Biomedical Engineering Reference
In-Depth Information
software to simulate and optimize experimental protocols for query processing
in Biomolecular Database systems.
4.
APPLYING OUR BIOMOLECULAR DATABASE SYSTEM
TO EXECUTE GENOMIC PROCESSING
There is tremendous potential to apply Biomolecular Databases to the solu-
tion of a number of biological problems. The huge amount of data provided by
the sequencing of the human genome has outstripped many conventional meth-
ods for DNA analysis.
4.1. Genomic Processing Applications
We now discuss applications of such a Biomolecular Database system to
provide key genomic processing capabilities. Three basic kinds of applications
are discussed, which demonstrate different ways in which the massive parallel-
ism of Biomolecular Databases can be used: (1)
Rapid identification of indi-
viduals either susceptible to or resistant to chemical or biological agents
. We
describe the selection of a group of DNA molecules based on a common prop-
erty, and then use the information tags to identify the individuals selected. (2)
Large-scale gene expression profiling using Biomolecular Databases
. Expressed
genes from multiple tissues are represented in a Biomolecular Database, from
which they can be selected individually or in groups for subsequent expression
analysis. (3)
High-throughput screening of candidate genes to optimize genetic
association analysis for complex diseases such as heart disease or Parkinson's
disease
. Pools of individuals are selected through use of the information tags
appended to each DNA molecule in the database. The pools so selected are then
subjected to genetic analysis. We describe in detail these three applications that
concern genomic information processing, and constitute important genomic
processing applications of Biomolecular Database systems for medical science.
4.1.1. Rapid Identification of All Individuals Possessing a Specific
Known Genotype
A single known genotype can confer properties making the individual either
susceptible to or resistant to a particular chemical or biological agent found in
the environment. It is certainly possible with existing biotechnology (e.g., hy-
bridization experiments) to screen individuals for a given genotype. This is done
one individual at a time, and is thus a relatively slow process. In addition, the
cost of traditional genotyping of an individual ranges from $300 to over $1,000.
