Gene expression profiling of cancer

Microarray analysis

Gene expression profiling of cancer

MALDI-TOF mass spectrometry

Analysis of proteins lH


High- Primer extension applied to resolution DNA analysis analysis of of DNA DNA

Y2H system

Y2H system invented lH

Yeast interactome mapped

Fruit fly interactome mapped Worm interactome mapped

processing of molecular sequences of DNA and proteins at the National Institutes of Health. As the collection of sequences of proteins and nucleic acids expanded, and the demand for efficient, rapid, and economical methods to perform searches on these molecules increased throughout the 1980s, older, computationally intensive, and costlier methods were replaced by new approaches to sequence comparisons that were much faster and more accessible than existing search tools for DNA and protein sequences, motifs, and gene identification. The invention of fluorescent detection systems made it possible to automate DNA sequencing and by 1986 the first automated sequencers became commercially available. Since then, the speed of DNA sequencing has increased by several orders of magnitude through the development of simpler chemistry and more sensitive dyes for DNA labeling, more powerful computers, and improved optical systems. Alternative sequencing methodologies have led to further increases in the speed, sensitivity, and accuracy of sequencing at reduced cost.

During the 1980s, as the density of information derived from sequencing, mapping, and identifying human genes increased, so did the demand for analytical tools capable of exploiting this information. In a sequence of events reminiscent of the evolution of conventional techniques for sequencing DNA, a means was developed of generating probe arrays on solid supports for highly parallel hybridization analysis of DNA. These probe arrays, termed ''DNA mi-croarrays,'' have come to occupy niches in nearly every area of basic biological and biomedical science, including genome mapping, genotyping and reference-based sequence checking (resequencing), and gene expression profiling. Later, the technology was transferred to the development of proteomic, glycomic, tissue arrays, and G-protein-coupled microarrays, and to the assessment of RNA and protein alterations as diagnostic markers, particularly in oncology. The dramatic increase in information that could be gathered from a single profiling experiment with DNA microarray technology and its ready adaptability to interdisciplinary research were highly advantageous.

Toward the end of the 1980s, the introduction of matrix-assisted laser desorption (MALDI) time of flight (TOF) mass spectrometry revolutionized the analysis of large biomolecules. Using this technique, proteins with masses of up to several hundred thousand could be analyzed. By combining improved signal resolution with less expensive, more efficient lasers to increase sequencing fidelity, large DNA biomolecules could also be analyzed. The simplicity of MALDI-TOF mass spectrometry increased its popularity and substantially expanded its range of applications to the discovery and identification of SNPs, sizing of nu-cleotide repeats, estimation of allele frequencies, and the quantitative analysis of gene expression and DNA methylation patterns. And finally, the invention of the yeast-two-hybrid (Y2H) system in 1989 provided a strategy for identifying interactions of pairs of proteins. With the aid of the Y2H system, partial maps of protein-protein interactions (''interactomes'') have been determined for the yeast, worm, and fruit fly genomes. The Y2H approach, a unique facility to target protein-protein interactions in model organisms, set the stage for the determination of human interactomes.

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