Genomic Analysis

What is genomics?

Genomics is the study of the entire complement of genetic material in a chromosome set. The science of genomics has allowed scientists to decode the human genome and to greatly speed discovery of new drugs by identifying the genes implicated in disease states.

What are some common methods of genomics analysis?

Microarrays have been used in the task of identifying and characterizing the tens of thousands of genes in the human genome. Methods of reverse dot-blot techniques are often used and can be done on thousands of genes simultaneously. The expression arrays are designed for the comparison of mRNA expression of normal versus diseased tissues and evaluating drug-induced transcriptional changes. To do the comparison, chromosome-specific, tissue specific, or signal-transduction pathway specific microarrays carrying thousands of cloned cDNA fragments or nucleotides are used as hybridization probes to compare gene expression profiles.

In the current methods, target mynas are isolated and reverse transcribed to cDNAs that are then PCR-amplified and hybridized against the subject microarrays. Sensitive and specific detection is essential for genomic microarray analysis to reflect the real dynamic mRNA expression pattern.

What are the downfalls of current genomic analysis techniques?

Unfortunately, the predominant chip methods have pitfalls and limitations.

The reverse transcription reaction requires large amounts of starting materials. In many cases, the samples to generate the nRNAs can be rare or limiting, for example, micro-dissected tumor sections or fixed tumor cells. Additionally, low amount mRNAs could be missed in the reverse transcription and PCR amplification steps.
In general, the format of chip analysis is multiplex nucleotide hybridization. The existence of hundreds of different nucleotides in one hybridization reaction can be problematic since the signal-to-noise ratio is subject to many parameters and can be hard to adjust by hybridization stringency alone. To interpret a weak signal as specific rather than background can be a tricky task.
The ratio of the mRNA populations could be changed upon PCR amplification.
Current cDNA chip methods involve multiple steps.

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What are the benefits of RAM/HSAM in genomic analysis?

The RAM/HSAM system has the potential to overcome the above limitations. Cell and tissue lysates containing mRNAs can be directly applied to probe arrays and the reverse transcription and PCR amplification steps are no longer needed. These advantages should generate higher sensitivity and maintain proportional signal profiling. The hybridization, as well as the ligation step confers higher specificity, enabling unambiguous quantitative assignment of signals. The RAM/HSAM system can also be used in automated detection systems for greater ease of use and better throughput.