements
identifi cation
(gene clusters) and
in yeast. It will soon be used to discover coregulated
then identify DNA sequence patterns
genes in other organisms (including humans).
Toxicology
Test drug-treated tissue samples for
These studies help drug companies eliminate from their
toxicological effects
pipelines - at an early stage of development - drugs that
are likely to have poor side-effect profi les. This approach
will make drug development more effi cient and cost
effective.
Transcript discovery
Find transcripts (genes) in genomic
In these experiments, arrays are made from genomic
sequence
DNA sequences, rather than from complementary DNAs
(cDNAs). Such studies can be used to confi rm
computational gene predictions and characterize
alternative splicing and the boundaries of exons (DNA
sequences destined to become part of the mature
messenger RNA [mRNA]).
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