Finding: Microarray-based Genomic Selection (MGS), is a research protocol that allows scientists to extract and enrich specific large-sized DNA regions, then compare genetic variation among individuals using DNA resequencing methods. Sequencing can be done by a small staff of researchers...it is inexpensive and not labor intensive.
The new technology will allow researchers to more easily discover subtle and overlooked genetic variations that may have serious consequences for health and disease.
Problem in genetic investigation
DNA sequencing platforms do not have a simple, inexpensive method of selecting specific regions to resequence; this has been a serious barrier to detecting subtle genetic variability among individuals.
The goal of most human genetics researchers is to find variations in the genome that contribute to disease. Despite the success of the human genome project and the availability of a number of next-generation The Emory scientists believe that goal will be much more obtainable thanks to MGS.
MGS uses DNA oligonucleotides (probes) arrayed on a chip at high density (microarray) to directly capture and extract the target region(s) from the genome. The probes are chosen from the reference human genome and are complementary to the target(s) to capture. Once the target is selected, resequencing arrays or other sequencing technologies can be used to identify variations.
The Emory scientists believe MGS will allow them to easily compare genetic variation among a number of individuals and relate that variation to health and disease.
The human genome project focused on sequencing just one human genome--an amazing technological feat that required a very large industrial infrastructure, hundreds of people and a great deal of money. The question since then has been, can we replicate the ability to resequence parts of the genome, or ultimately the entire genome, in a laboratory with a single investigator and a small staff" The answer is now 'yes.'"
Geneticists have found many different types of obvious gene mutations that are deleterious to health, but more subtle variations, or variations located in parts of the genome where scientists rarely look, may also have negative consequences but are not so easily discovered.
Other methods for isolating and studying a particular region of the genome, such as PCR and BAC cloning (bacterial artificial chromosomes) are comparatively labor intensive, difficult for single laboratories to scale to large sections of the genome, and relatively expensive, says Dr. Zwick.
Whereas typical microarray technology measures gene expression, MGS is a novel use of microarrays for capturing specific genomic sequences. For the published study, a third type of microarray--a resequencing array--was used to determine the DNA sequence in the patient samples.
The logic behind the resequencing chip is that you design the chip to have the identity of the base at every single site in a reference sequence. You use the human genome reference sequence as a shell and you search for variation on the theme. This alternative new technology allows a regular-sized laboratory and single investigator to generate a great deal of data at a cost significantly less than what a sequencing center would charge.
Showing posts with label Microarray. Show all posts
Showing posts with label Microarray. Show all posts
Tuesday, July 22, 2008
Friday, September 28, 2007
DNA microarray
A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to chemically suitable matrices.
DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
Microarray technology is often used for gene expression profiling. It makes use of the sequence resources created by the genome sequencing projects and other sequencing efforts to answer the question, what genes are expressed in a particular cell type of an organism, at a particular time, under particular conditions?
For instance, they allow comparison of gene expression between normal and diseased (e.g., cancerous) cells. There are several names for this technology - DNA microarrays, DNA arrays, DNA chips, gene chips, others. Sometimes a distinction is made between these names but in fact they are all synonyms as there are no standard definitions for which type of microarray technology should be called by which name.
Microarrays exploit the preferential binding of complementary nucleic acid sequences. A microarray is typically a glass slide, on to which DNA molecules are attached at fixed locations (spots or features). There may be tens of thousands of spots on an array, each containing a huge number of identical DNA molecules (or fragments of identical molecules), of lengths from twenty to hundreds of nucleotides. The spots on a microarray are either printed on the microarrays by a robot, or synthesized by photo-lithography (similar to computer chip productions) or by ink-jet printing. There are commercially available microarrays, however many academic labs produce their own microarrays.
Microarrays that contain all of the about 6000 genes of the yeast genome have been available since 1997. The latest generations of commercial microarrays represent the entire human genome, more than 30,000 genes, on two microarrays.
DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
Microarray technology is often used for gene expression profiling. It makes use of the sequence resources created by the genome sequencing projects and other sequencing efforts to answer the question, what genes are expressed in a particular cell type of an organism, at a particular time, under particular conditions?
For instance, they allow comparison of gene expression between normal and diseased (e.g., cancerous) cells. There are several names for this technology - DNA microarrays, DNA arrays, DNA chips, gene chips, others. Sometimes a distinction is made between these names but in fact they are all synonyms as there are no standard definitions for which type of microarray technology should be called by which name.
Microarrays exploit the preferential binding of complementary nucleic acid sequences. A microarray is typically a glass slide, on to which DNA molecules are attached at fixed locations (spots or features). There may be tens of thousands of spots on an array, each containing a huge number of identical DNA molecules (or fragments of identical molecules), of lengths from twenty to hundreds of nucleotides. The spots on a microarray are either printed on the microarrays by a robot, or synthesized by photo-lithography (similar to computer chip productions) or by ink-jet printing. There are commercially available microarrays, however many academic labs produce their own microarrays.
Microarrays that contain all of the about 6000 genes of the yeast genome have been available since 1997. The latest generations of commercial microarrays represent the entire human genome, more than 30,000 genes, on two microarrays.
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