Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

depending on the sophistication of the controls and analysis methods [10]. One aspect
our group has given particular attention to is the detection of SNPs in the 25-base
Affymetrix probe arrays.
2) Target Concentration. Target concentrations will vary as the gene transcript amounts
vary, and the variation extends to the presence of particular exons as well as genes
expressed across samples [31-33]. Given the scenario of low transcript (target)
concentration, some experimental conditions can be altered to drive the reaction
towards duplex formation (increase the rate at which it approaches equilibrium) [14,
15]. The duplex form of the nucleic acids is affected by too high heat, so
amplification of the target mass is the preferred method. The challenge is to keep the
relative concentrations of individual targets within the mixture identical in the
process, which generally utilizes some type of polymerase chain reaction, either as an
intermediate or end step [14]. Additionally, ‘hybridization accelerators’ such as
polyethylene glycol (PEG) and dextran sulfate are employed to create a diphasic
reagent solution, with the target reagents effectively concentrated in the aqueous
phase [34]. This allows the overall volume to be increased sufficiently to cover the
relatively wide array surface without diluting the target component. Similarly to the
nature of probe sequences, the composition of target sequences may allow the
formation of internal secondary structures; in the event that such regions block the
probe binding site this will affect the probe’s ability to associate with the
complementary target region [5, 10, 35]. Target sequences are minimally 1000
nucleotides long (depending on the effectiveness of the molecular biology
preparatory processes) and, unless shearing or fragmentation is performed, the
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