Biological Perspective - Biomedical Informatics in Translational Research - page 51

Microarrays
A number of high-throughput techniques characterizing DNA and RNA
utilize microarray technology. The basis for these methods is the specific-
ity of nucleic acid hybridization as discussed in the box titled “Polymerase
Chain Reaction.” Microarrays have been developed to quantify the
amounts of a particular DNA or RNA sequence in a mixture of nucleic
acids. The mixture is interrogated by labeling the nucleic acid found in the
mixture, usually by PCR, and hybridizing to a probe or set of probes spe-
cific to the species of interest. The amount of hybridization is proportional
to the concentration of the species of interest in the mixture.
The advantage of microarray techniques is that the concentration of
many species can be determined simultaneously by fixing many probes to a
surface in a grid (array) in which the location of each probe is fixed and,
hence, the hybridization signal at that position is a readout of the concen-
tration of the species interrogated by that probe. The spots for a given
probe can be very small, hence the needs for microarrays. Hundreds of
thousands to more than a million features might be present on a single
array. Copy number variation and gene expression analysis are two types
of measurements that use this approach and they will be discussed in detail
in Chapter 5.
Another type of analysis that is based on the same basic technology is
the determination of single nucleotide polymorphisms or specific sequence
(genetic) variants. Although the method used is similar to that described
earlier, that is, an array of probes to which a mixture of labeled DNA is
hybridized, the hybridization property being exploited is quite different.
For short probes (20 to 25 bases), the requirement for an exact match
between the probe and the sequence being interrogated is very stringent.
Conditions can be established so that a mismatch of even one base will
greatly reduce the signal. This specificity allows the technique to distin-
guish been two or more possible bases at a given position. The signal in
this analysis is based on the specificity of the hybridization, not the quan-
tity of the target species. This allows a single DNA sample to be
simultaneously genotyped for hundreds of thousands of variants. These
types of experiments will be discussed in Chapter 5.
sity of chemistry and structure that has enabled proteins to evolve into the vast array
of functions that enable and enrich life.
Humans are estimated to have more than 100,00 different proteins. (Although
the human genome contains about 25,000 protein encoding genes, alternative splic-
ing of mRNA and other forms of post-translational processing of proteins yields
more kinds of proteins than genes that encode them [12].) They are found
intercellularly and in most body fluids. The concentrations of individual proteins
vary by orders of magnitude.
All of these properties of proteins make them important targets for study of dis-
ease processes because they can be both markers of disease and targets for pharma-
cological therapeutics. Their great diversity and chemical heterogeneity make the